Index

_

__and__() (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask method) __array__() (phenotypic._core._image_parts.accessors._detect_mat_accessor.DetectMatAccessor method) (phenotypic._core._image_parts.accessors._grayscale_accessor.Grayscale method) (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap method) (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask method) (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) (phenotypic._core._image_parts.accessors._rgb_accessor.ImageRGB method) __contains__() (phenotypic._core._image_parts.accessors._metadata_accessor.MetadataAccessor method) (phenotypic.sdk_.constants_.IMAGE_MODE class method), [1] (phenotypic.sdk_.constants_.IMAGE_TYPES class method), [1] __copy__() (phenotypic.abc_.BackgroundSubtraction method), [1] (phenotypic.abc_.BaseOperation method), [1] (phenotypic.abc_.ContrastAdjustment method), [1] (phenotypic.abc_.FocusBlob method), [1] (phenotypic.abc_.FocusEdge method), [1] (phenotypic.abc_.GpuDetector method), [1] (phenotypic.abc_.GridCorrector method), [1] (phenotypic.abc_.GridFinder method), [1] (phenotypic.abc_.GridMeasureFeatures method), [1] (phenotypic.abc_.GridObjectDetector method), [1] (phenotypic.abc_.GridObjectRefiner method), [1] (phenotypic.abc_.GridOperation method), [1] (phenotypic.abc_.ImageCorrector method), [1] (phenotypic.abc_.ImageDenoiser method), [1] (phenotypic.abc_.ImageEnhancer method), [1] (phenotypic.abc_.ImageOperation method), [1] (phenotypic.abc_.MeasureFeatures method), [1] (phenotypic.abc_.MorphologicalFiltering method), [1] (phenotypic.abc_.ObjectDetector method), [1] (phenotypic.abc_.ObjectRefiner method), [1] (phenotypic.abc_.PostMeasurement method), [1] (phenotypic.abc_.PrefabPipeline method), [1] (phenotypic.abc_.Smoothing method), [1] (phenotypic.abc_.ThresholdDetector method), [1] (phenotypic.analysis.abc_.ModelFitter method) (phenotypic.analysis.abc_.QualityCheck method) (phenotypic.analysis.abc_.SetAnalyzer method) (phenotypic.analysis.DoubleSoftplus method), [1] (phenotypic.analysis.EdgeCorrector method), [1] (phenotypic.analysis.ErrorCutoffFinder method), [1] (phenotypic.analysis.ExpectedVsDetectedCount method), [1] (phenotypic.analysis.ICC method), [1] (phenotypic.analysis.LinearSoftplus method), [1] (phenotypic.analysis.LogGrowthModel method), [1] (phenotypic.analysis.MADOutlierRemover method), [1] (phenotypic.analysis.MaxModifiedZScore method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount method) (phenotypic.analysis.qc.ICC method) (phenotypic.analysis.qc.MaxModifiedZScore method) (phenotypic.analysis.qc.RelativeMAD method) (phenotypic.analysis.qc.ReplicateAgreement method) (phenotypic.analysis.qc.TukeyOutlierFraction method) (phenotypic.analysis.RelativeMAD method), [1] (phenotypic.analysis.ReplicateAgreement method), [1] (phenotypic.analysis.TukeyOutlierFraction method), [1] (phenotypic.analysis.TukeyOutlierRemover method), [1] (phenotypic.correction.BayesShrinkCorrector method), [1] (phenotypic.correction.CaptureMetadata method), [1] (phenotypic.correction.ColorCheckerProfile method), [1] (phenotypic.correction.ColorCorrector method), [1] (phenotypic.correction.ColorDenoise method), [1] (phenotypic.correction.DenoiseBlockMatch method), [1] (phenotypic.correction.GridAligner method), [1] (phenotypic.correction.ImageCropper method), [1] (phenotypic.correction.ImagePadder method), [1] (phenotypic.correction.VisuShrinkCorrector method), [1] (phenotypic.detect.CannyDetector method), [1] (phenotypic.detect.ChanVeseDetector method), [1] (phenotypic.detect.CompositeDetector method), [1] (phenotypic.detect.FilamentousFungiDetector method), [1] (phenotypic.detect.HysteresisDetector method), [1] (phenotypic.detect.InoculumDetector method), [1] (phenotypic.detect.IsodataDetector method), [1] (phenotypic.detect.LiDetector method), [1] (phenotypic.detect.MadHysteresisDetector method), [1] (phenotypic.detect.ManualGridPointDetector method), [1] (phenotypic.detect.ManualPointDetector method), [1] (phenotypic.detect.MeanDetector method), [1] (phenotypic.detect.MinimumDetector method), [1] (phenotypic.detect.OtsuDetector method), [1] (phenotypic.detect.RankOtsuDetector method), [1] (phenotypic.detect.RoundPeaksDetector method), [1] (phenotypic.detect.SecondaryOtsuDetector method), [1] (phenotypic.detect.SinePeakDetector method), [1] (phenotypic.detect.TriangleDetector method), [1] (phenotypic.detect.UserThreshold method), [1] (phenotypic.detect.WatershedDetector method), [1] (phenotypic.detect.YenDetector method), [1] (phenotypic.enhance.BayesShrinkEnhancer method), [1] (phenotypic.enhance.ContrastStretching method), [1] (phenotypic.enhance.EnhanceBlockMatch method), [1] (phenotypic.enhance.EnhanceLocalContrast method), [1] (phenotypic.enhance.FlattenIllumination method), [1] (phenotypic.enhance.FocusBlobLoG method), [1] (phenotypic.enhance.FocusEdgeFrangi method), [1] (phenotypic.enhance.FocusEdgeHessian method), [1] (phenotypic.enhance.FocusEdgeLaplace method), [1] (phenotypic.enhance.FocusEdgeMeijering method), [1] (phenotypic.enhance.FocusEdgePhase method), [1] (phenotypic.enhance.FocusEdgeSato method), [1] (phenotypic.enhance.FocusEdgeSobel method), [1] (phenotypic.enhance.GaussianBlur method), [1] (phenotypic.enhance.GrayOpening method), [1] (phenotypic.enhance.ImageInverter method), [1] (phenotypic.enhance.LocalEdgeDenoise method), [1] (phenotypic.enhance.MedianFilter method), [1] (phenotypic.enhance.NonLocalMeansDenoiser method), [1] (phenotypic.enhance.RankMedianEnhancer method), [1] (phenotypic.enhance.SetDetectMode method), [1] (phenotypic.enhance.SharpenEdgeGauss method), [1] (phenotypic.enhance.StructureSmoothing method), [1] (phenotypic.enhance.SubtractGaussian method), [1] (phenotypic.enhance.SubtractOpening method), [1] (phenotypic.enhance.SubtractRollingBall method), [1] (phenotypic.enhance.SubtractWhiteTophat method), [1] (phenotypic.enhance.VisuShrinkEnhancer method), [1] (phenotypic.enhance.WhiteTophatEnhance method), [1] (phenotypic.grid.AutoGridFinder method), [1] (phenotypic.grid.CenteredAutoGridFinder method), [1] (phenotypic.grid.GridApply method), [1] (phenotypic.grid.ManualGridFinder method), [1] (phenotypic.measure.MeasureBounds method), [1] (phenotypic.measure.MeasureColor method), [1] (phenotypic.measure.MeasureGridLinRegStats method), [1] (phenotypic.measure.MeasureGridSpatial method), [1] (phenotypic.measure.MeasureGridSpread method), [1] (phenotypic.measure.MeasureIntensity method), [1] (phenotypic.measure.MeasureShape method), [1] (phenotypic.measure.MeasureSize method), [1] (phenotypic.measure.MeasureSymmetricZones method), [1] (phenotypic.measure.MeasureTexture method), [1] (phenotypic.post.AppendString method) (phenotypic.post.ExpandMetadata method) (phenotypic.post.MergeMetadata method) (phenotypic.post.PrependString method) (phenotypic.prefab.FilamentousFungiPipeline method), [1] (phenotypic.prefab.GridSectionPipeline method), [1] (phenotypic.prefab.HeavyOtsuPipeline method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1] (phenotypic.prefab.HeavyWatershedPipeline method), [1] (phenotypic.prefab.RoundPeaksPipeline method), [1] (phenotypic.prefab.SpImagerPipeline method), [1] (phenotypic.refine.ExtractColonyCore method), [1] (phenotypic.refine.GridAlignmentRefiner method), [1] (phenotypic.refine.GridOversizedObjectRemover method), [1] (phenotypic.refine.KeepNearestCenter method), [1] (phenotypic.refine.KeepSectionLargest method), [1] (phenotypic.refine.ManualRefine method), [1] (phenotypic.refine.MaskClosing method), [1] (phenotypic.refine.MaskDilation method), [1] (phenotypic.refine.MaskErosion method), [1] (phenotypic.refine.MaskFill method), [1] (phenotypic.refine.MaskGradient method), [1] (phenotypic.refine.MaskOpening method), [1] (phenotypic.refine.MaskWhiteTophat method), [1] (phenotypic.refine.MergeFragmentChains method), [1] (phenotypic.refine.NearestNeighborMerger method), [1] (phenotypic.refine.ReduceSectionsByLine method), [1] (phenotypic.refine.RefineBySineFit method), [1] (phenotypic.refine.RemoveBorderObjects method), [1] (phenotypic.refine.RemoveByFeature method), [1] (phenotypic.refine.RemoveGridOutliers method), [1] (phenotypic.refine.RemoveLowCircularity method), [1] (phenotypic.refine.SeparateObjects method), [1] (phenotypic.refine.Skeletonize method), [1] (phenotypic.refine.SmallObjectRemover method), [1] (phenotypic.refine.SmallToLargeMerger method), [1] (phenotypic.refine.Thinning method), [1] (phenotypic.refine.TrimAsymmetry method), [1] (phenotypic.tune.Budget method), [1] (phenotypic.tune.Categorical method), [1] (phenotypic.tune.CompositeScorer method), [1] (phenotypic.tune.EvaluationResult method), [1] (phenotypic.tune.Evaluator method), [1] (phenotypic.tune.Excluded method), [1] (phenotypic.tune.Fixed method), [1] (phenotypic.tune.FloatRange method), [1] (phenotypic.tune.GridConfig method), [1] (phenotypic.tune.GroundTruthMasks method), [1] (phenotypic.tune.HeldOutConfig method), [1] (phenotypic.tune.ImportanceReport method), [1] (phenotypic.tune.InferredSearchSpace method), [1] (phenotypic.tune.IntRange method), [1] (phenotypic.tune.Knob method), [1] (phenotypic.tune.OptunaConfig method), [1] (phenotypic.tune.QCScorer method), [1] (phenotypic.tune.RandomConfig method), [1] (phenotypic.tune.ReferenceFreeScorer method), [1] (phenotypic.tune.Scorer method), [1] (phenotypic.tune.SearchSpace method), [1] (phenotypic.tune.StrategyConfig method), [1] (phenotypic.tune.SupervisedScorer method), [1] (phenotypic.tune.targets.Nested method) (phenotypic.tune.targets.Param method) (phenotypic.tune.targets.Presence method) (phenotypic.tune.targets.TunableParam method) (phenotypic.tune.Trial method), [1] (phenotypic.tune.TuningSpec method), [1] __deepcopy__() (phenotypic.abc_.BackgroundSubtraction method), [1] (phenotypic.abc_.BaseOperation method), [1] (phenotypic.abc_.ContrastAdjustment method), [1] (phenotypic.abc_.FocusBlob method), [1] (phenotypic.abc_.FocusEdge method), [1] (phenotypic.abc_.GpuDetector method), [1] (phenotypic.abc_.GridCorrector method), [1] (phenotypic.abc_.GridFinder method), [1] (phenotypic.abc_.GridMeasureFeatures method), [1] (phenotypic.abc_.GridObjectDetector method), [1] (phenotypic.abc_.GridObjectRefiner method), [1] (phenotypic.abc_.GridOperation method), [1] (phenotypic.abc_.ImageCorrector method), [1] (phenotypic.abc_.ImageDenoiser method), [1] (phenotypic.abc_.ImageEnhancer method), [1] (phenotypic.abc_.ImageOperation method), [1] (phenotypic.abc_.MeasureFeatures method), [1] (phenotypic.abc_.MorphologicalFiltering method), [1] (phenotypic.abc_.ObjectDetector method), [1] (phenotypic.abc_.ObjectRefiner method), [1] (phenotypic.abc_.PostMeasurement method), [1] (phenotypic.abc_.PrefabPipeline method), [1] (phenotypic.abc_.Smoothing method), [1] (phenotypic.abc_.ThresholdDetector method), [1] (phenotypic.analysis.abc_.ModelFitter method) (phenotypic.analysis.abc_.QualityCheck method) (phenotypic.analysis.abc_.SetAnalyzer method) (phenotypic.analysis.DoubleSoftplus method), [1] (phenotypic.analysis.EdgeCorrector method), [1] (phenotypic.analysis.ErrorCutoffFinder method), [1] (phenotypic.analysis.ExpectedVsDetectedCount method), [1] (phenotypic.analysis.ICC method), [1] (phenotypic.analysis.LinearSoftplus method), [1] (phenotypic.analysis.LogGrowthModel method), [1] (phenotypic.analysis.MADOutlierRemover method), [1] (phenotypic.analysis.MaxModifiedZScore method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount method) (phenotypic.analysis.qc.ICC method) (phenotypic.analysis.qc.MaxModifiedZScore method) (phenotypic.analysis.qc.RelativeMAD method) (phenotypic.analysis.qc.ReplicateAgreement method) (phenotypic.analysis.qc.TukeyOutlierFraction method) (phenotypic.analysis.RelativeMAD method), [1] (phenotypic.analysis.ReplicateAgreement method), [1] (phenotypic.analysis.TukeyOutlierFraction method), [1] (phenotypic.analysis.TukeyOutlierRemover method), [1] (phenotypic.correction.BayesShrinkCorrector method), [1] (phenotypic.correction.CaptureMetadata method), [1] (phenotypic.correction.ColorCheckerProfile method), [1] (phenotypic.correction.ColorCorrector method), [1] (phenotypic.correction.ColorDenoise method), [1] (phenotypic.correction.DenoiseBlockMatch method), [1] (phenotypic.correction.GridAligner method), [1] (phenotypic.correction.ImageCropper method), [1] (phenotypic.correction.ImagePadder method), [1] (phenotypic.correction.VisuShrinkCorrector method), [1] (phenotypic.detect.CannyDetector method), [1] (phenotypic.detect.ChanVeseDetector method), [1] (phenotypic.detect.CompositeDetector method), [1] (phenotypic.detect.FilamentousFungiDetector method), [1] (phenotypic.detect.HysteresisDetector method), [1] (phenotypic.detect.InoculumDetector method), [1] (phenotypic.detect.IsodataDetector method), [1] (phenotypic.detect.LiDetector method), [1] (phenotypic.detect.MadHysteresisDetector method), [1] (phenotypic.detect.ManualGridPointDetector method), [1] (phenotypic.detect.ManualPointDetector method), [1] (phenotypic.detect.MeanDetector method), [1] (phenotypic.detect.MinimumDetector method), [1] (phenotypic.detect.OtsuDetector method), [1] (phenotypic.detect.RankOtsuDetector method), [1] (phenotypic.detect.RoundPeaksDetector method), [1] (phenotypic.detect.SecondaryOtsuDetector method), [1] (phenotypic.detect.SinePeakDetector method), [1] (phenotypic.detect.TriangleDetector method), [1] (phenotypic.detect.UserThreshold method), [1] (phenotypic.detect.WatershedDetector method), [1] (phenotypic.detect.YenDetector method), [1] (phenotypic.enhance.BayesShrinkEnhancer method), [1] (phenotypic.enhance.ContrastStretching method), [1] (phenotypic.enhance.EnhanceBlockMatch method), [1] (phenotypic.enhance.EnhanceLocalContrast method), [1] (phenotypic.enhance.FlattenIllumination method), [1] (phenotypic.enhance.FocusBlobLoG method), [1] (phenotypic.enhance.FocusEdgeFrangi method), [1] (phenotypic.enhance.FocusEdgeHessian method), [1] (phenotypic.enhance.FocusEdgeLaplace method), [1] (phenotypic.enhance.FocusEdgeMeijering method), [1] (phenotypic.enhance.FocusEdgePhase method), [1] (phenotypic.enhance.FocusEdgeSato method), [1] (phenotypic.enhance.FocusEdgeSobel method), [1] (phenotypic.enhance.GaussianBlur method), [1] (phenotypic.enhance.GrayOpening method), [1] (phenotypic.enhance.ImageInverter method), [1] (phenotypic.enhance.LocalEdgeDenoise method), [1] (phenotypic.enhance.MedianFilter method), [1] (phenotypic.enhance.NonLocalMeansDenoiser method), [1] (phenotypic.enhance.RankMedianEnhancer method), [1] (phenotypic.enhance.SetDetectMode method), [1] (phenotypic.enhance.SharpenEdgeGauss method), [1] (phenotypic.enhance.StructureSmoothing method), [1] (phenotypic.enhance.SubtractGaussian method), [1] (phenotypic.enhance.SubtractOpening method), [1] (phenotypic.enhance.SubtractRollingBall method), [1] (phenotypic.enhance.SubtractWhiteTophat method), [1] (phenotypic.enhance.VisuShrinkEnhancer method), [1] (phenotypic.enhance.WhiteTophatEnhance method), [1] (phenotypic.grid.AutoGridFinder method), [1] (phenotypic.grid.CenteredAutoGridFinder method), [1] (phenotypic.grid.GridApply method), [1] (phenotypic.grid.ManualGridFinder method), [1] (phenotypic.measure.MeasureBounds method), [1] (phenotypic.measure.MeasureColor method), [1] (phenotypic.measure.MeasureGridLinRegStats method), [1] (phenotypic.measure.MeasureGridSpatial method), [1] (phenotypic.measure.MeasureGridSpread method), [1] (phenotypic.measure.MeasureIntensity method), [1] (phenotypic.measure.MeasureShape method), [1] (phenotypic.measure.MeasureSize method), [1] (phenotypic.measure.MeasureSymmetricZones method), [1] (phenotypic.measure.MeasureTexture method), [1] (phenotypic.post.AppendString method) (phenotypic.post.ExpandMetadata method) (phenotypic.post.MergeMetadata method) (phenotypic.post.PrependString method) (phenotypic.prefab.FilamentousFungiPipeline method), [1] (phenotypic.prefab.GridSectionPipeline method), [1] (phenotypic.prefab.HeavyOtsuPipeline method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1] (phenotypic.prefab.HeavyWatershedPipeline method), [1] (phenotypic.prefab.RoundPeaksPipeline method), [1] (phenotypic.prefab.SpImagerPipeline method), [1] (phenotypic.refine.ExtractColonyCore method), [1] (phenotypic.refine.GridAlignmentRefiner method), [1] (phenotypic.refine.GridOversizedObjectRemover method), [1] (phenotypic.refine.KeepNearestCenter method), [1] (phenotypic.refine.KeepSectionLargest method), [1] (phenotypic.refine.ManualRefine method), [1] (phenotypic.refine.MaskClosing method), [1] (phenotypic.refine.MaskDilation method), [1] (phenotypic.refine.MaskErosion method), [1] (phenotypic.refine.MaskFill method), [1] (phenotypic.refine.MaskGradient method), [1] (phenotypic.refine.MaskOpening method), [1] (phenotypic.refine.MaskWhiteTophat method), [1] (phenotypic.refine.MergeFragmentChains method), [1] (phenotypic.refine.NearestNeighborMerger method), [1] (phenotypic.refine.ReduceSectionsByLine method), [1] (phenotypic.refine.RefineBySineFit method), [1] (phenotypic.refine.RemoveBorderObjects method), [1] (phenotypic.refine.RemoveByFeature method), [1] (phenotypic.refine.RemoveGridOutliers method), [1] (phenotypic.refine.RemoveLowCircularity method), [1] (phenotypic.refine.SeparateObjects method), [1] (phenotypic.refine.Skeletonize method), [1] (phenotypic.refine.SmallObjectRemover method), [1] (phenotypic.refine.SmallToLargeMerger method), [1] (phenotypic.refine.Thinning method), [1] (phenotypic.refine.TrimAsymmetry method), [1] (phenotypic.tune.Budget method), [1] (phenotypic.tune.Categorical method), [1] (phenotypic.tune.CompositeScorer method), [1] (phenotypic.tune.EvaluationResult method), [1] (phenotypic.tune.Evaluator method), [1] (phenotypic.tune.Excluded method), [1] (phenotypic.tune.Fixed method), [1] (phenotypic.tune.FloatRange method), [1] (phenotypic.tune.GridConfig method), [1] (phenotypic.tune.GroundTruthMasks method), [1] (phenotypic.tune.HeldOutConfig method), [1] (phenotypic.tune.ImportanceReport method), [1] (phenotypic.tune.InferredSearchSpace method), [1] (phenotypic.tune.IntRange method), [1] (phenotypic.tune.Knob method), [1] (phenotypic.tune.OptunaConfig method), [1] (phenotypic.tune.QCScorer method), [1] (phenotypic.tune.RandomConfig method), [1] (phenotypic.tune.ReferenceFreeScorer method), [1] (phenotypic.tune.Scorer method), [1] (phenotypic.tune.SearchSpace method), [1] (phenotypic.tune.StrategyConfig method), [1] (phenotypic.tune.SupervisedScorer method), [1] (phenotypic.tune.targets.Nested method) (phenotypic.tune.targets.Param method) (phenotypic.tune.targets.Presence method) (phenotypic.tune.targets.TunableParam method) (phenotypic.tune.Trial method), [1] (phenotypic.tune.TuningSpec method), [1] __del__() (phenotypic.abc_.BackgroundSubtraction method), [1] (phenotypic.abc_.BaseOperation method), [1] (phenotypic.abc_.ContrastAdjustment method), [1] (phenotypic.abc_.FocusBlob method), [1] (phenotypic.abc_.FocusEdge method), [1] (phenotypic.abc_.GpuDetector method), [1] (phenotypic.abc_.GridCorrector method), [1] (phenotypic.abc_.GridFinder method), [1] (phenotypic.abc_.GridMeasureFeatures method), [1] (phenotypic.abc_.GridObjectDetector method), [1] (phenotypic.abc_.GridObjectRefiner method), [1] (phenotypic.abc_.GridOperation method), [1] (phenotypic.abc_.ImageCorrector method), [1] (phenotypic.abc_.ImageDenoiser method), [1] (phenotypic.abc_.ImageEnhancer method), [1] (phenotypic.abc_.ImageOperation method), [1] (phenotypic.abc_.MeasureFeatures method), [1] (phenotypic.abc_.MorphologicalFiltering method), [1] (phenotypic.abc_.ObjectDetector method), [1] (phenotypic.abc_.ObjectRefiner method), [1] (phenotypic.abc_.PostMeasurement method), [1] (phenotypic.abc_.PrefabPipeline method), [1] (phenotypic.abc_.Smoothing method), [1] (phenotypic.abc_.ThresholdDetector method), [1] (phenotypic.correction.BayesShrinkCorrector method), [1] (phenotypic.correction.ColorCorrector method), [1] (phenotypic.correction.ColorDenoise method), [1] (phenotypic.correction.DenoiseBlockMatch method), [1] (phenotypic.correction.GridAligner method), [1] (phenotypic.correction.ImageCropper method), [1] (phenotypic.correction.ImagePadder method), [1] (phenotypic.correction.VisuShrinkCorrector method), [1] (phenotypic.detect.CannyDetector method), [1] (phenotypic.detect.ChanVeseDetector method), [1] (phenotypic.detect.CompositeDetector method), [1] (phenotypic.detect.FilamentousFungiDetector method), [1] (phenotypic.detect.HysteresisDetector method), [1] (phenotypic.detect.InoculumDetector method), [1] (phenotypic.detect.IsodataDetector method), [1] (phenotypic.detect.LiDetector method), [1] (phenotypic.detect.MadHysteresisDetector method), [1] (phenotypic.detect.ManualGridPointDetector method), [1] (phenotypic.detect.ManualPointDetector method), [1] (phenotypic.detect.MeanDetector method), [1] (phenotypic.detect.MinimumDetector method), [1] (phenotypic.detect.OtsuDetector method), [1] (phenotypic.detect.RankOtsuDetector method), [1] (phenotypic.detect.RoundPeaksDetector method), [1] (phenotypic.detect.SecondaryOtsuDetector method), [1] (phenotypic.detect.SinePeakDetector method), [1] (phenotypic.detect.TriangleDetector method), [1] (phenotypic.detect.UserThreshold method), [1] (phenotypic.detect.WatershedDetector method), [1] (phenotypic.detect.YenDetector method), [1] (phenotypic.enhance.BayesShrinkEnhancer method), [1] (phenotypic.enhance.ContrastStretching method), [1] (phenotypic.enhance.EnhanceBlockMatch method), [1] (phenotypic.enhance.EnhanceLocalContrast method), [1] (phenotypic.enhance.FlattenIllumination method), [1] (phenotypic.enhance.FocusBlobLoG method), [1] (phenotypic.enhance.FocusEdgeFrangi method), [1] (phenotypic.enhance.FocusEdgeHessian method), [1] (phenotypic.enhance.FocusEdgeLaplace method), [1] (phenotypic.enhance.FocusEdgeMeijering method), [1] (phenotypic.enhance.FocusEdgePhase method), [1] (phenotypic.enhance.FocusEdgeSato method), [1] (phenotypic.enhance.FocusEdgeSobel method), [1] (phenotypic.enhance.GaussianBlur method), [1] (phenotypic.enhance.GrayOpening method), [1] (phenotypic.enhance.ImageInverter method), [1] (phenotypic.enhance.LocalEdgeDenoise method), [1] (phenotypic.enhance.MedianFilter method), [1] (phenotypic.enhance.NonLocalMeansDenoiser method), [1] (phenotypic.enhance.RankMedianEnhancer method), [1] (phenotypic.enhance.SetDetectMode method), [1] (phenotypic.enhance.SharpenEdgeGauss method), [1] (phenotypic.enhance.StructureSmoothing method), [1] (phenotypic.enhance.SubtractGaussian method), [1] (phenotypic.enhance.SubtractOpening method), [1] (phenotypic.enhance.SubtractRollingBall method), [1] (phenotypic.enhance.SubtractWhiteTophat method), [1] (phenotypic.enhance.VisuShrinkEnhancer method), [1] (phenotypic.enhance.WhiteTophatEnhance method), [1] (phenotypic.grid.AutoGridFinder method), [1] (phenotypic.grid.CenteredAutoGridFinder method), [1] (phenotypic.grid.GridApply method), [1] (phenotypic.grid.ManualGridFinder method), [1] (phenotypic.measure.MeasureBounds method), [1] (phenotypic.measure.MeasureColor method), [1] (phenotypic.measure.MeasureGridLinRegStats method), [1] (phenotypic.measure.MeasureGridSpatial method), [1] (phenotypic.measure.MeasureGridSpread method), [1] (phenotypic.measure.MeasureIntensity method), [1] (phenotypic.measure.MeasureShape method), [1] (phenotypic.measure.MeasureSize method), [1] (phenotypic.measure.MeasureSymmetricZones method), [1] (phenotypic.measure.MeasureTexture method), [1] (phenotypic.post.AppendString method) (phenotypic.post.ExpandMetadata method) (phenotypic.post.MergeMetadata method) (phenotypic.post.PrependString method) (phenotypic.prefab.FilamentousFungiPipeline method), [1] (phenotypic.prefab.GridSectionPipeline method), [1] (phenotypic.prefab.HeavyOtsuPipeline method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1] (phenotypic.prefab.HeavyWatershedPipeline method), [1] (phenotypic.prefab.RoundPeaksPipeline method), [1] (phenotypic.prefab.SpImagerPipeline method), [1] (phenotypic.refine.ExtractColonyCore method), [1] (phenotypic.refine.GridAlignmentRefiner method), [1] (phenotypic.refine.GridOversizedObjectRemover method), [1] (phenotypic.refine.KeepNearestCenter method), [1] (phenotypic.refine.KeepSectionLargest method), [1] (phenotypic.refine.ManualRefine method), [1] (phenotypic.refine.MaskClosing method), [1] (phenotypic.refine.MaskDilation method), [1] (phenotypic.refine.MaskErosion method), [1] (phenotypic.refine.MaskFill method), [1] (phenotypic.refine.MaskGradient method), [1] (phenotypic.refine.MaskOpening method), [1] (phenotypic.refine.MaskWhiteTophat method), [1] (phenotypic.refine.MergeFragmentChains method), [1] (phenotypic.refine.NearestNeighborMerger method), [1] (phenotypic.refine.ReduceSectionsByLine method), [1] (phenotypic.refine.RefineBySineFit method), [1] (phenotypic.refine.RemoveBorderObjects method), [1] (phenotypic.refine.RemoveByFeature method), [1] (phenotypic.refine.RemoveGridOutliers method), [1] (phenotypic.refine.RemoveLowCircularity method), [1] (phenotypic.refine.SeparateObjects method), [1] (phenotypic.refine.Skeletonize method), [1] (phenotypic.refine.SmallObjectRemover method), [1] (phenotypic.refine.SmallToLargeMerger method), [1] (phenotypic.refine.Thinning method), [1] (phenotypic.refine.TrimAsymmetry method), [1] __delitem__() (phenotypic._core._image_parts.accessors._metadata_accessor.MetadataAccessor method) __dir__() (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] __eq__() (phenotypic.Image method) __get_pydantic_json_schema__() (phenotypic.abc_.BackgroundSubtraction class method), [1] (phenotypic.abc_.BaseOperation class method), [1] (phenotypic.abc_.ContrastAdjustment class method), [1] (phenotypic.abc_.FocusBlob class method), [1] (phenotypic.abc_.FocusEdge class method), [1] (phenotypic.abc_.GpuDetector class method), [1] (phenotypic.abc_.GridCorrector class method), [1] (phenotypic.abc_.GridFinder class method), [1] (phenotypic.abc_.GridMeasureFeatures class method), [1] (phenotypic.abc_.GridObjectDetector class method), [1] (phenotypic.abc_.GridObjectRefiner class method), [1] (phenotypic.abc_.GridOperation class method), [1] (phenotypic.abc_.ImageCorrector class method), [1] (phenotypic.abc_.ImageDenoiser class method), [1] (phenotypic.abc_.ImageEnhancer class method), [1] (phenotypic.abc_.ImageOperation class method), [1] (phenotypic.abc_.MeasureFeatures class method), [1] (phenotypic.abc_.MorphologicalFiltering class method), [1] (phenotypic.abc_.ObjectDetector class method), [1] (phenotypic.abc_.ObjectRefiner class method), [1] (phenotypic.abc_.PostMeasurement class method), [1] (phenotypic.abc_.PrefabPipeline class method), [1] (phenotypic.abc_.Smoothing class method), [1] (phenotypic.abc_.ThresholdDetector class method), [1] (phenotypic.analysis.abc_.ModelFitter class method) (phenotypic.analysis.abc_.QualityCheck class method) (phenotypic.analysis.abc_.SetAnalyzer class method) (phenotypic.analysis.DoubleSoftplus class method), [1] (phenotypic.analysis.EdgeCorrector class method), [1] (phenotypic.analysis.ErrorCutoffFinder class method), [1] (phenotypic.analysis.ExpectedVsDetectedCount class method), [1] (phenotypic.analysis.ICC class method), [1] (phenotypic.analysis.LinearSoftplus class method), [1] (phenotypic.analysis.LogGrowthModel class method), [1] (phenotypic.analysis.MADOutlierRemover class method), [1] (phenotypic.analysis.MaxModifiedZScore class method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount class method) (phenotypic.analysis.qc.ICC class method) (phenotypic.analysis.qc.MaxModifiedZScore class method) (phenotypic.analysis.qc.RelativeMAD class method) (phenotypic.analysis.qc.ReplicateAgreement class method) (phenotypic.analysis.qc.TukeyOutlierFraction class method) (phenotypic.analysis.RelativeMAD class method), [1] (phenotypic.analysis.ReplicateAgreement class method), [1] (phenotypic.analysis.TukeyOutlierFraction class method), [1] (phenotypic.analysis.TukeyOutlierRemover class method), [1] (phenotypic.correction.BayesShrinkCorrector class method), [1] (phenotypic.correction.CaptureMetadata class method), [1] (phenotypic.correction.ColorCheckerProfile class method), [1] (phenotypic.correction.ColorCorrector class method), [1] (phenotypic.correction.ColorDenoise class method), [1] (phenotypic.correction.DenoiseBlockMatch class method), [1] (phenotypic.correction.GridAligner class method), [1] (phenotypic.correction.ImageCropper class method), [1] (phenotypic.correction.ImagePadder class method), [1] (phenotypic.correction.VisuShrinkCorrector class method), [1] (phenotypic.detect.CannyDetector class method), [1] (phenotypic.detect.ChanVeseDetector class method), [1] (phenotypic.detect.CompositeDetector class method), [1] (phenotypic.detect.FilamentousFungiDetector class method), [1] (phenotypic.detect.HysteresisDetector class method), [1] (phenotypic.detect.InoculumDetector class method), [1] (phenotypic.detect.IsodataDetector class method), [1] (phenotypic.detect.LiDetector class method), [1] (phenotypic.detect.MadHysteresisDetector class method), [1] (phenotypic.detect.ManualGridPointDetector class method), [1] (phenotypic.detect.ManualPointDetector class method), [1] (phenotypic.detect.MeanDetector class method), [1] (phenotypic.detect.MinimumDetector class method), [1] (phenotypic.detect.OtsuDetector class method), [1] (phenotypic.detect.RankOtsuDetector class method), [1] (phenotypic.detect.RoundPeaksDetector class method), [1] (phenotypic.detect.SecondaryOtsuDetector class method), [1] (phenotypic.detect.SinePeakDetector class method), [1] (phenotypic.detect.TriangleDetector class method), [1] (phenotypic.detect.UserThreshold class method), [1] (phenotypic.detect.WatershedDetector class method), [1] (phenotypic.detect.YenDetector class method), [1] (phenotypic.enhance.BayesShrinkEnhancer class method), [1] (phenotypic.enhance.ContrastStretching class method), [1] (phenotypic.enhance.EnhanceBlockMatch class method), [1] (phenotypic.enhance.EnhanceLocalContrast class method), [1] (phenotypic.enhance.FlattenIllumination class method), [1] (phenotypic.enhance.FocusBlobLoG class method), [1] (phenotypic.enhance.FocusEdgeFrangi class method), [1] (phenotypic.enhance.FocusEdgeHessian class method), [1] (phenotypic.enhance.FocusEdgeLaplace class method), [1] (phenotypic.enhance.FocusEdgeMeijering class method), [1] (phenotypic.enhance.FocusEdgePhase class method), [1] (phenotypic.enhance.FocusEdgeSato class method), [1] (phenotypic.enhance.FocusEdgeSobel class method), [1] (phenotypic.enhance.GaussianBlur class method), [1] (phenotypic.enhance.GrayOpening class method), [1] (phenotypic.enhance.ImageInverter class method), [1] (phenotypic.enhance.LocalEdgeDenoise class method), [1] (phenotypic.enhance.MedianFilter class method), [1] (phenotypic.enhance.NonLocalMeansDenoiser class method), [1] (phenotypic.enhance.RankMedianEnhancer class method), [1] (phenotypic.enhance.SetDetectMode class method), [1] (phenotypic.enhance.SharpenEdgeGauss class method), [1] (phenotypic.enhance.StructureSmoothing class method), [1] (phenotypic.enhance.SubtractGaussian class method), [1] (phenotypic.enhance.SubtractOpening class method), [1] (phenotypic.enhance.SubtractRollingBall class method), [1] (phenotypic.enhance.SubtractWhiteTophat class method), [1] (phenotypic.enhance.VisuShrinkEnhancer class method), [1] (phenotypic.enhance.WhiteTophatEnhance class method), [1] (phenotypic.grid.AutoGridFinder class method), [1] (phenotypic.grid.CenteredAutoGridFinder class method), [1] (phenotypic.grid.GridApply class method), [1] (phenotypic.grid.ManualGridFinder class method), [1] (phenotypic.measure.MeasureBounds class method), [1] (phenotypic.measure.MeasureColor class method), [1] (phenotypic.measure.MeasureGridLinRegStats class method), [1] (phenotypic.measure.MeasureGridSpatial class method), [1] (phenotypic.measure.MeasureGridSpread class method), [1] (phenotypic.measure.MeasureIntensity class method), [1] (phenotypic.measure.MeasureShape class method), [1] (phenotypic.measure.MeasureSize class method), [1] (phenotypic.measure.MeasureSymmetricZones class method), [1] (phenotypic.measure.MeasureTexture class method), [1] (phenotypic.post.AppendString class method) (phenotypic.post.ExpandMetadata class method) (phenotypic.post.MergeMetadata class method) (phenotypic.post.PrependString class method) (phenotypic.prefab.FilamentousFungiPipeline class method), [1] (phenotypic.prefab.GridSectionPipeline class method), [1] (phenotypic.prefab.HeavyOtsuPipeline class method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline class method), [1] (phenotypic.prefab.HeavyWatershedPipeline class method), [1] (phenotypic.prefab.RoundPeaksPipeline class method), [1] (phenotypic.prefab.SpImagerPipeline class method), [1] (phenotypic.refine.ExtractColonyCore class method), [1] (phenotypic.refine.GridAlignmentRefiner class method), [1] (phenotypic.refine.GridOversizedObjectRemover class method), [1] (phenotypic.refine.KeepNearestCenter class method), [1] (phenotypic.refine.KeepSectionLargest class method), [1] (phenotypic.refine.ManualRefine class method), [1] (phenotypic.refine.MaskClosing class method), [1] (phenotypic.refine.MaskDilation class method), [1] (phenotypic.refine.MaskErosion class method), [1] (phenotypic.refine.MaskFill class method), [1] (phenotypic.refine.MaskGradient class method), [1] (phenotypic.refine.MaskOpening class method), [1] (phenotypic.refine.MaskWhiteTophat class method), [1] (phenotypic.refine.MergeFragmentChains class method), [1] (phenotypic.refine.NearestNeighborMerger class method), [1] (phenotypic.refine.ReduceSectionsByLine class method), [1] (phenotypic.refine.RefineBySineFit class method), [1] (phenotypic.refine.RemoveBorderObjects class method), [1] (phenotypic.refine.RemoveByFeature class method), [1] (phenotypic.refine.RemoveGridOutliers class method), [1] (phenotypic.refine.RemoveLowCircularity class method), [1] (phenotypic.refine.SeparateObjects class method), [1] (phenotypic.refine.Skeletonize class method), [1] (phenotypic.refine.SmallObjectRemover class method), [1] (phenotypic.refine.SmallToLargeMerger class method), [1] (phenotypic.refine.Thinning class method), [1] (phenotypic.refine.TrimAsymmetry class method), [1] (phenotypic.tune.Budget class method), [1] (phenotypic.tune.Categorical class method), [1] (phenotypic.tune.CompositeScorer class method), [1] (phenotypic.tune.EvaluationResult class method), [1] (phenotypic.tune.Evaluator class method), [1] (phenotypic.tune.Excluded class method), [1] (phenotypic.tune.Fixed class method), [1] (phenotypic.tune.FloatRange class method), [1] (phenotypic.tune.GridConfig class method), [1] (phenotypic.tune.GroundTruthMasks class method), [1] (phenotypic.tune.HeldOutConfig class method), [1] (phenotypic.tune.ImportanceReport class method), [1] (phenotypic.tune.InferredSearchSpace class method), [1] (phenotypic.tune.IntRange class method), [1] (phenotypic.tune.Knob class method), [1] (phenotypic.tune.OptunaConfig class method), [1] (phenotypic.tune.QCScorer class method), [1] (phenotypic.tune.RandomConfig class method), [1] (phenotypic.tune.ReferenceFreeScorer class method), [1] (phenotypic.tune.Scorer class method), [1] (phenotypic.tune.SearchSpace class method), [1] (phenotypic.tune.StrategyConfig class method), [1] (phenotypic.tune.SupervisedScorer class method), [1] (phenotypic.tune.targets.Nested class method) (phenotypic.tune.targets.Param class method) (phenotypic.tune.targets.Presence class method) (phenotypic.tune.targets.TunableParam class method) (phenotypic.tune.Trial class method), [1] (phenotypic.tune.TuningSpec class method), [1] __getattr__() (in module phenotypic.gui) (in module phenotypic.gui.builder) (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) __getitem__() (phenotypic._core._image_parts.accessors._detect_mat_accessor.DetectMatAccessor method) (phenotypic._core._image_parts.accessors._grayscale_accessor.Grayscale method) (phenotypic._core._image_parts.accessors._metadata_accessor.MetadataAccessor method) (phenotypic._core._image_parts.accessors._objects_accessor.ObjectsAccessor method) (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap method) (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask method) (phenotypic._core._image_parts.accessors._rgb_accessor.ImageRGB method) (phenotypic.Image method) (phenotypic.sdk_.constants_.IMAGE_MODE class method), [1] (phenotypic.sdk_.constants_.IMAGE_TYPES class method), [1] __getstate__() (phenotypic.sdk_.LazyWidgetMixin method), [1] (phenotypic.sdk_.mixin.LazyWidgetMixin method) __hash__() (phenotypic.Image method) __iand__() (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask method) __init__() (phenotypic._core._image_parts.accessors._color_accessor.ColorAccessor method) (phenotypic._core._image_parts.accessors._metadata_accessor.MetadataAccessor method) (phenotypic._core._image_parts.accessors._objects_accessor.ObjectsAccessor method) (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) (phenotypic.abc_.BackgroundSubtraction method), [1] (phenotypic.abc_.BaseOperation method), [1] (phenotypic.abc_.ContrastAdjustment method), [1] (phenotypic.abc_.FocusBlob method), [1] (phenotypic.abc_.FocusEdge method), [1] (phenotypic.abc_.GpuDetector method), [1] (phenotypic.abc_.GridCorrector method), [1] (phenotypic.abc_.GridFinder method), [1] (phenotypic.abc_.GridMeasureFeatures method), [1] (phenotypic.abc_.GridObjectDetector method), [1] (phenotypic.abc_.GridObjectRefiner method), [1] (phenotypic.abc_.GridOperation method), [1] (phenotypic.abc_.ImageCorrector method), [1] (phenotypic.abc_.ImageDenoiser method), [1] (phenotypic.abc_.ImageEnhancer method), [1] (phenotypic.abc_.ImageOperation method), [1] (phenotypic.abc_.MeasureFeatures method), [1] (phenotypic.abc_.MorphologicalFiltering method), [1] (phenotypic.abc_.ObjectDetector method), [1] (phenotypic.abc_.ObjectRefiner method), [1] (phenotypic.abc_.PostMeasurement method), [1] (phenotypic.abc_.PrefabPipeline method), [1] (phenotypic.abc_.Smoothing method), [1] (phenotypic.abc_.ThresholdDetector method), [1] (phenotypic.analysis.abc_.ModelFitter method) (phenotypic.analysis.abc_.QualityCheck method) (phenotypic.analysis.abc_.SetAnalyzer method) (phenotypic.analysis.DoubleSoftplus method), [1] (phenotypic.analysis.EdgeCorrector method), [1] (phenotypic.analysis.ErrorCutoffFinder method), [1] (phenotypic.analysis.ExpectedVsDetectedCount method), [1] (phenotypic.analysis.ICC method), [1] (phenotypic.analysis.LinearSoftplus method), [1] (phenotypic.analysis.LogGrowthModel method), [1] (phenotypic.analysis.MADOutlierRemover method), [1] (phenotypic.analysis.MaxModifiedZScore method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount method) (phenotypic.analysis.qc.ICC method) (phenotypic.analysis.qc.MaxModifiedZScore method) (phenotypic.analysis.qc.RelativeMAD method) (phenotypic.analysis.qc.ReplicateAgreement method) (phenotypic.analysis.qc.TukeyOutlierFraction method) (phenotypic.analysis.RelativeMAD method), [1] (phenotypic.analysis.ReplicateAgreement method), [1] (phenotypic.analysis.TukeyOutlierFraction method), [1] (phenotypic.analysis.TukeyOutlierRemover method), [1] (phenotypic.correction.BayesShrinkCorrector method), [1] (phenotypic.correction.CaptureMetadata method), [1] (phenotypic.correction.ColorCheckerProfile method), [1] (phenotypic.correction.ColorCorrector method), [1] (phenotypic.correction.ColorDenoise method), [1] (phenotypic.correction.DenoiseBlockMatch method), [1] (phenotypic.correction.GridAligner method), [1] (phenotypic.correction.ImageCropper method), [1] (phenotypic.correction.ImagePadder method), [1] (phenotypic.correction.VisuShrinkCorrector method), [1] (phenotypic.detect.CannyDetector method), [1] (phenotypic.detect.ChanVeseDetector method), [1] (phenotypic.detect.CompositeDetector method), [1] (phenotypic.detect.FilamentousFungiDetector method), [1] (phenotypic.detect.HysteresisDetector method), [1] (phenotypic.detect.InoculumDetector method), [1] (phenotypic.detect.IsodataDetector method), [1] (phenotypic.detect.LiDetector method), [1] (phenotypic.detect.MadHysteresisDetector method), [1] (phenotypic.detect.ManualGridPointDetector method), [1] (phenotypic.detect.ManualPointDetector method), [1] (phenotypic.detect.MeanDetector method), [1] (phenotypic.detect.MinimumDetector method), [1] (phenotypic.detect.OtsuDetector method), [1] (phenotypic.detect.RankOtsuDetector method), [1] (phenotypic.detect.RoundPeaksDetector method), [1] (phenotypic.detect.SecondaryOtsuDetector method), [1] (phenotypic.detect.SinePeakDetector method), [1] (phenotypic.detect.TriangleDetector method), [1] (phenotypic.detect.UserThreshold method), [1] (phenotypic.detect.WatershedDetector method), [1] (phenotypic.detect.YenDetector method), [1] (phenotypic.enhance.BayesShrinkEnhancer method), [1] (phenotypic.enhance.ContrastStretching method), [1] (phenotypic.enhance.EnhanceBlockMatch method), [1] (phenotypic.enhance.EnhanceLocalContrast method), [1] (phenotypic.enhance.FlattenIllumination method), [1] (phenotypic.enhance.FocusBlobLoG method), [1] (phenotypic.enhance.FocusEdgeFrangi method), [1] (phenotypic.enhance.FocusEdgeHessian method), [1] (phenotypic.enhance.FocusEdgeLaplace method), [1] (phenotypic.enhance.FocusEdgeMeijering method), [1] (phenotypic.enhance.FocusEdgePhase method), [1] (phenotypic.enhance.FocusEdgeSato method), [1] (phenotypic.enhance.FocusEdgeSobel method), [1] (phenotypic.enhance.GaussianBlur method), [1] (phenotypic.enhance.GrayOpening method), [1] (phenotypic.enhance.ImageInverter method), [1] (phenotypic.enhance.LocalEdgeDenoise method), [1] (phenotypic.enhance.MedianFilter method), [1] (phenotypic.enhance.NonLocalMeansDenoiser method), [1] (phenotypic.enhance.RankMedianEnhancer method), [1] (phenotypic.enhance.SetDetectMode method), [1] (phenotypic.enhance.SharpenEdgeGauss method), [1] (phenotypic.enhance.StructureSmoothing method), [1] (phenotypic.enhance.SubtractGaussian method), [1] (phenotypic.enhance.SubtractOpening method), [1] (phenotypic.enhance.SubtractRollingBall method), [1] (phenotypic.enhance.SubtractWhiteTophat method), [1] (phenotypic.enhance.VisuShrinkEnhancer method), [1] (phenotypic.enhance.WhiteTophatEnhance method), [1] (phenotypic.grid.AutoGridFinder method), [1] (phenotypic.grid.CenteredAutoGridFinder method), [1] (phenotypic.grid.GridApply method), [1] (phenotypic.grid.ManualGridFinder method), [1] (phenotypic.GridImage method) (phenotypic.Image method) (phenotypic.ImagePipeline method) (phenotypic.measure.MeasureBounds method), [1] (phenotypic.measure.MeasureColor method), [1] (phenotypic.measure.MeasureGridLinRegStats method), [1] (phenotypic.measure.MeasureGridSpatial method), [1] (phenotypic.measure.MeasureGridSpread method), [1] (phenotypic.measure.MeasureIntensity method), [1] (phenotypic.measure.MeasureShape method), [1] (phenotypic.measure.MeasureSize method), [1] (phenotypic.measure.MeasureSymmetricZones method), [1] (phenotypic.measure.MeasureTexture method), [1] (phenotypic.post.AppendString method) (phenotypic.post.ExpandMetadata method) (phenotypic.post.MergeMetadata method) (phenotypic.post.PrependString method) (phenotypic.prefab.GridSectionPipeline method), [1] (phenotypic.prefab.HeavyOtsuPipeline method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1] (phenotypic.prefab.HeavyWatershedPipeline method), [1] (phenotypic.refine.ExtractColonyCore method), [1] (phenotypic.refine.GridAlignmentRefiner method), [1] (phenotypic.refine.GridOversizedObjectRemover method), [1] (phenotypic.refine.KeepNearestCenter method), [1] (phenotypic.refine.KeepSectionLargest method), [1] (phenotypic.refine.ManualRefine method), [1] (phenotypic.refine.MaskClosing method), [1] (phenotypic.refine.MaskDilation method), [1] (phenotypic.refine.MaskErosion method), [1] (phenotypic.refine.MaskFill method), [1] (phenotypic.refine.MaskGradient method), [1] (phenotypic.refine.MaskOpening method), [1] (phenotypic.refine.MaskWhiteTophat method), [1] (phenotypic.refine.MergeFragmentChains method), [1] (phenotypic.refine.NearestNeighborMerger method), [1] (phenotypic.refine.ReduceSectionsByLine method), [1] (phenotypic.refine.RefineBySineFit method), [1] (phenotypic.refine.RemoveBorderObjects method), [1] (phenotypic.refine.RemoveByFeature method), [1] (phenotypic.refine.RemoveGridOutliers method), [1] (phenotypic.refine.RemoveLowCircularity method), [1] (phenotypic.refine.SeparateObjects method), [1] (phenotypic.refine.Skeletonize method), [1] (phenotypic.refine.SmallObjectRemover method), [1] (phenotypic.refine.SmallToLargeMerger method), [1] (phenotypic.refine.Thinning method), [1] (phenotypic.refine.TrimAsymmetry method), [1] (phenotypic.sdk_.HDF method), [1] (phenotypic.sdk_.hdf_.HDF method) (phenotypic.tune.Budget method), [1] (phenotypic.tune.Categorical method), [1] (phenotypic.tune.CompositeScorer method), [1] (phenotypic.tune.EvaluationResult method), [1] (phenotypic.tune.Evaluator method), [1] (phenotypic.tune.Excluded method), [1] (phenotypic.tune.Fixed method), [1] (phenotypic.tune.FloatRange method), [1] (phenotypic.tune.GridConfig method), [1] (phenotypic.tune.GroundTruthMasks method), [1] (phenotypic.tune.HeldOutConfig method), [1] (phenotypic.tune.ImportanceReport method), [1] (phenotypic.tune.InferredSearchSpace method), [1] (phenotypic.tune.IntRange method), [1] (phenotypic.tune.JournalStudyStore method), [1] (phenotypic.tune.Knob method), [1] (phenotypic.tune.OptunaConfig method), [1] (phenotypic.tune.QCScorer method), [1] (phenotypic.tune.RandomConfig method), [1] (phenotypic.tune.ReferenceFreeScorer method), [1] (phenotypic.tune.Scorer method), [1] (phenotypic.tune.SearchSpace method), [1] (phenotypic.tune.StrategyConfig method), [1] (phenotypic.tune.SupervisedScorer method), [1] (phenotypic.tune.targets.Nested method) (phenotypic.tune.targets.Param method) (phenotypic.tune.targets.Presence method) (phenotypic.tune.targets.TunableParam method) (phenotypic.tune.Trial method), [1] (phenotypic.tune.TuningEngine method), [1] (phenotypic.tune.TuningSpec method), [1] __init_subclass__() (phenotypic.analysis.abc_.QualityCheck class method) (phenotypic.analysis.ExpectedVsDetectedCount class method), [1] (phenotypic.analysis.ICC class method), [1] (phenotypic.analysis.MaxModifiedZScore class method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount class method) (phenotypic.analysis.qc.ICC class method) 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(phenotypic.abc_.GridFinder method), [1] (phenotypic.abc_.GridMeasureFeatures method), [1] (phenotypic.abc_.GridObjectDetector method), [1] (phenotypic.abc_.GridObjectRefiner method), [1] (phenotypic.abc_.GridOperation method), [1] (phenotypic.abc_.ImageCorrector method), [1] (phenotypic.abc_.ImageDenoiser method), [1] (phenotypic.abc_.ImageEnhancer method), [1] (phenotypic.abc_.ImageOperation method), [1] (phenotypic.abc_.MeasureFeatures method), [1] (phenotypic.abc_.MorphologicalFiltering method), [1] (phenotypic.abc_.ObjectDetector method), [1] (phenotypic.abc_.ObjectRefiner method), [1] (phenotypic.abc_.PostMeasurement method), [1] (phenotypic.abc_.PrefabPipeline method), [1] (phenotypic.abc_.Smoothing method), [1] (phenotypic.abc_.ThresholdDetector method), [1] (phenotypic.analysis.abc_.ModelFitter method) (phenotypic.analysis.abc_.QualityCheck method) (phenotypic.analysis.abc_.SetAnalyzer method) (phenotypic.analysis.DoubleSoftplus method), [1] (phenotypic.analysis.EdgeCorrector method), [1] (phenotypic.analysis.ErrorCutoffFinder method), [1] (phenotypic.analysis.ExpectedVsDetectedCount method), [1] (phenotypic.analysis.ICC method), [1] (phenotypic.analysis.LinearSoftplus method), [1] (phenotypic.analysis.LogGrowthModel method), [1] (phenotypic.analysis.MADOutlierRemover method), [1] (phenotypic.analysis.MaxModifiedZScore method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount method) (phenotypic.analysis.qc.ICC method) (phenotypic.analysis.qc.MaxModifiedZScore method) (phenotypic.analysis.qc.RelativeMAD method) (phenotypic.analysis.qc.ReplicateAgreement method) (phenotypic.analysis.qc.TukeyOutlierFraction method) (phenotypic.analysis.RelativeMAD method), [1] (phenotypic.analysis.ReplicateAgreement method), [1] (phenotypic.analysis.TukeyOutlierFraction method), [1] (phenotypic.analysis.TukeyOutlierRemover method), [1] (phenotypic.correction.BayesShrinkCorrector method), [1] (phenotypic.correction.CaptureMetadata method), [1] (phenotypic.correction.ColorCheckerProfile method), [1] (phenotypic.correction.ColorCorrector method), [1] (phenotypic.correction.ColorDenoise method), [1] (phenotypic.correction.DenoiseBlockMatch method), [1] (phenotypic.correction.GridAligner method), [1] (phenotypic.correction.ImageCropper method), [1] (phenotypic.correction.ImagePadder method), [1] (phenotypic.correction.VisuShrinkCorrector method), [1] (phenotypic.detect.CannyDetector method), [1] (phenotypic.detect.ChanVeseDetector method), [1] (phenotypic.detect.CompositeDetector method), [1] (phenotypic.detect.FilamentousFungiDetector method), [1] (phenotypic.detect.HysteresisDetector method), [1] (phenotypic.detect.InoculumDetector method), [1] (phenotypic.detect.IsodataDetector method), [1] (phenotypic.detect.LiDetector method), [1] (phenotypic.detect.MadHysteresisDetector method), [1] (phenotypic.detect.ManualGridPointDetector method), [1] (phenotypic.detect.ManualPointDetector method), [1] (phenotypic.detect.MeanDetector method), [1] (phenotypic.detect.MinimumDetector method), [1] (phenotypic.detect.OtsuDetector method), [1] (phenotypic.detect.RankOtsuDetector method), [1] (phenotypic.detect.RoundPeaksDetector method), [1] (phenotypic.detect.SecondaryOtsuDetector method), [1] (phenotypic.detect.SinePeakDetector method), [1] (phenotypic.detect.TriangleDetector method), [1] (phenotypic.detect.UserThreshold method), [1] (phenotypic.detect.WatershedDetector method), [1] (phenotypic.detect.YenDetector method), [1] (phenotypic.enhance.BayesShrinkEnhancer method), [1] (phenotypic.enhance.ContrastStretching method), [1] (phenotypic.enhance.EnhanceBlockMatch method), [1] (phenotypic.enhance.EnhanceLocalContrast method), [1] (phenotypic.enhance.FlattenIllumination method), [1] (phenotypic.enhance.FocusBlobLoG method), [1] (phenotypic.enhance.FocusEdgeFrangi method), [1] (phenotypic.enhance.FocusEdgeHessian method), [1] (phenotypic.enhance.FocusEdgeLaplace method), [1] (phenotypic.enhance.FocusEdgeMeijering method), [1] (phenotypic.enhance.FocusEdgePhase method), [1] (phenotypic.enhance.FocusEdgeSato method), [1] (phenotypic.enhance.FocusEdgeSobel method), [1] (phenotypic.enhance.GaussianBlur method), [1] (phenotypic.enhance.GrayOpening method), [1] (phenotypic.enhance.ImageInverter method), [1] (phenotypic.enhance.LocalEdgeDenoise method), [1] (phenotypic.enhance.MedianFilter method), [1] (phenotypic.enhance.NonLocalMeansDenoiser method), [1] (phenotypic.enhance.RankMedianEnhancer method), [1] (phenotypic.enhance.SetDetectMode method), [1] (phenotypic.enhance.SharpenEdgeGauss method), [1] (phenotypic.enhance.StructureSmoothing method), [1] (phenotypic.enhance.SubtractGaussian method), [1] (phenotypic.enhance.SubtractOpening method), [1] (phenotypic.enhance.SubtractRollingBall method), [1] (phenotypic.enhance.SubtractWhiteTophat method), [1] (phenotypic.enhance.VisuShrinkEnhancer method), [1] (phenotypic.enhance.WhiteTophatEnhance method), [1] (phenotypic.grid.AutoGridFinder method), [1] (phenotypic.grid.CenteredAutoGridFinder method), [1] (phenotypic.grid.GridApply method), [1] (phenotypic.grid.ManualGridFinder method), [1] (phenotypic.measure.MeasureBounds method), [1] (phenotypic.measure.MeasureColor method), [1] (phenotypic.measure.MeasureGridLinRegStats method), [1] (phenotypic.measure.MeasureGridSpatial method), [1] (phenotypic.measure.MeasureGridSpread method), [1] (phenotypic.measure.MeasureIntensity method), [1] (phenotypic.measure.MeasureShape method), [1] (phenotypic.measure.MeasureSize method), [1] (phenotypic.measure.MeasureSymmetricZones method), [1] (phenotypic.measure.MeasureTexture method), [1] (phenotypic.post.AppendString method) (phenotypic.post.ExpandMetadata method) (phenotypic.post.MergeMetadata method) (phenotypic.post.PrependString method) (phenotypic.prefab.FilamentousFungiPipeline method), [1] (phenotypic.prefab.GridSectionPipeline method), [1] (phenotypic.prefab.HeavyOtsuPipeline method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1] (phenotypic.prefab.HeavyWatershedPipeline method), [1] (phenotypic.prefab.RoundPeaksPipeline method), [1] (phenotypic.prefab.SpImagerPipeline method), [1] (phenotypic.refine.ExtractColonyCore method), [1] (phenotypic.refine.GridAlignmentRefiner method), [1] (phenotypic.refine.GridOversizedObjectRemover method), [1] (phenotypic.refine.KeepNearestCenter method), [1] (phenotypic.refine.KeepSectionLargest method), [1] (phenotypic.refine.ManualRefine method), [1] (phenotypic.refine.MaskClosing method), [1] (phenotypic.refine.MaskDilation method), [1] (phenotypic.refine.MaskErosion method), [1] (phenotypic.refine.MaskFill method), [1] (phenotypic.refine.MaskGradient method), [1] (phenotypic.refine.MaskOpening method), [1] (phenotypic.refine.MaskWhiteTophat method), [1] (phenotypic.refine.MergeFragmentChains method), [1] (phenotypic.refine.NearestNeighborMerger method), [1] (phenotypic.refine.ReduceSectionsByLine method), [1] (phenotypic.refine.RefineBySineFit method), [1] (phenotypic.refine.RemoveBorderObjects method), [1] (phenotypic.refine.RemoveByFeature method), [1] (phenotypic.refine.RemoveGridOutliers method), [1] (phenotypic.refine.RemoveLowCircularity method), [1] (phenotypic.refine.SeparateObjects method), [1] (phenotypic.refine.Skeletonize method), [1] (phenotypic.refine.SmallObjectRemover method), [1] (phenotypic.refine.SmallToLargeMerger method), [1] (phenotypic.refine.Thinning method), [1] (phenotypic.refine.TrimAsymmetry method), [1] (phenotypic.sdk_.constants_.IMAGE_MODE class method), [1] (phenotypic.sdk_.constants_.IMAGE_TYPES class method), [1] (phenotypic.tune.Budget method), [1] (phenotypic.tune.Categorical method), [1] (phenotypic.tune.CompositeScorer method), [1] (phenotypic.tune.EvaluationResult method), [1] (phenotypic.tune.Evaluator method), [1] (phenotypic.tune.Excluded method), [1] (phenotypic.tune.Fixed method), [1] (phenotypic.tune.FloatRange method), [1] (phenotypic.tune.GridConfig method), [1] 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(phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1]

__or__() (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask method) __pretty__() (phenotypic.abc_.BackgroundSubtraction method), [1] (phenotypic.abc_.BaseOperation method), [1] (phenotypic.abc_.ContrastAdjustment method), [1] (phenotypic.abc_.FocusBlob method), [1] (phenotypic.abc_.FocusEdge method), [1] (phenotypic.abc_.GpuDetector method), [1] (phenotypic.abc_.GridCorrector method), [1] (phenotypic.abc_.GridFinder method), [1] (phenotypic.abc_.GridMeasureFeatures method), [1] (phenotypic.abc_.GridObjectDetector method), [1] (phenotypic.abc_.GridObjectRefiner method), [1] (phenotypic.abc_.GridOperation method), [1] (phenotypic.abc_.ImageCorrector method), [1] (phenotypic.abc_.ImageDenoiser method), [1] (phenotypic.abc_.ImageEnhancer method), [1] (phenotypic.abc_.ImageOperation method), [1] (phenotypic.abc_.MeasureFeatures method), [1] (phenotypic.abc_.MorphologicalFiltering method), [1] (phenotypic.abc_.ObjectDetector method), [1] (phenotypic.abc_.ObjectRefiner 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(phenotypic.analysis.qc.ReplicateAgreement method) (phenotypic.analysis.qc.TukeyOutlierFraction method) (phenotypic.analysis.RelativeMAD method), [1] (phenotypic.analysis.ReplicateAgreement method), [1] (phenotypic.analysis.TukeyOutlierFraction method), [1] (phenotypic.analysis.TukeyOutlierRemover method), [1] (phenotypic.correction.BayesShrinkCorrector method), [1] (phenotypic.correction.CaptureMetadata method), [1] (phenotypic.correction.ColorCheckerProfile method), [1] (phenotypic.correction.ColorCorrector method), [1] (phenotypic.correction.ColorDenoise method), [1] (phenotypic.correction.DenoiseBlockMatch method), [1] (phenotypic.correction.GridAligner method), [1] (phenotypic.correction.ImageCropper method), [1] (phenotypic.correction.ImagePadder method), [1] (phenotypic.correction.VisuShrinkCorrector method), [1] (phenotypic.detect.CannyDetector method), [1] (phenotypic.detect.ChanVeseDetector method), [1] (phenotypic.detect.CompositeDetector method), [1] (phenotypic.detect.FilamentousFungiDetector method), [1] (phenotypic.detect.HysteresisDetector method), [1] (phenotypic.detect.InoculumDetector method), [1] (phenotypic.detect.IsodataDetector method), [1] (phenotypic.detect.LiDetector method), [1] (phenotypic.detect.MadHysteresisDetector method), [1] (phenotypic.detect.ManualGridPointDetector method), [1] (phenotypic.detect.ManualPointDetector method), [1] (phenotypic.detect.MeanDetector method), [1] (phenotypic.detect.MinimumDetector method), [1] (phenotypic.detect.OtsuDetector method), [1] (phenotypic.detect.RankOtsuDetector method), [1] (phenotypic.detect.RoundPeaksDetector method), [1] (phenotypic.detect.SecondaryOtsuDetector method), [1] (phenotypic.detect.SinePeakDetector method), [1] (phenotypic.detect.TriangleDetector method), [1] (phenotypic.detect.UserThreshold method), [1] (phenotypic.detect.WatershedDetector method), [1] (phenotypic.detect.YenDetector method), [1] (phenotypic.enhance.BayesShrinkEnhancer method), [1] (phenotypic.enhance.ContrastStretching method), [1] (phenotypic.enhance.EnhanceBlockMatch method), [1] (phenotypic.enhance.EnhanceLocalContrast method), [1] (phenotypic.enhance.FlattenIllumination method), [1] (phenotypic.enhance.FocusBlobLoG method), [1] (phenotypic.enhance.FocusEdgeFrangi method), [1] (phenotypic.enhance.FocusEdgeHessian method), [1] (phenotypic.enhance.FocusEdgeLaplace method), [1] (phenotypic.enhance.FocusEdgeMeijering method), [1] (phenotypic.enhance.FocusEdgePhase method), [1] (phenotypic.enhance.FocusEdgeSato method), [1] (phenotypic.enhance.FocusEdgeSobel method), [1] (phenotypic.enhance.GaussianBlur method), [1] (phenotypic.enhance.GrayOpening method), [1] (phenotypic.enhance.ImageInverter method), [1] (phenotypic.enhance.LocalEdgeDenoise method), [1] (phenotypic.enhance.MedianFilter method), [1] (phenotypic.enhance.NonLocalMeansDenoiser method), [1] (phenotypic.enhance.RankMedianEnhancer method), [1] (phenotypic.enhance.SetDetectMode method), [1] 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(phenotypic.measure.MeasureSymmetricZones method), [1] (phenotypic.measure.MeasureTexture method), [1] (phenotypic.post.AppendString method) (phenotypic.post.ExpandMetadata method) (phenotypic.post.MergeMetadata method) (phenotypic.post.PrependString method) (phenotypic.prefab.FilamentousFungiPipeline method), [1] (phenotypic.prefab.GridSectionPipeline method), [1] (phenotypic.prefab.HeavyOtsuPipeline method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1] (phenotypic.prefab.HeavyWatershedPipeline method), [1] (phenotypic.prefab.RoundPeaksPipeline method), [1] (phenotypic.prefab.SpImagerPipeline method), [1] (phenotypic.refine.ExtractColonyCore method), [1] (phenotypic.refine.GridAlignmentRefiner method), [1] (phenotypic.refine.GridOversizedObjectRemover method), [1] (phenotypic.refine.KeepNearestCenter method), [1] (phenotypic.refine.KeepSectionLargest method), [1] (phenotypic.refine.ManualRefine method), [1] (phenotypic.refine.MaskClosing method), [1] (phenotypic.refine.MaskDilation method), [1] (phenotypic.refine.MaskErosion method), [1] (phenotypic.refine.MaskFill method), [1] (phenotypic.refine.MaskGradient method), [1] (phenotypic.refine.MaskOpening method), [1] (phenotypic.refine.MaskWhiteTophat method), [1] (phenotypic.refine.MergeFragmentChains method), [1] (phenotypic.refine.NearestNeighborMerger method), [1] (phenotypic.refine.ReduceSectionsByLine method), [1] (phenotypic.refine.RefineBySineFit method), [1] (phenotypic.refine.RemoveBorderObjects method), [1] (phenotypic.refine.RemoveByFeature method), [1] (phenotypic.refine.RemoveGridOutliers method), [1] (phenotypic.refine.RemoveLowCircularity method), [1] (phenotypic.refine.SeparateObjects method), [1] (phenotypic.refine.Skeletonize method), [1] (phenotypic.refine.SmallObjectRemover method), [1] (phenotypic.refine.SmallToLargeMerger method), [1] (phenotypic.refine.Thinning method), [1] (phenotypic.refine.TrimAsymmetry method), [1] (phenotypic.tune.Budget method), [1] 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(phenotypic.tune.targets.Param method) (phenotypic.tune.targets.Presence method) (phenotypic.tune.targets.TunableParam method) (phenotypic.tune.Trial method), [1] (phenotypic.tune.TuningSpec method), [1] __pydantic_init_subclass__() (phenotypic.abc_.BackgroundSubtraction class method), [1] (phenotypic.abc_.BaseOperation class method), [1] (phenotypic.abc_.ContrastAdjustment class method), [1] (phenotypic.abc_.FocusBlob class method), [1] (phenotypic.abc_.FocusEdge class method), [1] (phenotypic.abc_.GpuDetector class method), [1] (phenotypic.abc_.GridCorrector class method), [1] (phenotypic.abc_.GridFinder class method), [1] (phenotypic.abc_.GridMeasureFeatures class method), [1] (phenotypic.abc_.GridObjectDetector class method), [1] (phenotypic.abc_.GridObjectRefiner class method), [1] (phenotypic.abc_.GridOperation class method), [1] (phenotypic.abc_.ImageCorrector class method), [1] (phenotypic.abc_.ImageDenoiser class method), [1] (phenotypic.abc_.ImageEnhancer class method), [1] (phenotypic.abc_.ImageOperation class method), [1] (phenotypic.abc_.MeasureFeatures class method), [1] (phenotypic.abc_.MorphologicalFiltering class method), [1] (phenotypic.abc_.ObjectDetector class method), [1] (phenotypic.abc_.ObjectRefiner class method), [1] (phenotypic.abc_.PostMeasurement class method), [1] (phenotypic.abc_.PrefabPipeline class method), [1] (phenotypic.abc_.Smoothing class method), [1] (phenotypic.abc_.ThresholdDetector class method), [1] (phenotypic.analysis.abc_.ModelFitter class method) (phenotypic.analysis.abc_.QualityCheck class method) (phenotypic.analysis.abc_.SetAnalyzer class method) (phenotypic.analysis.DoubleSoftplus class method), [1] (phenotypic.analysis.EdgeCorrector class method), [1] (phenotypic.analysis.ErrorCutoffFinder class method), [1] (phenotypic.analysis.ExpectedVsDetectedCount class method), [1] (phenotypic.analysis.ICC class method), [1] (phenotypic.analysis.LinearSoftplus class method), [1] (phenotypic.analysis.LogGrowthModel class method), [1] (phenotypic.analysis.MADOutlierRemover class method), [1] (phenotypic.analysis.MaxModifiedZScore class method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount class method) (phenotypic.analysis.qc.ICC class method) (phenotypic.analysis.qc.MaxModifiedZScore class method) (phenotypic.analysis.qc.RelativeMAD class method) (phenotypic.analysis.qc.ReplicateAgreement class method) (phenotypic.analysis.qc.TukeyOutlierFraction class method) (phenotypic.analysis.RelativeMAD class method), [1] (phenotypic.analysis.ReplicateAgreement class method), [1] (phenotypic.analysis.TukeyOutlierFraction class method), [1] (phenotypic.analysis.TukeyOutlierRemover class method), [1] (phenotypic.correction.BayesShrinkCorrector class method), [1] (phenotypic.correction.CaptureMetadata class method), [1] (phenotypic.correction.ColorCheckerProfile class method), [1] (phenotypic.correction.ColorCorrector class method), [1] (phenotypic.correction.ColorDenoise class method), [1] (phenotypic.correction.DenoiseBlockMatch class method), [1] (phenotypic.correction.GridAligner class method), [1] (phenotypic.correction.ImageCropper class method), [1] (phenotypic.correction.ImagePadder class method), [1] (phenotypic.correction.VisuShrinkCorrector class method), [1] (phenotypic.detect.CannyDetector class method), [1] (phenotypic.detect.ChanVeseDetector class method), [1] (phenotypic.detect.CompositeDetector class method), [1] (phenotypic.detect.FilamentousFungiDetector class method), [1] (phenotypic.detect.HysteresisDetector class method), [1] (phenotypic.detect.InoculumDetector class method), [1] (phenotypic.detect.IsodataDetector class method), [1] (phenotypic.detect.LiDetector class method), [1] (phenotypic.detect.MadHysteresisDetector class method), [1] (phenotypic.detect.ManualGridPointDetector class method), [1] (phenotypic.detect.ManualPointDetector class method), [1] (phenotypic.detect.MeanDetector class method), [1] (phenotypic.detect.MinimumDetector class method), [1] (phenotypic.detect.OtsuDetector class method), [1] (phenotypic.detect.RankOtsuDetector class method), [1] (phenotypic.detect.RoundPeaksDetector class method), [1] (phenotypic.detect.SecondaryOtsuDetector class method), [1] (phenotypic.detect.SinePeakDetector class method), [1] (phenotypic.detect.TriangleDetector class method), [1] (phenotypic.detect.UserThreshold class method), [1] (phenotypic.detect.WatershedDetector class method), [1] (phenotypic.detect.YenDetector class method), [1] (phenotypic.enhance.BayesShrinkEnhancer class method), [1] (phenotypic.enhance.ContrastStretching class method), [1] (phenotypic.enhance.EnhanceBlockMatch class method), [1] (phenotypic.enhance.EnhanceLocalContrast class method), [1] (phenotypic.enhance.FlattenIllumination class method), [1] (phenotypic.enhance.FocusBlobLoG class method), [1] (phenotypic.enhance.FocusEdgeFrangi class method), [1] (phenotypic.enhance.FocusEdgeHessian class method), [1] (phenotypic.enhance.FocusEdgeLaplace class method), [1] (phenotypic.enhance.FocusEdgeMeijering class method), [1] (phenotypic.enhance.FocusEdgePhase class method), [1] (phenotypic.enhance.FocusEdgeSato class method), [1] (phenotypic.enhance.FocusEdgeSobel class method), [1] (phenotypic.enhance.GaussianBlur class method), [1] (phenotypic.enhance.GrayOpening class method), [1] (phenotypic.enhance.ImageInverter class method), [1] (phenotypic.enhance.LocalEdgeDenoise class method), [1] (phenotypic.enhance.MedianFilter class method), [1] (phenotypic.enhance.NonLocalMeansDenoiser class method), [1] (phenotypic.enhance.RankMedianEnhancer class method), [1] (phenotypic.enhance.SetDetectMode class method), [1] (phenotypic.enhance.SharpenEdgeGauss class method), [1] (phenotypic.enhance.StructureSmoothing class method), [1] (phenotypic.enhance.SubtractGaussian class method), [1] (phenotypic.enhance.SubtractOpening class method), [1] (phenotypic.enhance.SubtractRollingBall class method), [1] (phenotypic.enhance.SubtractWhiteTophat class method), [1] (phenotypic.enhance.VisuShrinkEnhancer class method), [1] (phenotypic.enhance.WhiteTophatEnhance class method), [1] (phenotypic.grid.AutoGridFinder class method), [1] (phenotypic.grid.CenteredAutoGridFinder class method), [1] (phenotypic.grid.GridApply class method), [1] (phenotypic.grid.ManualGridFinder class method), [1] (phenotypic.measure.MeasureBounds class method), [1] (phenotypic.measure.MeasureColor class method), [1] (phenotypic.measure.MeasureGridLinRegStats class method), [1] (phenotypic.measure.MeasureGridSpatial class method), [1] (phenotypic.measure.MeasureGridSpread class method), [1] (phenotypic.measure.MeasureIntensity class method), [1] (phenotypic.measure.MeasureShape class method), [1] (phenotypic.measure.MeasureSize class method), [1] (phenotypic.measure.MeasureSymmetricZones class method), [1] (phenotypic.measure.MeasureTexture class method), [1] (phenotypic.post.AppendString class method) (phenotypic.post.ExpandMetadata class method) (phenotypic.post.MergeMetadata class method) (phenotypic.post.PrependString class method) (phenotypic.prefab.FilamentousFungiPipeline class method), [1] (phenotypic.prefab.GridSectionPipeline class method), [1] (phenotypic.prefab.HeavyOtsuPipeline class method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline class method), [1] (phenotypic.prefab.HeavyWatershedPipeline class method), [1] (phenotypic.prefab.RoundPeaksPipeline class method), [1] (phenotypic.prefab.SpImagerPipeline class method), [1] (phenotypic.refine.ExtractColonyCore class method), [1] (phenotypic.refine.GridAlignmentRefiner class method), [1] (phenotypic.refine.GridOversizedObjectRemover class method), [1] (phenotypic.refine.KeepNearestCenter class method), [1] (phenotypic.refine.KeepSectionLargest class method), [1] (phenotypic.refine.ManualRefine class method), [1] (phenotypic.refine.MaskClosing class method), [1] (phenotypic.refine.MaskDilation class method), [1] (phenotypic.refine.MaskErosion class method), [1] (phenotypic.refine.MaskFill class method), [1] (phenotypic.refine.MaskGradient class method), [1] (phenotypic.refine.MaskOpening class method), [1] (phenotypic.refine.MaskWhiteTophat class method), [1] (phenotypic.refine.MergeFragmentChains class method), [1] (phenotypic.refine.NearestNeighborMerger class method), [1] (phenotypic.refine.ReduceSectionsByLine class method), [1] (phenotypic.refine.RefineBySineFit class method), [1] (phenotypic.refine.RemoveBorderObjects class method), [1] (phenotypic.refine.RemoveByFeature class method), [1] (phenotypic.refine.RemoveGridOutliers class method), [1] (phenotypic.refine.RemoveLowCircularity class method), [1] (phenotypic.refine.SeparateObjects class method), [1] (phenotypic.refine.Skeletonize class method), [1] (phenotypic.refine.SmallObjectRemover class method), [1] (phenotypic.refine.SmallToLargeMerger class method), [1] (phenotypic.refine.Thinning class method), [1] (phenotypic.refine.TrimAsymmetry class method), [1] (phenotypic.tune.Budget class method), [1] (phenotypic.tune.Categorical class method), [1] (phenotypic.tune.CompositeScorer class method), [1] (phenotypic.tune.EvaluationResult class method), [1] (phenotypic.tune.Evaluator class method), [1] (phenotypic.tune.Excluded class method), [1] (phenotypic.tune.Fixed class method), [1] (phenotypic.tune.FloatRange class method), [1] (phenotypic.tune.GridConfig class method), [1] (phenotypic.tune.GroundTruthMasks class method), [1] (phenotypic.tune.HeldOutConfig class method), [1] (phenotypic.tune.ImportanceReport class method), [1] (phenotypic.tune.InferredSearchSpace class method), [1] (phenotypic.tune.IntRange class method), [1] (phenotypic.tune.Knob class method), [1] (phenotypic.tune.OptunaConfig class method), [1] (phenotypic.tune.QCScorer class method), [1] (phenotypic.tune.RandomConfig class method), [1] (phenotypic.tune.ReferenceFreeScorer class method), [1] (phenotypic.tune.Scorer class method), [1] (phenotypic.tune.SearchSpace class method), [1] (phenotypic.tune.StrategyConfig class method), [1] (phenotypic.tune.SupervisedScorer class method), [1] (phenotypic.tune.targets.Nested class method) (phenotypic.tune.targets.Param class method) (phenotypic.tune.targets.Presence class method) (phenotypic.tune.targets.TunableParam class method) (phenotypic.tune.Trial class method), [1] (phenotypic.tune.TuningSpec class method), [1] __pydantic_on_complete__() (phenotypic.abc_.BackgroundSubtraction class method), [1] (phenotypic.abc_.BaseOperation class method), [1] (phenotypic.abc_.ContrastAdjustment class method), [1] (phenotypic.abc_.FocusBlob class method), [1] (phenotypic.abc_.FocusEdge class method), [1] (phenotypic.abc_.GpuDetector class method), [1] (phenotypic.abc_.GridCorrector class method), [1] (phenotypic.abc_.GridFinder class method), [1] (phenotypic.abc_.GridMeasureFeatures class method), [1] (phenotypic.abc_.GridObjectDetector class method), [1] (phenotypic.abc_.GridObjectRefiner class method), [1] (phenotypic.abc_.GridOperation class method), [1] (phenotypic.abc_.ImageCorrector class method), [1] (phenotypic.abc_.ImageDenoiser class method), [1] (phenotypic.abc_.ImageEnhancer class method), [1] (phenotypic.abc_.ImageOperation class method), [1] (phenotypic.abc_.MeasureFeatures class method), [1] (phenotypic.abc_.MorphologicalFiltering class method), [1] (phenotypic.abc_.ObjectDetector class method), [1] (phenotypic.abc_.ObjectRefiner class method), [1] (phenotypic.abc_.PostMeasurement class method), [1] (phenotypic.abc_.PrefabPipeline class method), [1] (phenotypic.abc_.Smoothing class method), [1] (phenotypic.abc_.ThresholdDetector class method), [1] (phenotypic.analysis.abc_.ModelFitter class method) (phenotypic.analysis.abc_.QualityCheck class method) (phenotypic.analysis.abc_.SetAnalyzer class method) (phenotypic.analysis.DoubleSoftplus class method), [1] (phenotypic.analysis.EdgeCorrector class method), [1] (phenotypic.analysis.ErrorCutoffFinder class method), [1] (phenotypic.analysis.ExpectedVsDetectedCount class method), [1] (phenotypic.analysis.ICC class method), [1] (phenotypic.analysis.LinearSoftplus class method), [1] (phenotypic.analysis.LogGrowthModel class method), [1] (phenotypic.analysis.MADOutlierRemover class method), [1] (phenotypic.analysis.MaxModifiedZScore class method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount class method) (phenotypic.analysis.qc.ICC class method) (phenotypic.analysis.qc.MaxModifiedZScore class method) (phenotypic.analysis.qc.RelativeMAD class method) (phenotypic.analysis.qc.ReplicateAgreement class method) (phenotypic.analysis.qc.TukeyOutlierFraction class method) (phenotypic.analysis.RelativeMAD class method), [1] (phenotypic.analysis.ReplicateAgreement class method), [1] (phenotypic.analysis.TukeyOutlierFraction class method), [1] (phenotypic.analysis.TukeyOutlierRemover class method), [1] (phenotypic.correction.BayesShrinkCorrector class method), [1] (phenotypic.correction.CaptureMetadata class method), [1] (phenotypic.correction.ColorCheckerProfile class method), [1] (phenotypic.correction.ColorCorrector class method), [1] (phenotypic.correction.ColorDenoise class method), [1] (phenotypic.correction.DenoiseBlockMatch class method), [1] (phenotypic.correction.GridAligner class method), [1] (phenotypic.correction.ImageCropper class method), [1] (phenotypic.correction.ImagePadder class method), [1] (phenotypic.correction.VisuShrinkCorrector class method), [1] (phenotypic.detect.CannyDetector class method), [1] (phenotypic.detect.ChanVeseDetector class method), [1] (phenotypic.detect.CompositeDetector class method), [1] (phenotypic.detect.FilamentousFungiDetector class method), [1] (phenotypic.detect.HysteresisDetector class method), [1] (phenotypic.detect.InoculumDetector class method), [1] (phenotypic.detect.IsodataDetector class method), [1] (phenotypic.detect.LiDetector class method), [1] (phenotypic.detect.MadHysteresisDetector class method), [1] (phenotypic.detect.ManualGridPointDetector class method), [1] (phenotypic.detect.ManualPointDetector class method), [1] (phenotypic.detect.MeanDetector class method), [1] (phenotypic.detect.MinimumDetector class method), [1] (phenotypic.detect.OtsuDetector class method), [1] (phenotypic.detect.RankOtsuDetector class method), [1] (phenotypic.detect.RoundPeaksDetector class method), [1] (phenotypic.detect.SecondaryOtsuDetector class method), [1] (phenotypic.detect.SinePeakDetector class method), [1] (phenotypic.detect.TriangleDetector class method), [1] (phenotypic.detect.UserThreshold class method), [1] (phenotypic.detect.WatershedDetector class method), [1] (phenotypic.detect.YenDetector class method), [1] (phenotypic.enhance.BayesShrinkEnhancer class method), [1] (phenotypic.enhance.ContrastStretching class method), [1] (phenotypic.enhance.EnhanceBlockMatch class method), [1] (phenotypic.enhance.EnhanceLocalContrast class method), [1] (phenotypic.enhance.FlattenIllumination class method), [1] (phenotypic.enhance.FocusBlobLoG class method), [1] (phenotypic.enhance.FocusEdgeFrangi class method), [1] (phenotypic.enhance.FocusEdgeHessian class method), [1] (phenotypic.enhance.FocusEdgeLaplace class method), [1] (phenotypic.enhance.FocusEdgeMeijering class method), [1] (phenotypic.enhance.FocusEdgePhase class method), [1] (phenotypic.enhance.FocusEdgeSato class method), [1] (phenotypic.enhance.FocusEdgeSobel class method), [1] (phenotypic.enhance.GaussianBlur class method), [1] (phenotypic.enhance.GrayOpening class method), [1] (phenotypic.enhance.ImageInverter class method), [1] (phenotypic.enhance.LocalEdgeDenoise class method), [1] (phenotypic.enhance.MedianFilter class method), [1] (phenotypic.enhance.NonLocalMeansDenoiser class method), [1] (phenotypic.enhance.RankMedianEnhancer class method), [1] (phenotypic.enhance.SetDetectMode class method), [1] (phenotypic.enhance.SharpenEdgeGauss class method), [1] (phenotypic.enhance.StructureSmoothing class method), [1] (phenotypic.enhance.SubtractGaussian class method), [1] (phenotypic.enhance.SubtractOpening class method), [1] (phenotypic.enhance.SubtractRollingBall class method), [1] (phenotypic.enhance.SubtractWhiteTophat class method), [1] (phenotypic.enhance.VisuShrinkEnhancer class method), [1] (phenotypic.enhance.WhiteTophatEnhance class method), [1] (phenotypic.grid.AutoGridFinder class method), [1] (phenotypic.grid.CenteredAutoGridFinder class method), [1] (phenotypic.grid.GridApply class method), [1] (phenotypic.grid.ManualGridFinder class method), [1] (phenotypic.measure.MeasureBounds class method), [1] (phenotypic.measure.MeasureColor class method), [1] (phenotypic.measure.MeasureGridLinRegStats class method), [1] (phenotypic.measure.MeasureGridSpatial class method), [1] (phenotypic.measure.MeasureGridSpread class method), [1] (phenotypic.measure.MeasureIntensity class method), [1] (phenotypic.measure.MeasureShape class method), [1] (phenotypic.measure.MeasureSize class method), [1] (phenotypic.measure.MeasureSymmetricZones class method), [1] (phenotypic.measure.MeasureTexture class method), [1] (phenotypic.post.AppendString class method) (phenotypic.post.ExpandMetadata class method) (phenotypic.post.MergeMetadata class method) (phenotypic.post.PrependString class method) (phenotypic.prefab.FilamentousFungiPipeline class method), [1] (phenotypic.prefab.GridSectionPipeline class method), [1] (phenotypic.prefab.HeavyOtsuPipeline class method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline class method), [1] (phenotypic.prefab.HeavyWatershedPipeline class method), [1] (phenotypic.prefab.RoundPeaksPipeline class method), [1] (phenotypic.prefab.SpImagerPipeline class method), [1] (phenotypic.refine.ExtractColonyCore class method), [1] (phenotypic.refine.GridAlignmentRefiner class method), [1] (phenotypic.refine.GridOversizedObjectRemover class method), [1] (phenotypic.refine.KeepNearestCenter class method), [1] (phenotypic.refine.KeepSectionLargest class method), [1] (phenotypic.refine.ManualRefine class method), [1] (phenotypic.refine.MaskClosing class method), [1] (phenotypic.refine.MaskDilation class method), [1] (phenotypic.refine.MaskErosion class method), [1] (phenotypic.refine.MaskFill class method), [1] (phenotypic.refine.MaskGradient class method), [1] (phenotypic.refine.MaskOpening class method), [1] (phenotypic.refine.MaskWhiteTophat class method), [1] (phenotypic.refine.MergeFragmentChains class method), [1] (phenotypic.refine.NearestNeighborMerger class method), [1] (phenotypic.refine.ReduceSectionsByLine class method), [1] (phenotypic.refine.RefineBySineFit class method), [1] (phenotypic.refine.RemoveBorderObjects class method), [1] (phenotypic.refine.RemoveByFeature class method), [1] (phenotypic.refine.RemoveGridOutliers class method), [1] (phenotypic.refine.RemoveLowCircularity class method), [1] (phenotypic.refine.SeparateObjects class method), [1] (phenotypic.refine.Skeletonize class method), [1] (phenotypic.refine.SmallObjectRemover class method), [1] (phenotypic.refine.SmallToLargeMerger class method), [1] (phenotypic.refine.Thinning class method), [1] (phenotypic.refine.TrimAsymmetry class method), [1] (phenotypic.tune.Budget class method), [1] (phenotypic.tune.Categorical class method), [1] (phenotypic.tune.CompositeScorer class method), [1] (phenotypic.tune.EvaluationResult class method), [1] (phenotypic.tune.Evaluator class method), [1] (phenotypic.tune.Excluded class method), [1] (phenotypic.tune.Fixed class method), [1] (phenotypic.tune.FloatRange class method), [1] (phenotypic.tune.GridConfig class method), [1] (phenotypic.tune.GroundTruthMasks class method), [1] (phenotypic.tune.HeldOutConfig class method), [1] (phenotypic.tune.ImportanceReport class method), [1] (phenotypic.tune.InferredSearchSpace class method), [1] (phenotypic.tune.IntRange class method), [1] (phenotypic.tune.Knob class method), [1] (phenotypic.tune.OptunaConfig class method), [1] (phenotypic.tune.QCScorer class method), [1] (phenotypic.tune.RandomConfig class method), [1] (phenotypic.tune.ReferenceFreeScorer class method), [1] (phenotypic.tune.Scorer class method), [1] (phenotypic.tune.SearchSpace class method), [1] (phenotypic.tune.StrategyConfig class method), [1] (phenotypic.tune.SupervisedScorer class method), [1] (phenotypic.tune.targets.Nested class method) (phenotypic.tune.targets.Param class method) (phenotypic.tune.targets.Presence class method) (phenotypic.tune.targets.TunableParam class method) (phenotypic.tune.Trial class method), [1] (phenotypic.tune.TuningSpec class method), [1] __repr__() (phenotypic.Image method) __repr_name__() (phenotypic.abc_.BackgroundSubtraction method), [1] (phenotypic.abc_.BaseOperation method), [1] (phenotypic.abc_.ContrastAdjustment method), [1] (phenotypic.abc_.FocusBlob method), [1] (phenotypic.abc_.FocusEdge method), [1] (phenotypic.abc_.GpuDetector method), [1] (phenotypic.abc_.GridCorrector method), [1] (phenotypic.abc_.GridFinder method), [1] (phenotypic.abc_.GridMeasureFeatures method), [1] (phenotypic.abc_.GridObjectDetector method), [1] (phenotypic.abc_.GridObjectRefiner method), [1] (phenotypic.abc_.GridOperation method), [1] (phenotypic.abc_.ImageCorrector method), [1] (phenotypic.abc_.ImageDenoiser method), [1] (phenotypic.abc_.ImageEnhancer method), [1] (phenotypic.abc_.ImageOperation method), [1] (phenotypic.abc_.MeasureFeatures method), [1] (phenotypic.abc_.MorphologicalFiltering method), [1] (phenotypic.abc_.ObjectDetector method), [1] (phenotypic.abc_.ObjectRefiner method), [1] (phenotypic.abc_.PostMeasurement method), [1] (phenotypic.abc_.PrefabPipeline method), [1] (phenotypic.abc_.Smoothing method), [1] (phenotypic.abc_.ThresholdDetector method), [1] (phenotypic.analysis.abc_.ModelFitter method) (phenotypic.analysis.abc_.QualityCheck method) (phenotypic.analysis.abc_.SetAnalyzer method) (phenotypic.analysis.DoubleSoftplus method), [1] (phenotypic.analysis.EdgeCorrector method), [1] (phenotypic.analysis.ErrorCutoffFinder method), [1] (phenotypic.analysis.ExpectedVsDetectedCount method), [1] (phenotypic.analysis.ICC method), [1] (phenotypic.analysis.LinearSoftplus method), [1] (phenotypic.analysis.LogGrowthModel method), [1] (phenotypic.analysis.MADOutlierRemover method), [1] (phenotypic.analysis.MaxModifiedZScore method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount method) (phenotypic.analysis.qc.ICC method) (phenotypic.analysis.qc.MaxModifiedZScore method) (phenotypic.analysis.qc.RelativeMAD method) (phenotypic.analysis.qc.ReplicateAgreement method) (phenotypic.analysis.qc.TukeyOutlierFraction method) (phenotypic.analysis.RelativeMAD method), [1] (phenotypic.analysis.ReplicateAgreement method), [1] (phenotypic.analysis.TukeyOutlierFraction method), [1] (phenotypic.analysis.TukeyOutlierRemover method), [1] (phenotypic.correction.BayesShrinkCorrector method), [1] (phenotypic.correction.CaptureMetadata method), [1] (phenotypic.correction.ColorCheckerProfile method), [1] (phenotypic.correction.ColorCorrector method), [1] (phenotypic.correction.ColorDenoise method), [1] (phenotypic.correction.DenoiseBlockMatch method), [1] (phenotypic.correction.GridAligner method), [1] (phenotypic.correction.ImageCropper method), [1] (phenotypic.correction.ImagePadder method), [1] (phenotypic.correction.VisuShrinkCorrector method), [1] (phenotypic.detect.CannyDetector method), [1] (phenotypic.detect.ChanVeseDetector method), [1] (phenotypic.detect.CompositeDetector method), [1] (phenotypic.detect.FilamentousFungiDetector method), [1] (phenotypic.detect.HysteresisDetector method), [1] (phenotypic.detect.InoculumDetector method), [1] (phenotypic.detect.IsodataDetector method), [1] (phenotypic.detect.LiDetector method), [1] (phenotypic.detect.MadHysteresisDetector method), [1] (phenotypic.detect.ManualGridPointDetector method), [1] (phenotypic.detect.ManualPointDetector method), [1] (phenotypic.detect.MeanDetector method), [1] (phenotypic.detect.MinimumDetector method), [1] (phenotypic.detect.OtsuDetector method), [1] (phenotypic.detect.RankOtsuDetector method), [1] (phenotypic.detect.RoundPeaksDetector method), [1] (phenotypic.detect.SecondaryOtsuDetector method), [1] (phenotypic.detect.SinePeakDetector method), [1] (phenotypic.detect.TriangleDetector method), [1] (phenotypic.detect.UserThreshold method), [1] (phenotypic.detect.WatershedDetector method), [1] (phenotypic.detect.YenDetector method), [1] (phenotypic.enhance.BayesShrinkEnhancer method), [1] (phenotypic.enhance.ContrastStretching method), [1] (phenotypic.enhance.EnhanceBlockMatch method), [1] (phenotypic.enhance.EnhanceLocalContrast method), [1] (phenotypic.enhance.FlattenIllumination method), [1] (phenotypic.enhance.FocusBlobLoG method), [1] (phenotypic.enhance.FocusEdgeFrangi method), [1] (phenotypic.enhance.FocusEdgeHessian method), [1] (phenotypic.enhance.FocusEdgeLaplace method), [1] (phenotypic.enhance.FocusEdgeMeijering method), [1] (phenotypic.enhance.FocusEdgePhase method), [1] (phenotypic.enhance.FocusEdgeSato method), [1] (phenotypic.enhance.FocusEdgeSobel method), [1] (phenotypic.enhance.GaussianBlur method), [1] (phenotypic.enhance.GrayOpening method), [1] (phenotypic.enhance.ImageInverter method), [1] (phenotypic.enhance.LocalEdgeDenoise method), [1] (phenotypic.enhance.MedianFilter method), [1] (phenotypic.enhance.NonLocalMeansDenoiser method), [1] (phenotypic.enhance.RankMedianEnhancer method), [1] (phenotypic.enhance.SetDetectMode method), [1] (phenotypic.enhance.SharpenEdgeGauss method), [1] (phenotypic.enhance.StructureSmoothing method), [1] (phenotypic.enhance.SubtractGaussian method), [1] (phenotypic.enhance.SubtractOpening method), [1] (phenotypic.enhance.SubtractRollingBall method), [1] (phenotypic.enhance.SubtractWhiteTophat method), [1] (phenotypic.enhance.VisuShrinkEnhancer method), [1] (phenotypic.enhance.WhiteTophatEnhance method), [1] (phenotypic.grid.AutoGridFinder method), [1] 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method), [1] (phenotypic.tune.GroundTruthMasks method), [1] (phenotypic.tune.HeldOutConfig method), [1] (phenotypic.tune.ImportanceReport method), [1] (phenotypic.tune.InferredSearchSpace method), [1] (phenotypic.tune.IntRange method), [1] (phenotypic.tune.Knob method), [1] (phenotypic.tune.OptunaConfig method), [1] (phenotypic.tune.QCScorer method), [1] (phenotypic.tune.RandomConfig method), [1] (phenotypic.tune.ReferenceFreeScorer method), [1] (phenotypic.tune.Scorer method), [1] (phenotypic.tune.SearchSpace method), [1] (phenotypic.tune.StrategyConfig method), [1] (phenotypic.tune.SupervisedScorer method), [1] (phenotypic.tune.targets.Nested method) (phenotypic.tune.targets.Param method) (phenotypic.tune.targets.Presence method) (phenotypic.tune.targets.TunableParam method) (phenotypic.tune.Trial method), [1] (phenotypic.tune.TuningSpec method), [1] __setitem__() (phenotypic._core._image_parts.accessors._detect_mat_accessor.DetectMatAccessor method) (phenotypic._core._image_parts.accessors._grayscale_accessor.Grayscale method) (phenotypic._core._image_parts.accessors._metadata_accessor.MetadataAccessor method) (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap method) (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask method) (phenotypic._core._image_parts.accessors._rgb_accessor.ImageRGB method) __str__() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.abc_.PrefabPipeline method), [1] (phenotypic.Image method) (phenotypic.prefab.FilamentousFungiPipeline method), [1] (phenotypic.prefab.GridSectionPipeline method), [1] (phenotypic.prefab.HeavyOtsuPipeline method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1] (phenotypic.prefab.HeavyWatershedPipeline method), [1] (phenotypic.prefab.RoundPeaksPipeline method), [1] (phenotypic.prefab.SpImagerPipeline method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] __xor__() (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask method) _accessor_property_name (phenotypic._core._image_parts.accessors._grayscale_accessor.Grayscale attribute) (phenotypic._core._image_parts.accessors._rgb_accessor.ImageRGB attribute) _apply_to_single_image() (phenotypic.abc_.ImageOperation method), [1] _cielab (phenotypic._core._image_parts.accessors._color_accessor.ColorAccessor attribute) _DagBuilderScope (class in phenotypic.gui.builder._state) _DagBuilderState (class in phenotypic.gui.builder._state) _hsv (phenotypic._core._image_parts.accessors._color_accessor.ColorAccessor attribute) _logger (phenotypic.abc_.BaseOperation attribute), [1] _make_footprint() (phenotypic.abc_.ImageEnhancer method), [1] (phenotypic.abc_.ObjectRefiner method), [1] _operate() (phenotypic.abc_.ImageEnhancer method), [1] (phenotypic.abc_.ImageOperation method), [1] (phenotypic.abc_.ObjectDetector method), [1] (phenotypic.abc_.ObjectRefiner method), [1] _parent_image (phenotypic._core._image_parts.accessors._metadata_accessor.MetadataAccessor attribute) _point_picker_param_name (phenotypic.sdk_.mixin.PointPickerMixin attribute) _root_image (phenotypic._core._image_parts.accessors._color_accessor.ColorAccessor attribute) (phenotypic._core._image_parts.accessors._objects_accessor.ObjectsAccessor attribute) (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap attribute) (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask attribute) _seed_input_image() (in module phenotypic.gui.builder._state) _tracemalloc_started (phenotypic.abc_.BaseOperation attribute), [1] _xy (phenotypic._core._image_parts.accessors._color_accessor.ColorAccessor attribute) _xyz (phenotypic._core._image_parts.accessors._color_accessor.ColorAccessor attribute) _xyz_d65 (phenotypic._core._image_parts.accessors._color_accessor.ColorAccessor attribute)

A

A_STAR_GEOMEDIAN (phenotypic.schema.ColorLab attribute) A_STAR_MEDOID (phenotypic.schema.ColorLab attribute) ABOVE_DISTANCE (phenotypic.schema.GRID_SPATIAL attribute) ABOVE_NEIGHBOR_OBJ_LABEL (phenotypic.schema.GRID_SPATIAL attribute) absolute_drop (phenotypic.tune.GeneralizationReport attribute), [1] ABSOLUTE_FLOOR (phenotypic.grid.CenteredAutoGridFinder attribute), [1] ACCEPTED_FILE_EXTENSIONS (phenotypic.sdk_.constants_.IO attribute), [1] accessor ACQUISITION_METADATA (class in phenotypic.schema) ACTIVE_CHUNKS (phenotypic.sdk_.DashboardManifestSlurmInfoKey attribute), [1] add_image_layer() (in module phenotypic.sdk_.napari_), [1] add_note() (phenotypic.grid.CenteredAutoGridFinderFallbackWarning method), [1] (phenotypic.gui.tune.TuneRunRootError method) (phenotypic.sdk_.exceptions_.ArrayKeyValueShapeMismatchError method), [1] (phenotypic.sdk_.exceptions_.DataIntegrityError method), [1] (phenotypic.sdk_.exceptions_.EmptyImageError method), [1] (phenotypic.sdk_.exceptions_.GrayscaleOutOfRangeError method), [1] (phenotypic.sdk_.exceptions_.GridImageInputError method), [1] (phenotypic.sdk_.exceptions_.IllegalAssignmentError method), [1] (phenotypic.sdk_.exceptions_.IllegalElementAssignmentError method), [1] (phenotypic.sdk_.exceptions_.ImageOperationError method), [1] (phenotypic.sdk_.exceptions_.ImmutableComponentError method), [1] (phenotypic.sdk_.exceptions_.InputShapeMismatchError method), [1] (phenotypic.sdk_.exceptions_.InterfaceError method), [1] (phenotypic.sdk_.exceptions_.InvalidHsvSchemaError method), [1] (phenotypic.sdk_.exceptions_.InvalidMapValueError method), [1] (phenotypic.sdk_.exceptions_.InvalidMaskScalarValueError method), [1] (phenotypic.sdk_.exceptions_.InvalidMaskValueError method), [1] (phenotypic.sdk_.exceptions_.InvalidShapeError method), [1] (phenotypic.sdk_.exceptions_.MetadataKeySpacesError method), [1] (phenotypic.sdk_.exceptions_.MetadataKeyValueError method), [1] (phenotypic.sdk_.exceptions_.MetadataValueNonScalarError method), [1] (phenotypic.sdk_.exceptions_.NoArrayError method), [1] (phenotypic.sdk_.exceptions_.NoComponentError method), [1] (phenotypic.sdk_.exceptions_.NoImageDataError method), [1] (phenotypic.sdk_.exceptions_.NoObjectsError method), [1] (phenotypic.sdk_.exceptions_.NoOutputError method), [1] (phenotypic.sdk_.exceptions_.ObjectNotFoundError method), [1] (phenotypic.sdk_.exceptions_.OperationFailedError method), [1] (phenotypic.sdk_.exceptions_.OperationIntegrityError method), [1] (phenotypic.sdk_.exceptions_.OutputValueError method), [1] (phenotypic.sdk_.exceptions_.PhenoTypicError method), [1] (phenotypic.sdk_.exceptions_.UnknownError method), [1] (phenotypic.sdk_.exceptions_.UnsupportedFileTypeError method), [1] (phenotypic.sdk_.exceptions_.UnsupportedImageFormat method), [1] (phenotypic.sdk_.exceptions_.UuidAssignmentError method), [1] (phenotypic.sdk_.exceptions_.UUIDReassignmentError method), [1] agg_func (phenotypic.analysis.abc_.ModelFitter attribute) (phenotypic.analysis.abc_.QualityCheck attribute) (phenotypic.analysis.abc_.SetAnalyzer attribute) (phenotypic.analysis.DoubleSoftplus attribute), [1] (phenotypic.analysis.EdgeCorrector attribute), [1] (phenotypic.analysis.ExpectedVsDetectedCount attribute), [1] (phenotypic.analysis.ICC attribute), [1] (phenotypic.analysis.LinearSoftplus attribute), [1] (phenotypic.analysis.LogGrowthModel attribute), [1] (phenotypic.analysis.MADOutlierRemover attribute), [1] (phenotypic.analysis.MaxModifiedZScore attribute), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount attribute) (phenotypic.analysis.qc.ICC attribute) (phenotypic.analysis.qc.MaxModifiedZScore attribute) (phenotypic.analysis.qc.RelativeMAD attribute) (phenotypic.analysis.qc.ReplicateAgreement attribute) (phenotypic.analysis.qc.TukeyOutlierFraction attribute) (phenotypic.analysis.RelativeMAD attribute), [1] (phenotypic.analysis.ReplicateAgreement attribute), [1] (phenotypic.analysis.TukeyOutlierFraction attribute), [1] (phenotypic.analysis.TukeyOutlierRemover attribute), [1] all() (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) all_headers() (phenotypic.schema.ColorComposition class method) ALLELE (phenotypic.schema.GENETIC_METADATA attribute) alpha (phenotypic.enhance.FocusEdgeFrangi attribute), [1] (phenotypic.enhance.FocusEdgeHessian attribute), [1] (phenotypic.enhance.FocusEdgeMeijering attribute), [1] (phenotypic.enhance.StructureSmoothing attribute), [1] (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL attribute) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL attribute) AMBIGUOUS_FORMATS (phenotypic.sdk_.constants_.IMAGE_MODE attribute), [1] amount (phenotypic.enhance.SharpenEdgeGauss attribute), [1] ANALYSIS (phenotypic.sdk_.ModulePath attribute), [1] analysis_csv_path() (in module phenotypic.sdk_), [1] ANALYSIS_DATA_VERSION (phenotypic.sdk_.DashboardManifestKey attribute), [1] analysis_full_parquet_path() (in module phenotypic.sdk_), [1] analysis_html_path() (in module phenotypic.sdk_), [1] analysis_parquet_path() (in module phenotypic.sdk_), [1] analysis_scatter_json_path() (in module phenotypic.sdk_), [1] AnalysisPluginRegistry (class in phenotypic.sdk_.register), [1] analyze() (phenotypic.abc_.PrefabPipeline method), [1] (phenotypic.analysis.abc_.ModelFitter method) (phenotypic.analysis.abc_.QualityCheck method) (phenotypic.analysis.abc_.SetAnalyzer method) (phenotypic.analysis.DoubleSoftplus method), [1] (phenotypic.analysis.EdgeCorrector method), [1] (phenotypic.analysis.ErrorCutoffFinder method), [1] (phenotypic.analysis.ExpectedVsDetectedCount method), [1] (phenotypic.analysis.ICC method), [1] (phenotypic.analysis.LinearSoftplus method), [1] (phenotypic.analysis.LogGrowthModel method), [1] (phenotypic.analysis.MADOutlierRemover method), [1] (phenotypic.analysis.MaxModifiedZScore method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount method) (phenotypic.analysis.qc.ICC method) (phenotypic.analysis.qc.MaxModifiedZScore method) (phenotypic.analysis.qc.RelativeMAD method) (phenotypic.analysis.qc.ReplicateAgreement method) (phenotypic.analysis.qc.TukeyOutlierFraction method) (phenotypic.analysis.RelativeMAD method), [1] (phenotypic.analysis.ReplicateAgreement method), [1] (phenotypic.analysis.TukeyOutlierFraction method), [1] (phenotypic.analysis.TukeyOutlierRemover method), [1] (phenotypic.prefab.FilamentousFungiPipeline method), [1] (phenotypic.prefab.GridSectionPipeline method), [1] (phenotypic.prefab.HeavyOtsuPipeline method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1] (phenotypic.prefab.HeavyWatershedPipeline method), [1] (phenotypic.prefab.RoundPeaksPipeline method), [1] (phenotypic.prefab.SpImagerPipeline method), [1] ANGULAR_SECOND_MOMENT (phenotypic.schema.TEXTURE attribute) ANTIBIOTIC (phenotypic.schema.CONDITION_METADATA attribute) append() (phenotypic.tune.JournalStudyStore method), [1] append_rst_to_doc() (phenotypic.abc_.MeasurementInfo class method), [1] (phenotypic.schema.ACQUISITION_METADATA class method) (phenotypic.schema.BBOX class method) (phenotypic.schema.ColorComposition class method) (phenotypic.schema.ColorHSV class method) (phenotypic.schema.ColorLab class method) (phenotypic.schema.Colorxy class method) (phenotypic.schema.ColorXYZ class method) (phenotypic.schema.CONDITION_METADATA class method) (phenotypic.schema.CURATION class method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL class method) (phenotypic.schema.EDGE_CORRECTION class method) (phenotypic.schema.ErrorCategory class method) (phenotypic.schema.EXPERIMENT_METADATA class method) (phenotypic.schema.GENETIC_METADATA class method) (phenotypic.schema.GRID class method) (phenotypic.schema.GRID_LINREG_STATS class method) (phenotypic.schema.GRID_SPATIAL class method) (phenotypic.schema.GRID_SPREAD class method) (phenotypic.schema.INCUBATION_METADATA class method) (phenotypic.schema.INTENSITY class method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL class method) (phenotypic.schema.LOG_GROWTH_MODEL class method) (phenotypic.schema.MeasurementInfo class method) (phenotypic.schema.METADATA class method) (phenotypic.schema.MODEL_METRICS class method) (phenotypic.schema.OBJECT class method) (phenotypic.schema.PLATE_METADATA class method) (phenotypic.schema.QUALITY_CHECK class method) (phenotypic.schema.QUALITY_COUNT class method) (phenotypic.schema.QUALITY_ICC class method) (phenotypic.schema.QUALITY_MAD class method) (phenotypic.schema.QUALITY_SE class method) (phenotypic.schema.QUALITY_TUKEY class method) (phenotypic.schema.QUALITY_ZMAX class method) (phenotypic.schema.RADIAL_EXPANSION class method) (phenotypic.schema.SAMPLE_METADATA class method) (phenotypic.schema.SHAPE class method) (phenotypic.schema.SIZE class method) (phenotypic.schema.SYMMETRIC_ZONES class method) (phenotypic.schema.TEXTURE class method) (phenotypic.sdk_.constants_.ConstantLabels class method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS class method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS class method), [1] AppendString (class in phenotypic.post) apply() (phenotypic.abc_.BackgroundSubtraction method), [1] (phenotypic.abc_.ContrastAdjustment method), [1] (phenotypic.abc_.FocusBlob method), [1] (phenotypic.abc_.FocusEdge method), [1] (phenotypic.abc_.GpuDetector method), [1] (phenotypic.abc_.GridCorrector method), [1] (phenotypic.abc_.GridObjectDetector method), [1] (phenotypic.abc_.GridObjectRefiner method), [1] (phenotypic.abc_.GridOperation method), [1] (phenotypic.abc_.ImageCorrector method), [1] (phenotypic.abc_.ImageDenoiser method), [1] (phenotypic.abc_.ImageEnhancer method), [1], [2], [3] (phenotypic.abc_.ImageOperation method), [1], [2], [3] (phenotypic.abc_.MorphologicalFiltering method), [1] (phenotypic.abc_.ObjectDetector method), [1], [2], [3] (phenotypic.abc_.ObjectRefiner method), [1], [2], [3] (phenotypic.abc_.PostMeasurement method), [1] (phenotypic.abc_.PrefabPipeline method), [1] (phenotypic.abc_.Smoothing method), [1] (phenotypic.abc_.ThresholdDetector method), [1] (phenotypic.correction.BayesShrinkCorrector method), [1] (phenotypic.correction.ColorCorrector method), [1] (phenotypic.correction.ColorDenoise method), [1] (phenotypic.correction.DenoiseBlockMatch method), [1] (phenotypic.correction.GridAligner method), [1] (phenotypic.correction.ImageCropper method), [1] (phenotypic.correction.ImagePadder method), [1] (phenotypic.correction.VisuShrinkCorrector method), [1] (phenotypic.detect.CannyDetector method), [1] (phenotypic.detect.ChanVeseDetector method), [1] (phenotypic.detect.CompositeDetector method), [1] (phenotypic.detect.FilamentousFungiDetector method), [1] (phenotypic.detect.HysteresisDetector method), [1] (phenotypic.detect.InoculumDetector method), [1] (phenotypic.detect.IsodataDetector method), [1] (phenotypic.detect.LiDetector method), [1] (phenotypic.detect.MadHysteresisDetector method), [1] (phenotypic.detect.ManualGridPointDetector method), [1] (phenotypic.detect.ManualPointDetector method), [1] (phenotypic.detect.MeanDetector method), [1] (phenotypic.detect.MinimumDetector method), [1] (phenotypic.detect.OtsuDetector method), [1] (phenotypic.detect.RankOtsuDetector method), [1] (phenotypic.detect.RoundPeaksDetector method), [1] (phenotypic.detect.SecondaryOtsuDetector method), [1] (phenotypic.detect.SinePeakDetector method), [1] (phenotypic.detect.TriangleDetector method), [1] (phenotypic.detect.UserThreshold method), [1] (phenotypic.detect.WatershedDetector method), [1] (phenotypic.detect.YenDetector method), [1] (phenotypic.enhance.BayesShrinkEnhancer method), [1] (phenotypic.enhance.ContrastStretching method), [1] (phenotypic.enhance.EnhanceBlockMatch method), [1] (phenotypic.enhance.EnhanceLocalContrast method), [1] (phenotypic.enhance.FlattenIllumination method), [1] (phenotypic.enhance.FocusBlobLoG method), [1] (phenotypic.enhance.FocusEdgeFrangi method), [1] (phenotypic.enhance.FocusEdgeHessian method), [1] (phenotypic.enhance.FocusEdgeLaplace method), [1] (phenotypic.enhance.FocusEdgeMeijering method), [1] (phenotypic.enhance.FocusEdgePhase method), [1] (phenotypic.enhance.FocusEdgeSato method), [1] (phenotypic.enhance.FocusEdgeSobel method), [1] (phenotypic.enhance.GaussianBlur method), [1] (phenotypic.enhance.GrayOpening method), [1] (phenotypic.enhance.ImageInverter method), [1] (phenotypic.enhance.LocalEdgeDenoise method), [1] (phenotypic.enhance.MedianFilter method), [1] (phenotypic.enhance.NonLocalMeansDenoiser method), [1] (phenotypic.enhance.RankMedianEnhancer method), [1] (phenotypic.enhance.SetDetectMode method), [1] (phenotypic.enhance.SharpenEdgeGauss method), [1] (phenotypic.enhance.StructureSmoothing method), [1] (phenotypic.enhance.SubtractGaussian method), [1] (phenotypic.enhance.SubtractOpening method), [1] (phenotypic.enhance.SubtractRollingBall method), [1] (phenotypic.enhance.SubtractWhiteTophat method), [1] (phenotypic.enhance.VisuShrinkEnhancer method), [1] (phenotypic.enhance.WhiteTophatEnhance method), [1] (phenotypic.grid.GridApply method), [1] (phenotypic.ImagePipeline method) (phenotypic.post.AppendString method) (phenotypic.post.ExpandMetadata method) (phenotypic.post.MergeMetadata method) (phenotypic.post.PrependString method) (phenotypic.prefab.FilamentousFungiPipeline method), [1] (phenotypic.prefab.GridSectionPipeline method), [1] (phenotypic.prefab.HeavyOtsuPipeline method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1] (phenotypic.prefab.HeavyWatershedPipeline method), [1] (phenotypic.prefab.RoundPeaksPipeline method), [1] (phenotypic.prefab.SpImagerPipeline method), [1] (phenotypic.refine.ExtractColonyCore method), [1] (phenotypic.refine.GridAlignmentRefiner method), [1] (phenotypic.refine.GridOversizedObjectRemover method), [1] (phenotypic.refine.KeepNearestCenter method), [1] (phenotypic.refine.KeepSectionLargest method), [1] (phenotypic.refine.ManualRefine method), [1] (phenotypic.refine.MaskClosing method), [1] (phenotypic.refine.MaskDilation method), [1] (phenotypic.refine.MaskErosion method), [1] (phenotypic.refine.MaskFill method), [1] (phenotypic.refine.MaskGradient method), [1] (phenotypic.refine.MaskOpening method), [1] (phenotypic.refine.MaskWhiteTophat method), [1] (phenotypic.refine.MergeFragmentChains method), [1] (phenotypic.refine.NearestNeighborMerger method), [1] (phenotypic.refine.ReduceSectionsByLine method), [1] (phenotypic.refine.RefineBySineFit method), [1] (phenotypic.refine.RemoveBorderObjects method), [1] (phenotypic.refine.RemoveByFeature method), [1] (phenotypic.refine.RemoveGridOutliers method), [1] (phenotypic.refine.RemoveLowCircularity method), [1] (phenotypic.refine.SeparateObjects method), [1] (phenotypic.refine.Skeletonize method), [1] (phenotypic.refine.SmallObjectRemover method), [1] (phenotypic.refine.SmallToLargeMerger method), [1] (phenotypic.refine.Thinning method), [1] (phenotypic.refine.TrimAsymmetry method), [1]

apply_and_measure() (phenotypic.abc_.PrefabPipeline method), [1] (phenotypic.ImagePipeline method) (phenotypic.prefab.FilamentousFungiPipeline method), [1] (phenotypic.prefab.GridSectionPipeline method), [1] (phenotypic.prefab.HeavyOtsuPipeline method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1] (phenotypic.prefab.HeavyWatershedPipeline method), [1] (phenotypic.prefab.RoundPeaksPipeline method), [1] (phenotypic.prefab.SpImagerPipeline method), [1] apply_border_penalty() (in module phenotypic.sdk_.branch_pathfinding) apply_distance_gap_penalty() (in module phenotypic.sdk_.branch_pathfinding) apply_filter_cascade() (in module phenotypic.sdk_.branch_pathfinding) apply_napari() (phenotypic.abc_.PrefabPipeline method), [1] (phenotypic.prefab.FilamentousFungiPipeline method), [1] (phenotypic.prefab.GridSectionPipeline method), [1] (phenotypic.prefab.HeavyOtsuPipeline method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1] (phenotypic.prefab.HeavyWatershedPipeline method), [1] (phenotypic.prefab.RoundPeaksPipeline method), [1] (phenotypic.prefab.SpImagerPipeline method), [1] apply_structure_mask() (in module phenotypic.sdk_.branch_pathfinding) apply_theme() (in module phenotypic.sdk_.viz) (in module phenotypic.sdk_.viz.figures) apply_with_intermediates() (phenotypic.abc_.PrefabPipeline method), [1] (phenotypic.prefab.FilamentousFungiPipeline method), [1] (phenotypic.prefab.GridSectionPipeline method), [1] (phenotypic.prefab.HeavyOtsuPipeline method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1] (phenotypic.prefab.HeavyWatershedPipeline method), [1] (phenotypic.prefab.RoundPeaksPipeline method), [1] (phenotypic.prefab.SpImagerPipeline method), [1] AREA (phenotypic.schema.SHAPE attribute) (phenotypic.schema.SIZE attribute) args (phenotypic.grid.CenteredAutoGridFinderFallbackWarning attribute), [1] (phenotypic.gui.tune.TuneRunRootError attribute) (phenotypic.sdk_.exceptions_.ArrayKeyValueShapeMismatchError attribute), [1] (phenotypic.sdk_.exceptions_.DataIntegrityError attribute), [1] (phenotypic.sdk_.exceptions_.EmptyImageError attribute), [1] (phenotypic.sdk_.exceptions_.GrayscaleOutOfRangeError attribute), [1] (phenotypic.sdk_.exceptions_.GridImageInputError attribute), [1] (phenotypic.sdk_.exceptions_.IllegalAssignmentError attribute), [1] (phenotypic.sdk_.exceptions_.IllegalElementAssignmentError attribute), [1] (phenotypic.sdk_.exceptions_.ImageOperationError attribute), [1] (phenotypic.sdk_.exceptions_.ImmutableComponentError attribute), [1] (phenotypic.sdk_.exceptions_.InputShapeMismatchError attribute), [1] (phenotypic.sdk_.exceptions_.InterfaceError attribute), [1] (phenotypic.sdk_.exceptions_.InvalidHsvSchemaError attribute), [1] (phenotypic.sdk_.exceptions_.InvalidMapValueError attribute), [1] (phenotypic.sdk_.exceptions_.InvalidMaskScalarValueError attribute), [1] (phenotypic.sdk_.exceptions_.InvalidMaskValueError attribute), [1] (phenotypic.sdk_.exceptions_.InvalidShapeError attribute), [1] (phenotypic.sdk_.exceptions_.MetadataKeySpacesError attribute), [1] (phenotypic.sdk_.exceptions_.MetadataKeyValueError attribute), [1] (phenotypic.sdk_.exceptions_.MetadataValueNonScalarError attribute), [1] (phenotypic.sdk_.exceptions_.NoArrayError attribute), [1] (phenotypic.sdk_.exceptions_.NoComponentError attribute), [1] (phenotypic.sdk_.exceptions_.NoImageDataError attribute), [1] (phenotypic.sdk_.exceptions_.NoObjectsError attribute), [1] (phenotypic.sdk_.exceptions_.NoOutputError attribute), [1] (phenotypic.sdk_.exceptions_.ObjectNotFoundError attribute), [1] (phenotypic.sdk_.exceptions_.OperationFailedError attribute), [1] (phenotypic.sdk_.exceptions_.OperationIntegrityError attribute), [1] (phenotypic.sdk_.exceptions_.OutputValueError attribute), [1] (phenotypic.sdk_.exceptions_.PhenoTypicError attribute), [1] (phenotypic.sdk_.exceptions_.UnknownError attribute), [1] (phenotypic.sdk_.exceptions_.UnsupportedFileTypeError attribute), [1] (phenotypic.sdk_.exceptions_.UnsupportedImageFormat attribute), [1] (phenotypic.sdk_.exceptions_.UuidAssignmentError attribute), [1] (phenotypic.sdk_.exceptions_.UUIDReassignmentError attribute), [1] ARRAY_DENSITY (phenotypic.schema.PLATE_METADATA attribute) ArrayKeyValueShapeMismatchError, [1] as_coo() (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap method) as_csc() (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap method) assemble_composite_cost() (in module phenotypic.sdk_.branch_pathfinding) assemble_connected_mask() (in module phenotypic.sdk_.branch_pathfinding) assert_swmr_on() (phenotypic.sdk_.HDF static method), [1] (phenotypic.sdk_.hdf_.HDF static method) assign_fragments_to_colonies() (in module phenotypic.sdk_.branch_pathfinding) ATMOSPHERE (phenotypic.schema.INCUBATION_METADATA attribute) atomic_write_bytes() (in module phenotypic.sdk_), [1] atomic_write_text() (in module phenotypic.sdk_), [1] AutoGridFinder (class in phenotypic.grid), [1] availability() (phenotypic.tune.CompositeScorer method), [1] (phenotypic.tune.QCScorer method), [1] (phenotypic.tune.ReferenceFreeScorer method), [1] (phenotypic.tune.Scorer method), [1] (phenotypic.tune.SupervisedScorer method), [1] available() (phenotypic.sdk_.register.AnalysisPluginRegistry class method), [1] (phenotypic.sdk_.register.BaseRegistry class method), [1] (phenotypic.sdk_.register.PlotterRegistry class method), [1] available_analysis_plugins() (in module phenotypic.sdk_.register), [1] available_names() (phenotypic.tune.GroundTruthMasks method), [1] available_plotters() (in module phenotypic.sdk_.register), [1] axis (phenotypic.correction.GridAligner attribute), [1] (phenotypic.refine.RemoveGridOutliers attribute), [1]

B

B_STAR_GEOMEDIAN (phenotypic.schema.ColorLab attribute) B_STAR_MEDOID (phenotypic.schema.ColorLab attribute) BACKGROUND (phenotypic.schema.GENETIC_METADATA attribute) background_estimate (phenotypic.util.BackgroundMetrics attribute), [1] (phenotypic.util.image_metrics.BackgroundMetrics attribute) BACKGROUND_NOISE (phenotypic.schema.ErrorCategory attribute) BackgroundMetrics (class in phenotypic.util), [1] (class in phenotypic.util.image_metrics) BackgroundSubtraction (class in phenotypic.abc_), [1] backtrack_path() (in module phenotypic.sdk_.branch_pathfinding) band_cost_variance (phenotypic.sdk_.branch_pathfinding.PathMetrics attribute), [1] band_variance_values (phenotypic.sdk_.branch_pathfinding.CalibrationData attribute), [1] BARCODE (phenotypic.schema.SAMPLE_METADATA attribute) BASE (phenotypic.sdk_.constants_.IMAGE_TYPES attribute), [1] BaseOperation (class in phenotypic.abc_), [1] BaseRegistry (class in phenotypic.sdk_.register), [1] BATCH (phenotypic.schema.PLATE_METADATA attribute) BayesShrinkCorrector (class in phenotypic.correction), [1] BayesShrinkEnhancer (class in phenotypic.enhance), [1] BBOX (class in phenotypic.schema) BBOX_AREA (phenotypic.schema.SHAPE attribute) beehive_threshold (phenotypic.refine.TrimAsymmetry attribute), [1] benchmark (phenotypic.abc_.PrefabPipeline attribute), [1] (phenotypic.prefab.FilamentousFungiPipeline attribute), [1] (phenotypic.prefab.GridSectionPipeline attribute), [1] (phenotypic.prefab.HeavyOtsuPipeline attribute), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1], [2], [3] (phenotypic.prefab.HeavyWatershedPipeline attribute), [1] (phenotypic.prefab.RoundPeaksPipeline attribute), [1] (phenotypic.prefab.SpImagerPipeline attribute), [1] benchmark_results() (phenotypic.abc_.PrefabPipeline method), [1] (phenotypic.ImagePipeline method) (phenotypic.prefab.FilamentousFungiPipeline method), [1] (phenotypic.prefab.GridSectionPipeline method), [1] (phenotypic.prefab.HeavyOtsuPipeline method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1] (phenotypic.prefab.HeavyWatershedPipeline method), [1] (phenotypic.prefab.RoundPeaksPipeline method), [1] (phenotypic.prefab.SpImagerPipeline method), [1] best() (phenotypic.tune.JournalStudyStore method), [1] best_params_path() (in module phenotypic.sdk_), [1] best_pipeline() (phenotypic.tune.TuningEngine method), [1] best_pipeline_path (phenotypic.gui.tune.TuneRunRoot attribute) best_pipeline_path() (in module phenotypic.sdk_), [1] beta (phenotypic.analysis.DoubleSoftplus attribute), [1] (phenotypic.analysis.LogGrowthModel attribute), [1] (phenotypic.detect.FilamentousFungiDetector attribute), [1] (phenotypic.enhance.FocusEdgeFrangi attribute), [1] (phenotypic.enhance.FocusEdgeHessian attribute), [1] (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL attribute) BETA (phenotypic.schema.LOG_GROWTH_MODEL attribute) BGR (phenotypic.sdk_.constants_.IMAGE_MODE attribute), [1] BGRA (phenotypic.sdk_.constants_.IMAGE_MODE attribute), [1] bio_desc (phenotypic.abc_.MeasurementInfo attribute), [1], [2], [3] (phenotypic.schema.ACQUISITION_METADATA attribute) (phenotypic.schema.BBOX attribute) (phenotypic.schema.ColorComposition attribute) (phenotypic.schema.ColorHSV attribute) (phenotypic.schema.ColorLab attribute) (phenotypic.schema.Colorxy attribute) (phenotypic.schema.ColorXYZ attribute) (phenotypic.schema.CONDITION_METADATA attribute) (phenotypic.schema.CURATION attribute) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL attribute) (phenotypic.schema.EDGE_CORRECTION attribute) (phenotypic.schema.Entry attribute) (phenotypic.schema.ErrorCategory attribute) (phenotypic.schema.EXPERIMENT_METADATA attribute) (phenotypic.schema.GENETIC_METADATA attribute) (phenotypic.schema.GRID attribute) (phenotypic.schema.GRID_LINREG_STATS attribute) (phenotypic.schema.GRID_SPATIAL attribute) (phenotypic.schema.GRID_SPREAD attribute) (phenotypic.schema.INCUBATION_METADATA attribute) (phenotypic.schema.INTENSITY attribute) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL attribute) (phenotypic.schema.LOG_GROWTH_MODEL attribute) (phenotypic.schema.MeasurementInfo attribute), [1] (phenotypic.schema.METADATA attribute) (phenotypic.schema.MODEL_METRICS attribute) (phenotypic.schema.OBJECT attribute) (phenotypic.schema.PLATE_METADATA attribute) (phenotypic.schema.QUALITY_CHECK attribute) (phenotypic.schema.QUALITY_COUNT attribute) (phenotypic.schema.QUALITY_ICC attribute) (phenotypic.schema.QUALITY_MAD attribute) (phenotypic.schema.QUALITY_SE attribute) (phenotypic.schema.QUALITY_TUKEY attribute) (phenotypic.schema.QUALITY_ZMAX attribute) (phenotypic.schema.RADIAL_EXPANSION attribute) (phenotypic.schema.SAMPLE_METADATA attribute) (phenotypic.schema.SHAPE attribute) (phenotypic.schema.SIZE attribute) (phenotypic.schema.SYMMETRIC_ZONES attribute) (phenotypic.schema.TEXTURE attribute) (phenotypic.sdk_.constants_.ConstantLabels attribute), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS attribute), [1] (phenotypic.sdk_.constants_.PIPE_STATUS attribute), [1]

BIT_DEPTH (phenotypic.schema.METADATA attribute) bit_depth (phenotypic.util.image_metrics.ImageMetricsCalculator attribute) (phenotypic.util.image_metrics.ImageMetricsCalculator property) (phenotypic.util.ImageMetricsCalculator attribute), [1] (phenotypic.util.ImageMetricsCalculator property), [1] BLACK_PCT (phenotypic.schema.ColorComposition attribute) black_ridges (phenotypic.enhance.FocusEdgeFrangi attribute), [1] (phenotypic.enhance.FocusEdgeHessian attribute), [1] (phenotypic.enhance.FocusEdgeMeijering attribute), [1] (phenotypic.enhance.FocusEdgeSato attribute), [1] blend (phenotypic.tune.CompositeScorer attribute), [1] block_id (phenotypic.gui.builder._state.BlockNode attribute), [1] (phenotypic.gui.builder._validation.Issue attribute), [1] block_size (phenotypic.correction.ColorDenoise attribute), [1] (phenotypic.correction.DenoiseBlockMatch attribute), [1] (phenotypic.enhance.EnhanceBlockMatch attribute), [1] BlockNode (class in phenotypic.gui.builder._state) blocks (phenotypic.gui.builder._state._DagBuilderScope attribute), [1] BLUE_PCT (phenotypic.schema.ColorComposition attribute) bm3d_block_size (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] bm3d_clip (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] bm3d_sigma (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] bm3d_stage_arg (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] border_margin_px (phenotypic.detect.FilamentousFungiDetector attribute), [1] border_remover_size (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] border_size (phenotypic.refine.RemoveBorderObjects attribute), [1] bottom (phenotypic.correction.ImageCropper attribute), [1] (phenotypic.correction.ImagePadder attribute), [1] boundary_displacement() (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) BoundFigures (class in phenotypic.abc_), [1] bounds (phenotypic.abc_.Control attribute), [1] breadcrumb (phenotypic.gui.builder._state._DagBuilderState attribute), [1] BROWN_PCT (phenotypic.schema.ColorComposition attribute) Budget (class in phenotypic.tune), [1] budget (phenotypic.tune.TuningSpec attribute), [1] build() (phenotypic.tune.GridConfig method), [1] (phenotypic.tune.OptunaConfig method), [1] (phenotypic.tune.RandomConfig method), [1] (phenotypic.tune.StrategyConfig method), [1] build_notebook_dashboard() (in module phenotypic.sdk_.viz.notebook) build_pipeline() (in module phenotypic.tune), [1] build_reduced_space() (in module phenotypic.tune), [1]

C

C (phenotypic.enhance.StructureSmoothing attribute), [1] calculate_optimal_array_chunks() (in module phenotypic.sdk_.slurm), [1] calibrate_screening_threshold() (in module phenotypic.sdk_.branch_pathfinding) calibrate_thresholds() (in module phenotypic.sdk_.branch_pathfinding) calibration_score (phenotypic.tune.GeneralizationReport attribute), [1] calibration_stability (phenotypic.tune.GeneralizationReport attribute), [1] CalibrationData (class in phenotypic.sdk_.branch_pathfinding) camera_make (phenotypic.correction.CaptureMetadata attribute), [1], [2], [3] camera_model (phenotypic.correction.CaptureMetadata attribute), [1], [2], [3] CannyDetector (class in phenotypic.detect), [1] capitalize() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] capture_metadata (phenotypic.correction.ColorCheckerProfile attribute), [1], [2], [3] CaptureMetadata (class in phenotypic.correction), [1] CARBON_SOURCE (phenotypic.schema.CONDITION_METADATA attribute) casefold() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] Categorical (class in phenotypic.tune), [1] categories (phenotypic.sdk_.typing_.TuneSpec attribute) (phenotypic.tune.TuneSpec attribute), [1] CATEGORY (phenotypic.abc_.MeasurementInfo attribute), [1] (phenotypic.abc_.MeasurementInfo property), [1] (phenotypic.schema.ACQUISITION_METADATA property) (phenotypic.schema.BBOX property) (phenotypic.schema.ColorComposition property) (phenotypic.schema.ColorHSV property) (phenotypic.schema.ColorLab property) (phenotypic.schema.Colorxy property) (phenotypic.schema.ColorXYZ property) (phenotypic.schema.CONDITION_METADATA property) (phenotypic.schema.CURATION property) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL property) (phenotypic.schema.EDGE_CORRECTION property) (phenotypic.schema.ErrorCategory property) (phenotypic.schema.EXPERIMENT_METADATA property) (phenotypic.schema.GENETIC_METADATA property) (phenotypic.schema.GRID property) (phenotypic.schema.GRID_LINREG_STATS property) (phenotypic.schema.GRID_SPATIAL property) (phenotypic.schema.GRID_SPREAD property) (phenotypic.schema.INCUBATION_METADATA property) (phenotypic.schema.INTENSITY property) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL property) (phenotypic.schema.LOG_GROWTH_MODEL property) (phenotypic.schema.MeasurementInfo attribute) (phenotypic.schema.MeasurementInfo property) (phenotypic.schema.METADATA property) (phenotypic.schema.MODEL_METRICS property) (phenotypic.schema.OBJECT property) (phenotypic.schema.PLATE_METADATA property) (phenotypic.schema.QUALITY_CHECK property) (phenotypic.schema.QUALITY_COUNT property) (phenotypic.schema.QUALITY_ICC property) (phenotypic.schema.QUALITY_MAD property) (phenotypic.schema.QUALITY_SE property) (phenotypic.schema.QUALITY_TUKEY property) (phenotypic.schema.QUALITY_ZMAX property) (phenotypic.schema.RADIAL_EXPANSION property) (phenotypic.schema.SAMPLE_METADATA property) (phenotypic.schema.SHAPE property) (phenotypic.schema.SIZE property) (phenotypic.schema.SYMMETRIC_ZONES property) (phenotypic.schema.TEXTURE property) (phenotypic.sdk_.constants_.ConstantLabels property), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS property), [1] (phenotypic.sdk_.constants_.PIPE_STATUS property), [1] category() (phenotypic.abc_.MeasurementInfo class method), [1] (phenotypic.schema.ACQUISITION_METADATA class method) (phenotypic.schema.BBOX class method) (phenotypic.schema.ColorComposition class method) (phenotypic.schema.ColorHSV class method) (phenotypic.schema.ColorLab class method) (phenotypic.schema.Colorxy class method) (phenotypic.schema.ColorXYZ class method) (phenotypic.schema.CONDITION_METADATA class method) (phenotypic.schema.CURATION class method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL class method) (phenotypic.schema.EDGE_CORRECTION class method) (phenotypic.schema.ErrorCategory class method) (phenotypic.schema.EXPERIMENT_METADATA class method) (phenotypic.schema.GENETIC_METADATA class method) (phenotypic.schema.GRID class method) (phenotypic.schema.GRID_LINREG_STATS class method) (phenotypic.schema.GRID_SPATIAL class method) (phenotypic.schema.GRID_SPREAD class method) (phenotypic.schema.INCUBATION_METADATA class method) (phenotypic.schema.INTENSITY class method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL class method) (phenotypic.schema.LOG_GROWTH_MODEL class method) (phenotypic.schema.MeasurementInfo class method) (phenotypic.schema.METADATA class method) (phenotypic.schema.MODEL_METRICS class method) (phenotypic.schema.OBJECT class method) (phenotypic.schema.PLATE_METADATA class method) (phenotypic.schema.QUALITY_CHECK class method) (phenotypic.schema.QUALITY_COUNT class method) (phenotypic.schema.QUALITY_ICC class method) (phenotypic.schema.QUALITY_MAD class method) (phenotypic.schema.QUALITY_SE class method) (phenotypic.schema.QUALITY_TUKEY class method) (phenotypic.schema.QUALITY_ZMAX class method) (phenotypic.schema.RADIAL_EXPANSION class method) (phenotypic.schema.SAMPLE_METADATA class method) (phenotypic.schema.SHAPE class method) (phenotypic.schema.SIZE class method) (phenotypic.schema.SYMMETRIC_ZONES class method) (phenotypic.schema.TEXTURE class method) (phenotypic.sdk_.constants_.ConstantLabels class method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS class method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS class method), [1] center() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] CENTER_CC (phenotypic.schema.BBOX attribute) CENTER_RR (phenotypic.schema.BBOX attribute) CenteredAutoGridFinder (class in phenotypic.grid), [1] CenteredAutoGridFinderFallbackWarning, [1] centers (phenotypic.detect.ManualPointDetector attribute), [1] (phenotypic.refine.ManualRefine attribute), [1] CHANNELS_DEFAULT (phenotypic.sdk_.constants_.IMAGE_MODE attribute), [1] ChanVeseDetector (class in phenotypic.detect), [1] check (phenotypic.tune.QCScorer attribute), [1] checker_type (phenotypic.correction.ColorCheckerProfile attribute), [1] checkpoint_lock_filename() (in module phenotypic.sdk_), [1] checkpoint_lock_path() (in module phenotypic.sdk_), [1] CheckpointType (in module phenotypic.sdk_.typing_) choices (phenotypic.tune.Categorical attribute), [1] CHUNK_JOB_IDS (phenotypic.sdk_.DashboardManifestSlurmInfoKey attribute), [1] (phenotypic.sdk_.JobMetadataKey attribute), [1] chunk_lock_path() (in module phenotypic.sdk_), [1] chunk_manifest_path() (in module phenotypic.sdk_), [1] chunk_parquet_filename() (in module phenotypic.sdk_), [1] chunk_parquet_path() (in module phenotypic.sdk_), [1] CHUNK_SCRIPTS (phenotypic.sdk_.DashboardManifestSlurmInfoKey attribute), [1] (phenotypic.sdk_.JobMetadataKey attribute), [1] chunk_state_path() (in module phenotypic.sdk_), [1] CHUNKED_FILES (phenotypic.sdk_.ChunkStateKey attribute), [1] ChunkManifestKey (class in phenotypic.sdk_), [1] CHUNKS (phenotypic.sdk_.ChunkManifestKey attribute), [1] chunks_dir() (in module phenotypic.sdk_), [1] ChunkStateKey (class in phenotypic.sdk_), [1] cieX_headers() (phenotypic.schema.ColorXYZ class method) cieY_headers() (phenotypic.schema.ColorXYZ class method) cieZ_headers() (phenotypic.schema.ColorXYZ class method) CIRCULARITY (phenotypic.schema.SHAPE attribute) clahe_clip_limit (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] clahe_kernel_size (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] class_name (phenotypic.gui.builder._state.BlockNode attribute), [1] clear() (phenotypic.util.BackgroundMetrics method), [1] (phenotypic.util.ContrastMetrics method), [1] (phenotypic.util.image_metrics.BackgroundMetrics method) (phenotypic.util.image_metrics.ContrastMetrics method) (phenotypic.util.image_metrics.NoiseMetrics method) (phenotypic.util.image_metrics.QualityScores method) (phenotypic.util.image_metrics.StructureMetrics method) (phenotypic.util.NoiseMetrics method), [1] (phenotypic.util.QualityScores method), [1] (phenotypic.util.StructureMetrics method), [1] clear_machine_state() (in module phenotypic.sdk_), [1] CliMode (in module phenotypic.sdk_.typing_) clip (phenotypic.correction.BayesShrinkCorrector attribute), [1] (phenotypic.correction.ColorDenoise attribute), [1] (phenotypic.correction.VisuShrinkCorrector attribute), [1] (phenotypic.enhance.BayesShrinkEnhancer attribute), [1] (phenotypic.enhance.EnhanceBlockMatch attribute), [1] (phenotypic.enhance.LocalEdgeDenoise attribute), [1] (phenotypic.enhance.VisuShrinkEnhancer attribute), [1] clip_limit (phenotypic.enhance.EnhanceLocalContrast attribute), [1] ClipControlMixin (class in phenotypic.sdk_), [1] (class in phenotypic.sdk_.mixin) CLONE (phenotypic.schema.SAMPLE_METADATA attribute) close_handle() (phenotypic.sdk_.HDF static method), [1] (phenotypic.sdk_.hdf_.HDF static method) COEFFICIENT_VARIANCE_INTENSITY (phenotypic.schema.INTENSITY attribute) Coherence (phenotypic.util.image_metrics.QualityScores attribute) (phenotypic.util.QualityScores attribute), [1] coherence_map (phenotypic.util.image_metrics.StructureMetrics attribute) (phenotypic.util.StructureMetrics attribute), [1] coherence_window_radius (phenotypic.detect.FilamentousFungiDetector attribute), [1] col_edges (phenotypic.grid.ManualGridFinder attribute), [1], [2], [3] COL_INTERVAL_END (phenotypic.schema.GRID attribute) COL_INTERVAL_START (phenotypic.schema.GRID attribute) COL_LINREG_B (phenotypic.schema.GRID_LINREG_STATS attribute) (phenotypic.sdk_.constants_.GRID_LINREG_STATS_EXTRACTOR attribute), [1] COL_LINREG_M (phenotypic.schema.GRID_LINREG_STATS attribute) (phenotypic.sdk_.constants_.GRID_LINREG_STATS_EXTRACTOR attribute), [1] COL_MAJOR_IDX (phenotypic.schema.GRID attribute) COL_NUM (phenotypic.schema.GRID attribute) collapsed (phenotypic.gui.builder._state.BlockNode attribute), [1] collate() (phenotypic.abc_.GpuDetector method), [1] colony colony_centroids (phenotypic.sdk_.branch_pathfinding.DijkstraResult attribute), [1] colony_id (phenotypic.sdk_.branch_pathfinding.DijkstraResult attribute), [1] (phenotypic.sdk_.branch_pathfinding.FragmentAssignment attribute), [1] (phenotypic.sdk_.branch_pathfinding.FragmentPath attribute), [1] color_chroma_min (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] color_include_XYZ (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] color_white_chroma_max (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] ColorAccessor (class in phenotypic._core._image_parts.accessors._color_accessor) ColorCheckerProfile (class in phenotypic.correction), [1] ColorComposition (class in phenotypic.schema) ColorCorrector (class in phenotypic.correction), [1] ColorDenoise (class in phenotypic.correction), [1] ColorHSV (class in phenotypic.schema) ColorLab (class in phenotypic.schema) Colorxy (class in phenotypic.schema) ColorXYZ (class in phenotypic.schema) column (phenotypic.post.AppendString attribute) (phenotypic.post.ExpandMetadata attribute) (phenotypic.post.PrependString attribute) columns (phenotypic.post.MergeMetadata attribute) compactness (phenotypic.detect.WatershedDetector attribute), [1] COMPACTNESS (phenotypic.schema.SHAPE attribute) compare() (phenotypic.correction.CaptureMetadata method), [1] COMPLETED (phenotypic.sdk_.DashboardManifestKey attribute), [1] (phenotypic.sdk_.ProcessingStateKey attribute), [1] COMPLETED_CHUNKS (phenotypic.sdk_.DashboardManifestSlurmInfoKey attribute), [1] completed_count() (phenotypic.tune.JournalStudyStore method), [1] CompositeBlend (in module phenotypic.sdk_.typing_) CompositeDetector (class in phenotypic.detect), [1] CompositeScorer (class in phenotypic.tune), [1] COMPOUND (phenotypic.schema.CONDITION_METADATA attribute) compute() (phenotypic.abc_.DetectionMode method), [1] compute_all() (phenotypic.util.image_metrics.ImageMetricsCalculator method) (phenotypic.util.ImageMetricsCalculator method), [1] compute_anisotropy() (in module phenotypic.sdk_.branch_pathfinding) compute_background_metrics() (phenotypic.util.image_metrics.ImageMetricsCalculator method) (phenotypic.util.ImageMetricsCalculator method), [1] compute_contrast_metrics() (phenotypic.util.image_metrics.ImageMetricsCalculator method) (phenotypic.util.ImageMetricsCalculator method), [1] compute_generalization_gap() (in module phenotypic.tune), [1] compute_local_contrast() (phenotypic.util.image_metrics.ImageMetricsCalculator method) (phenotypic.util.ImageMetricsCalculator method), [1] compute_local_mad_map() (in module phenotypic.sdk_.branch_pathfinding) compute_local_variance() (phenotypic.util.image_metrics.ImageMetricsCalculator method) (phenotypic.util.ImageMetricsCalculator method), [1] compute_min_cost_envelope() (in module phenotypic.sdk_.branch_pathfinding) compute_noise_metrics() (phenotypic.util.image_metrics.ImageMetricsCalculator method) (phenotypic.util.ImageMetricsCalculator method), [1] compute_orientation_coherence() (in module phenotypic.sdk_.branch_pathfinding) compute_param_importance() (in module phenotypic.tune), [1] compute_param_importance_report() (in module phenotypic.tune), [1] compute_path_metrics() (in module phenotypic.sdk_.branch_pathfinding) compute_psd() (phenotypic.util.image_metrics.ImageMetricsCalculator method) (phenotypic.util.ImageMetricsCalculator method), [1] compute_quality_scores() (phenotypic.util.image_metrics.ImageMetricsCalculator method) (phenotypic.util.ImageMetricsCalculator method), [1] compute_structure_metrics() (phenotypic.util.image_metrics.ImageMetricsCalculator method) (phenotypic.util.ImageMetricsCalculator method), [1] CONCENTRATION (phenotypic.schema.CONDITION_METADATA attribute) CONDITION_METADATA (class in phenotypic.schema) conditional_on (phenotypic.tune.Knob attribute), [1] cone_to_hsv() (in module phenotypic.util), [1] CONFIG (phenotypic.sdk_.ProcessingStateKey attribute), [1] connectivity (phenotypic.analysis.EdgeCorrector attribute), [1] (phenotypic.detect.CannyDetector attribute), [1] (phenotypic.detect.ChanVeseDetector attribute), [1] (phenotypic.detect.MadHysteresisDetector attribute), [1] (phenotypic.detect.WatershedDetector attribute), [1] connectivity_correct_labels() (in module phenotypic.sdk_.branch_pathfinding) constant_value (phenotypic.correction.ImagePadder attribute), [1] ConstantLabels (class in phenotypic.sdk_.constants_), [1] construct() (phenotypic.abc_.BackgroundSubtraction class method), [1] (phenotypic.abc_.BaseOperation class method), [1] (phenotypic.abc_.ContrastAdjustment class method), [1] (phenotypic.abc_.FocusBlob class method), [1] (phenotypic.abc_.FocusEdge class method), [1] (phenotypic.abc_.GpuDetector class method), [1] (phenotypic.abc_.GridCorrector class method), [1] (phenotypic.abc_.GridFinder class method), [1] (phenotypic.abc_.GridMeasureFeatures class method), [1] (phenotypic.abc_.GridObjectDetector class method), [1] (phenotypic.abc_.GridObjectRefiner class method), [1] (phenotypic.abc_.GridOperation class method), [1] (phenotypic.abc_.ImageCorrector class method), [1] (phenotypic.abc_.ImageDenoiser class method), [1] (phenotypic.abc_.ImageEnhancer class method), [1] (phenotypic.abc_.ImageOperation class method), [1] (phenotypic.abc_.MeasureFeatures class method), [1] (phenotypic.abc_.MorphologicalFiltering class method), [1] (phenotypic.abc_.ObjectDetector class method), [1] (phenotypic.abc_.ObjectRefiner class method), [1] (phenotypic.abc_.PostMeasurement class method), [1] (phenotypic.abc_.PrefabPipeline class method), [1] (phenotypic.abc_.Smoothing class method), [1] (phenotypic.abc_.ThresholdDetector class method), [1] (phenotypic.analysis.abc_.ModelFitter class method) (phenotypic.analysis.abc_.QualityCheck class method) (phenotypic.analysis.abc_.SetAnalyzer class method) (phenotypic.analysis.DoubleSoftplus class method), [1] (phenotypic.analysis.EdgeCorrector class method), [1] (phenotypic.analysis.ErrorCutoffFinder class method), [1] (phenotypic.analysis.ExpectedVsDetectedCount class method), [1] (phenotypic.analysis.ICC class method), [1] (phenotypic.analysis.LinearSoftplus class method), [1] (phenotypic.analysis.LogGrowthModel class method), [1] (phenotypic.analysis.MADOutlierRemover class method), [1] (phenotypic.analysis.MaxModifiedZScore class method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount class method) (phenotypic.analysis.qc.ICC class method) (phenotypic.analysis.qc.MaxModifiedZScore class method) (phenotypic.analysis.qc.RelativeMAD class method) (phenotypic.analysis.qc.ReplicateAgreement class method) (phenotypic.analysis.qc.TukeyOutlierFraction class method) (phenotypic.analysis.RelativeMAD class method), [1] (phenotypic.analysis.ReplicateAgreement class method), [1] (phenotypic.analysis.TukeyOutlierFraction class method), [1] (phenotypic.analysis.TukeyOutlierRemover class method), [1] (phenotypic.correction.BayesShrinkCorrector class method), [1] (phenotypic.correction.CaptureMetadata class method), [1] (phenotypic.correction.ColorCheckerProfile class method), [1] (phenotypic.correction.ColorCorrector class method), [1] (phenotypic.correction.ColorDenoise class method), [1] (phenotypic.correction.DenoiseBlockMatch class method), [1] (phenotypic.correction.GridAligner class method), [1] (phenotypic.correction.ImageCropper class method), [1] (phenotypic.correction.ImagePadder class method), [1] (phenotypic.correction.VisuShrinkCorrector class method), [1] (phenotypic.detect.CannyDetector class method), [1] (phenotypic.detect.ChanVeseDetector class method), [1] (phenotypic.detect.CompositeDetector class method), [1] (phenotypic.detect.FilamentousFungiDetector class method), [1] (phenotypic.detect.HysteresisDetector class method), [1] (phenotypic.detect.InoculumDetector class method), [1] (phenotypic.detect.IsodataDetector class method), [1] (phenotypic.detect.LiDetector class method), [1] (phenotypic.detect.MadHysteresisDetector class method), [1] (phenotypic.detect.ManualGridPointDetector class method), [1] (phenotypic.detect.ManualPointDetector class method), [1] (phenotypic.detect.MeanDetector class method), [1] (phenotypic.detect.MinimumDetector class method), [1] (phenotypic.detect.OtsuDetector class method), [1] (phenotypic.detect.RankOtsuDetector class method), [1] (phenotypic.detect.RoundPeaksDetector class method), [1] (phenotypic.detect.SecondaryOtsuDetector class method), [1] (phenotypic.detect.SinePeakDetector class method), [1] (phenotypic.detect.TriangleDetector class method), [1] (phenotypic.detect.UserThreshold class method), [1] (phenotypic.detect.WatershedDetector class method), [1] (phenotypic.detect.YenDetector class method), [1] (phenotypic.enhance.BayesShrinkEnhancer class method), [1] (phenotypic.enhance.ContrastStretching class method), [1] (phenotypic.enhance.EnhanceBlockMatch class method), [1] (phenotypic.enhance.EnhanceLocalContrast class method), [1] (phenotypic.enhance.FlattenIllumination class method), [1] (phenotypic.enhance.FocusBlobLoG class method), [1] (phenotypic.enhance.FocusEdgeFrangi class method), [1] (phenotypic.enhance.FocusEdgeHessian class method), [1] (phenotypic.enhance.FocusEdgeLaplace class method), [1] (phenotypic.enhance.FocusEdgeMeijering class method), [1] (phenotypic.enhance.FocusEdgePhase class method), [1] (phenotypic.enhance.FocusEdgeSato class method), [1] (phenotypic.enhance.FocusEdgeSobel class method), [1] (phenotypic.enhance.GaussianBlur class method), [1] (phenotypic.enhance.GrayOpening class method), [1] (phenotypic.enhance.ImageInverter class method), [1] (phenotypic.enhance.LocalEdgeDenoise class method), [1] (phenotypic.enhance.MedianFilter class method), [1] (phenotypic.enhance.NonLocalMeansDenoiser class method), [1] (phenotypic.enhance.RankMedianEnhancer class method), [1] (phenotypic.enhance.SetDetectMode class method), [1] (phenotypic.enhance.SharpenEdgeGauss class method), [1] (phenotypic.enhance.StructureSmoothing class method), [1] (phenotypic.enhance.SubtractGaussian class method), [1] (phenotypic.enhance.SubtractOpening class method), [1] (phenotypic.enhance.SubtractRollingBall class method), [1] (phenotypic.enhance.SubtractWhiteTophat class method), [1] (phenotypic.enhance.VisuShrinkEnhancer class method), [1] (phenotypic.enhance.WhiteTophatEnhance class method), [1] (phenotypic.grid.AutoGridFinder class method), [1] (phenotypic.grid.CenteredAutoGridFinder class method), [1] (phenotypic.grid.GridApply class method), [1] (phenotypic.grid.ManualGridFinder class method), [1] (phenotypic.measure.MeasureBounds class method), [1] (phenotypic.measure.MeasureColor class method), [1] (phenotypic.measure.MeasureGridLinRegStats class method), [1] (phenotypic.measure.MeasureGridSpatial class method), [1] (phenotypic.measure.MeasureGridSpread class method), [1] (phenotypic.measure.MeasureIntensity class method), [1] (phenotypic.measure.MeasureShape class method), [1] (phenotypic.measure.MeasureSize class method), [1] (phenotypic.measure.MeasureSymmetricZones class method), [1] (phenotypic.measure.MeasureTexture class method), [1] (phenotypic.post.AppendString class method) (phenotypic.post.ExpandMetadata class method) (phenotypic.post.MergeMetadata class method) (phenotypic.post.PrependString class method) (phenotypic.prefab.FilamentousFungiPipeline class method), [1] (phenotypic.prefab.GridSectionPipeline class method), [1] (phenotypic.prefab.HeavyOtsuPipeline class method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline class method), [1] (phenotypic.prefab.HeavyWatershedPipeline class method), [1] (phenotypic.prefab.RoundPeaksPipeline class method), [1] (phenotypic.prefab.SpImagerPipeline class method), [1] (phenotypic.refine.ExtractColonyCore class method), [1] (phenotypic.refine.GridAlignmentRefiner class method), [1] (phenotypic.refine.GridOversizedObjectRemover class method), [1] (phenotypic.refine.KeepNearestCenter class method), [1] (phenotypic.refine.KeepSectionLargest class method), [1] (phenotypic.refine.ManualRefine class method), [1] (phenotypic.refine.MaskClosing class method), [1] (phenotypic.refine.MaskDilation class method), [1] (phenotypic.refine.MaskErosion class method), [1] (phenotypic.refine.MaskFill class method), [1] (phenotypic.refine.MaskGradient class method), [1] (phenotypic.refine.MaskOpening class method), [1] (phenotypic.refine.MaskWhiteTophat class method), [1] (phenotypic.refine.MergeFragmentChains class method), [1] (phenotypic.refine.NearestNeighborMerger class method), [1] (phenotypic.refine.ReduceSectionsByLine class method), [1] (phenotypic.refine.RefineBySineFit class method), [1] (phenotypic.refine.RemoveBorderObjects class method), [1] (phenotypic.refine.RemoveByFeature class method), [1] (phenotypic.refine.RemoveGridOutliers class method), [1] (phenotypic.refine.RemoveLowCircularity class method), [1] (phenotypic.refine.SeparateObjects class method), [1] (phenotypic.refine.Skeletonize class method), [1] (phenotypic.refine.SmallObjectRemover class method), [1] (phenotypic.refine.SmallToLargeMerger class method), [1] (phenotypic.refine.Thinning class method), [1] (phenotypic.refine.TrimAsymmetry class method), [1] (phenotypic.tune.Budget class method), [1] (phenotypic.tune.Categorical class method), [1] (phenotypic.tune.CompositeScorer class method), [1] (phenotypic.tune.EvaluationResult class method), [1] (phenotypic.tune.Evaluator class method), [1] (phenotypic.tune.Excluded class method), [1] (phenotypic.tune.Fixed class method), [1] (phenotypic.tune.FloatRange class method), [1] (phenotypic.tune.GridConfig class method), [1] (phenotypic.tune.GroundTruthMasks class method), [1] (phenotypic.tune.HeldOutConfig class method), [1] (phenotypic.tune.ImportanceReport class method), [1] (phenotypic.tune.InferredSearchSpace class method), [1] (phenotypic.tune.IntRange class method), [1] (phenotypic.tune.Knob class method), [1] (phenotypic.tune.OptunaConfig class method), [1] (phenotypic.tune.QCScorer class method), [1] (phenotypic.tune.RandomConfig class method), [1] (phenotypic.tune.ReferenceFreeScorer class method), [1] (phenotypic.tune.Scorer class method), [1] (phenotypic.tune.SearchSpace class method), [1] (phenotypic.tune.StrategyConfig class method), [1] (phenotypic.tune.SupervisedScorer class method), [1] (phenotypic.tune.targets.Nested class method) (phenotypic.tune.targets.Param class method) (phenotypic.tune.targets.Presence class method) (phenotypic.tune.targets.TunableParam class method) (phenotypic.tune.Trial class method), [1] (phenotypic.tune.TuningSpec class method), [1]

contains() (phenotypic.gui.shell.SandboxRoot method) CONTRAST (phenotypic.schema.TEXTURE attribute) Contrast (phenotypic.util.image_metrics.QualityScores attribute) (phenotypic.util.QualityScores attribute), [1] ContrastAdjustment (class in phenotypic.abc_), [1] ContrastMetrics (class in phenotypic.util), [1] (class in phenotypic.util.image_metrics) ContrastStretching (class in phenotypic.enhance), [1] Control (class in phenotypic.abc_), [1] CONTROL (phenotypic.schema.SAMPLE_METADATA attribute) controls (phenotypic.abc_.FigureSpec attribute), [1], [2], [3] convert2ycbcr (phenotypic.correction.BayesShrinkCorrector attribute), [1] (phenotypic.correction.VisuShrinkCorrector attribute), [1] CONVEX_AREA (phenotypic.schema.SHAPE attribute) CONVEX_DENSITY (phenotypic.schema.INTENSITY attribute) coord1 (phenotypic.detect.ManualGridPointDetector attribute), [1] coord2 (phenotypic.detect.ManualGridPointDetector attribute), [1] coords (phenotypic.sdk_.branch_pathfinding.FragmentPath attribute), [1] copy() (phenotypic._core._image_parts.accessors._detect_mat_accessor.DetectMatAccessor method) (phenotypic._core._image_parts.accessors._grayscale_accessor.Grayscale method) (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap method) (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask method) (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) (phenotypic._core._image_parts.accessors._rgb_accessor.ImageRGB method) (phenotypic.abc_.BackgroundSubtraction method), [1] (phenotypic.abc_.BaseOperation method), [1] (phenotypic.abc_.ContrastAdjustment method), [1] (phenotypic.abc_.FocusBlob method), [1] (phenotypic.abc_.FocusEdge method), [1] (phenotypic.abc_.GpuDetector method), [1] (phenotypic.abc_.GridCorrector method), [1] (phenotypic.abc_.GridFinder method), [1] (phenotypic.abc_.GridMeasureFeatures method), [1] (phenotypic.abc_.GridObjectDetector method), [1] (phenotypic.abc_.GridObjectRefiner method), [1] (phenotypic.abc_.GridOperation method), [1] (phenotypic.abc_.ImageCorrector method), [1] (phenotypic.abc_.ImageDenoiser method), [1] (phenotypic.abc_.ImageEnhancer method), [1] (phenotypic.abc_.ImageOperation method), [1] (phenotypic.abc_.MeasureFeatures method), [1] (phenotypic.abc_.MorphologicalFiltering method), [1] (phenotypic.abc_.ObjectDetector method), [1] (phenotypic.abc_.ObjectRefiner method), [1] (phenotypic.abc_.PostMeasurement method), [1] (phenotypic.abc_.PrefabPipeline method), [1] (phenotypic.abc_.Smoothing method), [1] (phenotypic.abc_.ThresholdDetector method), [1] (phenotypic.analysis.abc_.ModelFitter method) (phenotypic.analysis.abc_.QualityCheck method) (phenotypic.analysis.abc_.SetAnalyzer method) (phenotypic.analysis.DoubleSoftplus method), [1] (phenotypic.analysis.EdgeCorrector method), [1] (phenotypic.analysis.ErrorCutoffFinder method), [1] (phenotypic.analysis.ExpectedVsDetectedCount method), [1] (phenotypic.analysis.ICC method), [1] (phenotypic.analysis.LinearSoftplus method), [1] (phenotypic.analysis.LogGrowthModel method), [1] (phenotypic.analysis.MADOutlierRemover method), [1] (phenotypic.analysis.MaxModifiedZScore method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount method) (phenotypic.analysis.qc.ICC method) (phenotypic.analysis.qc.MaxModifiedZScore method) (phenotypic.analysis.qc.RelativeMAD method) (phenotypic.analysis.qc.ReplicateAgreement method) (phenotypic.analysis.qc.TukeyOutlierFraction method) (phenotypic.analysis.RelativeMAD method), [1] (phenotypic.analysis.ReplicateAgreement method), [1] (phenotypic.analysis.TukeyOutlierFraction method), [1] (phenotypic.analysis.TukeyOutlierRemover method), [1] (phenotypic.correction.BayesShrinkCorrector method), [1] (phenotypic.correction.CaptureMetadata method), [1] (phenotypic.correction.ColorCheckerProfile method), [1] (phenotypic.correction.ColorCorrector method), [1] (phenotypic.correction.ColorDenoise method), [1] (phenotypic.correction.DenoiseBlockMatch method), [1] (phenotypic.correction.GridAligner method), [1] (phenotypic.correction.ImageCropper method), [1] (phenotypic.correction.ImagePadder method), [1] (phenotypic.correction.VisuShrinkCorrector method), [1] (phenotypic.detect.CannyDetector method), [1] (phenotypic.detect.ChanVeseDetector method), [1] (phenotypic.detect.CompositeDetector method), [1] (phenotypic.detect.FilamentousFungiDetector method), [1] (phenotypic.detect.HysteresisDetector method), [1] (phenotypic.detect.InoculumDetector method), [1] (phenotypic.detect.IsodataDetector method), [1] (phenotypic.detect.LiDetector method), [1] (phenotypic.detect.MadHysteresisDetector method), [1] (phenotypic.detect.ManualGridPointDetector method), [1] (phenotypic.detect.ManualPointDetector method), [1] (phenotypic.detect.MeanDetector method), [1] (phenotypic.detect.MinimumDetector method), [1] (phenotypic.detect.OtsuDetector method), [1] (phenotypic.detect.RankOtsuDetector method), [1] (phenotypic.detect.RoundPeaksDetector method), [1] (phenotypic.detect.SecondaryOtsuDetector method), [1] (phenotypic.detect.SinePeakDetector method), [1] (phenotypic.detect.TriangleDetector method), [1] (phenotypic.detect.UserThreshold method), [1] (phenotypic.detect.WatershedDetector method), [1] (phenotypic.detect.YenDetector method), [1] (phenotypic.enhance.BayesShrinkEnhancer method), [1] (phenotypic.enhance.ContrastStretching method), [1] (phenotypic.enhance.EnhanceBlockMatch method), [1] (phenotypic.enhance.EnhanceLocalContrast method), [1] (phenotypic.enhance.FlattenIllumination method), [1] (phenotypic.enhance.FocusBlobLoG method), [1] (phenotypic.enhance.FocusEdgeFrangi method), [1] (phenotypic.enhance.FocusEdgeHessian method), [1] (phenotypic.enhance.FocusEdgeLaplace method), [1] (phenotypic.enhance.FocusEdgeMeijering method), [1] (phenotypic.enhance.FocusEdgePhase method), [1] (phenotypic.enhance.FocusEdgeSato method), [1] (phenotypic.enhance.FocusEdgeSobel method), [1] (phenotypic.enhance.GaussianBlur method), [1] (phenotypic.enhance.GrayOpening method), [1] (phenotypic.enhance.ImageInverter method), [1] (phenotypic.enhance.LocalEdgeDenoise method), [1] (phenotypic.enhance.MedianFilter method), [1] (phenotypic.enhance.NonLocalMeansDenoiser method), [1] (phenotypic.enhance.RankMedianEnhancer method), [1] (phenotypic.enhance.SetDetectMode method), [1] (phenotypic.enhance.SharpenEdgeGauss method), [1] (phenotypic.enhance.StructureSmoothing method), [1] (phenotypic.enhance.SubtractGaussian method), [1] (phenotypic.enhance.SubtractOpening method), [1] (phenotypic.enhance.SubtractRollingBall method), [1] (phenotypic.enhance.SubtractWhiteTophat method), [1] (phenotypic.enhance.VisuShrinkEnhancer method), [1] (phenotypic.enhance.WhiteTophatEnhance method), [1] (phenotypic.grid.AutoGridFinder method), [1] (phenotypic.grid.CenteredAutoGridFinder method), [1] (phenotypic.grid.GridApply method), [1] (phenotypic.grid.ManualGridFinder method), [1] (phenotypic.GridImage method) (phenotypic.Image method) (phenotypic.measure.MeasureBounds method), [1] (phenotypic.measure.MeasureColor method), [1] (phenotypic.measure.MeasureGridLinRegStats method), [1] (phenotypic.measure.MeasureGridSpatial method), [1] (phenotypic.measure.MeasureGridSpread method), [1] (phenotypic.measure.MeasureIntensity method), [1] (phenotypic.measure.MeasureShape method), [1] (phenotypic.measure.MeasureSize method), [1] (phenotypic.measure.MeasureSymmetricZones method), [1] (phenotypic.measure.MeasureTexture method), [1] (phenotypic.post.AppendString method) (phenotypic.post.ExpandMetadata method) (phenotypic.post.MergeMetadata method) (phenotypic.post.PrependString method) (phenotypic.prefab.FilamentousFungiPipeline method), [1] (phenotypic.prefab.GridSectionPipeline method), [1] (phenotypic.prefab.HeavyOtsuPipeline method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1] (phenotypic.prefab.HeavyWatershedPipeline method), [1] (phenotypic.prefab.RoundPeaksPipeline method), [1] (phenotypic.prefab.SpImagerPipeline method), [1] (phenotypic.refine.ExtractColonyCore method), [1] (phenotypic.refine.GridAlignmentRefiner method), [1] (phenotypic.refine.GridOversizedObjectRemover method), [1] (phenotypic.refine.KeepNearestCenter method), [1] (phenotypic.refine.KeepSectionLargest method), [1] (phenotypic.refine.ManualRefine method), [1] (phenotypic.refine.MaskClosing method), [1] (phenotypic.refine.MaskDilation method), [1] (phenotypic.refine.MaskErosion method), [1] (phenotypic.refine.MaskFill method), [1] (phenotypic.refine.MaskGradient method), [1] (phenotypic.refine.MaskOpening method), [1] (phenotypic.refine.MaskWhiteTophat method), [1] (phenotypic.refine.MergeFragmentChains method), [1] (phenotypic.refine.NearestNeighborMerger method), [1] (phenotypic.refine.ReduceSectionsByLine method), [1] (phenotypic.refine.RefineBySineFit method), [1] (phenotypic.refine.RemoveBorderObjects method), [1] (phenotypic.refine.RemoveByFeature method), [1] (phenotypic.refine.RemoveGridOutliers method), [1] (phenotypic.refine.RemoveLowCircularity method), [1] (phenotypic.refine.SeparateObjects method), [1] (phenotypic.refine.Skeletonize method), [1] (phenotypic.refine.SmallObjectRemover method), [1] (phenotypic.refine.SmallToLargeMerger method), [1] (phenotypic.refine.Thinning method), [1] (phenotypic.refine.TrimAsymmetry method), [1] (phenotypic.tune.Budget method), [1] (phenotypic.tune.Categorical method), [1] (phenotypic.tune.CompositeScorer method), [1] (phenotypic.tune.EvaluationResult method), [1] (phenotypic.tune.Evaluator method), [1] (phenotypic.tune.Excluded method), [1] (phenotypic.tune.Fixed method), [1] (phenotypic.tune.FloatRange method), [1] (phenotypic.tune.GridConfig method), [1] (phenotypic.tune.GroundTruthMasks method), [1] (phenotypic.tune.HeldOutConfig method), [1] (phenotypic.tune.ImportanceReport method), [1] (phenotypic.tune.InferredSearchSpace method), [1] (phenotypic.tune.IntRange method), [1] (phenotypic.tune.Knob method), [1] (phenotypic.tune.OptunaConfig method), [1] (phenotypic.tune.QCScorer method), [1] (phenotypic.tune.RandomConfig method), [1] (phenotypic.tune.ReferenceFreeScorer method), [1] (phenotypic.tune.Scorer method), [1] (phenotypic.tune.SearchSpace method), [1] (phenotypic.tune.StrategyConfig method), [1] (phenotypic.tune.SupervisedScorer method), [1] (phenotypic.tune.targets.Nested method) (phenotypic.tune.targets.Param method) (phenotypic.tune.targets.Presence method) (phenotypic.tune.targets.TunableParam method) (phenotypic.tune.Trial method), [1] (phenotypic.tune.TuningSpec method), [1] (phenotypic.util.BackgroundMetrics method), [1] (phenotypic.util.ContrastMetrics method), [1] (phenotypic.util.image_metrics.BackgroundMetrics method) (phenotypic.util.image_metrics.ContrastMetrics method) (phenotypic.util.image_metrics.NoiseMetrics method) (phenotypic.util.image_metrics.QualityScores method) (phenotypic.util.image_metrics.StructureMetrics method) (phenotypic.util.NoiseMetrics method), [1] (phenotypic.util.QualityScores method), [1] (phenotypic.util.StructureMetrics method), [1] CORE_AREA (phenotypic.schema.SYMMETRIC_ZONES attribute) CORE_END_RADIUS (phenotypic.schema.SYMMETRIC_ZONES attribute) core_fraction (phenotypic.correction.ColorCheckerProfile attribute), [1] CORE_RADIUS (phenotypic.schema.RADIAL_EXPANSION attribute) (phenotypic.schema.SYMMETRIC_ZONES attribute) CORRECTED_CAP (phenotypic.schema.EDGE_CORRECTION attribute) correction_matrix (phenotypic.correction.ColorCheckerProfile attribute), [1], [2], [3] (phenotypic.correction.ColorCorrector property), [1] CORRELATION (phenotypic.schema.TEXTURE attribute) correlation_length (phenotypic.util.image_metrics.NoiseMetrics attribute) (phenotypic.util.NoiseMetrics attribute), [1] correlation_threshold (phenotypic.detect.SinePeakDetector attribute), [1] (phenotypic.refine.RefineBySineFit attribute), [1] cost_distance (phenotypic.sdk_.branch_pathfinding.DijkstraResult attribute), [1] cost_profile (phenotypic.sdk_.branch_pathfinding.FragmentPath attribute), [1] count() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] count_check (phenotypic.tune.ReferenceFreeScorer attribute), [1] (phenotypic.tune.SupervisedScorer attribute), [1] count_free_params() (in module phenotypic.tune), [1] count_term_name (phenotypic.tune.ReferenceFreeScorer attribute), [1] (phenotypic.tune.SupervisedScorer attribute), [1] create_app() (in module phenotypic.gui.analysis) (in module phenotypic.gui.results_viewer) (in module phenotypic.gui.shell) (in module phenotypic.gui.tune) CROP (phenotypic.sdk_.constants_.IMAGE_TYPES attribute), [1] CURATION (class in phenotypic.schema) curation_labels_parquet_path() (in module phenotypic.sdk_), [1] custom_categories_json_path() (in module phenotypic.sdk_), [1] cutoff (phenotypic.enhance.FocusEdgePhase attribute), [1] (phenotypic.refine.RemoveLowCircularity attribute), [1] cutoff_multiplier (phenotypic.refine.RemoveGridOutliers attribute), [1] CV (phenotypic.schema.QUALITY_SE attribute) cv_deferred (phenotypic.tune.GeneralizationReport attribute), [1] cval (phenotypic.enhance.FocusEdgeHessian attribute), [1] (phenotypic.enhance.FocusEdgeMeijering attribute), [1] (phenotypic.enhance.FocusEdgeSato attribute), [1] (phenotypic.enhance.GaussianBlur attribute), [1] (phenotypic.enhance.LocalEdgeDenoise attribute), [1] (phenotypic.enhance.MedianFilter attribute), [1] (phenotypic.enhance.SubtractGaussian attribute), [1] CYAN_PCT (phenotypic.schema.ColorComposition attribute)

D

dash (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor property) dash() (phenotypic._core._image_parts.accessors._detect_mat_accessor.DetectMatAccessor method) (phenotypic._core._image_parts.accessors._grayscale_accessor.Grayscale method) (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap method) (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask method) (phenotypic._core._image_parts.accessors._rgb_accessor.ImageRGB method) (phenotypic.abc_.FigureProvider method), [1] (phenotypic.analysis.abc_.ModelFitter method) (phenotypic.analysis.abc_.QualityCheck method) (phenotypic.analysis.abc_.SetAnalyzer method) (phenotypic.analysis.DoubleSoftplus method), [1] (phenotypic.analysis.EdgeCorrector method), [1] (phenotypic.analysis.ExpectedVsDetectedCount method), [1] (phenotypic.analysis.ICC method), [1] (phenotypic.analysis.LinearSoftplus method), [1] (phenotypic.analysis.LogGrowthModel method), [1] (phenotypic.analysis.MADOutlierRemover method), [1] (phenotypic.analysis.MaxModifiedZScore method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount method) (phenotypic.analysis.qc.ICC method) (phenotypic.analysis.qc.MaxModifiedZScore method) (phenotypic.analysis.qc.RelativeMAD method) (phenotypic.analysis.qc.ReplicateAgreement method) (phenotypic.analysis.qc.TukeyOutlierFraction method) (phenotypic.analysis.RelativeMAD method), [1] (phenotypic.analysis.ReplicateAgreement method), [1] (phenotypic.analysis.TukeyOutlierFraction method), [1] (phenotypic.analysis.TukeyOutlierRemover method), [1] (phenotypic.measure.MeasureSymmetricZones method), [1] dashboard() (phenotypic.correction.ColorCheckerProfile method), [1] (phenotypic.correction.ColorCorrector method), [1] (phenotypic.grid.AutoGridFinder method), [1] dashboard_html_path() (in module phenotypic.sdk_), [1] DashboardManifestKey (class in phenotypic.sdk_), [1] DashboardManifestSlurmInfoKey (class in phenotypic.sdk_), [1] DataIntegrityError, [1] DATASET (phenotypic.schema.EXPERIMENT_METADATA attribute) dataset_changed (phenotypic.tune.GeneralizationReport attribute), [1] dataset_hdf_dir() (in module phenotypic.sdk_), [1] dataset_measurements_dir() (in module phenotypic.sdk_), [1] dataset_overlays_dir() (in module phenotypic.sdk_), [1] dataset_results_dir() (in module phenotypic.sdk_), [1] DATASETS (phenotypic.sdk_.ChunkManifestKey attribute), [1] (phenotypic.sdk_.DashboardManifestKey attribute), [1] (phenotypic.sdk_.JobMetadataKey attribute), [1] (phenotypic.sdk_.ProcessingStateKey attribute), [1] DAY (phenotypic.schema.INCUBATION_METADATA attribute) DEBRIS (phenotypic.schema.ErrorCategory attribute) decode_srgb() (in module phenotypic.sdk_.colourspace), [1] decode_well_position() (in module phenotypic.util), [1] default (phenotypic.abc_.Control attribute), [1] (phenotypic.tune.targets.TunableParam attribute) default_output_dir_name() (in module phenotypic.sdk_), [1] DEFAULT_SCHEMA (phenotypic.sdk_.constants_.IMAGE_MODE attribute), [1] degree (phenotypic.correction.ColorCheckerProfile attribute), [1] (phenotypic.correction.ColorCorrector property), [1] delimiter (phenotypic.post.ExpandMetadata attribute) (phenotypic.post.MergeMetadata attribute) deliverables_dir() (in module phenotypic.sdk_), [1] delta (phenotypic.detect.FilamentousFungiDetector attribute), [1] DELTA (phenotypic.schema.QUALITY_COUNT attribute) DELTA_E2000_MEAN (phenotypic.schema.ColorLab attribute) DELTA_E2000_MEDIAN (phenotypic.schema.ColorLab attribute) DELTA_E2000_P95 (phenotypic.schema.ColorLab attribute) delta_e2000_spread() (in module phenotypic.util), [1] DenoiseBlockMatch (class in phenotypic.correction), [1] DENSE_AREA (phenotypic.schema.SYMMETRIC_ZONES attribute) DENSE_END_RADIUS (phenotypic.schema.SYMMETRIC_ZONES attribute) DENSITY (phenotypic.schema.INTENSITY attribute) desc (phenotypic.abc_.MeasurementInfo attribute), [1], [2], [3] (phenotypic.abc_.PrefabPipeline property), [1] (phenotypic.gui.builder._state._DagBuilderScope attribute), [1] (phenotypic.prefab.FilamentousFungiPipeline property), [1] (phenotypic.prefab.GridSectionPipeline property), [1] (phenotypic.prefab.HeavyOtsuPipeline property), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline property), [1] (phenotypic.prefab.HeavyWatershedPipeline property), [1] (phenotypic.prefab.RoundPeaksPipeline property), [1] (phenotypic.prefab.SpImagerPipeline property), [1] (phenotypic.schema.ACQUISITION_METADATA attribute) (phenotypic.schema.BBOX attribute) (phenotypic.schema.ColorComposition attribute) (phenotypic.schema.ColorHSV attribute) (phenotypic.schema.ColorLab attribute) (phenotypic.schema.Colorxy attribute) (phenotypic.schema.ColorXYZ attribute) (phenotypic.schema.CONDITION_METADATA attribute) (phenotypic.schema.CURATION attribute) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL attribute) (phenotypic.schema.EDGE_CORRECTION attribute) (phenotypic.schema.Entry attribute) (phenotypic.schema.ErrorCategory attribute) (phenotypic.schema.EXPERIMENT_METADATA attribute) (phenotypic.schema.GENETIC_METADATA attribute) (phenotypic.schema.GRID attribute) (phenotypic.schema.GRID_LINREG_STATS attribute) (phenotypic.schema.GRID_SPATIAL attribute) (phenotypic.schema.GRID_SPREAD attribute) (phenotypic.schema.INCUBATION_METADATA attribute) (phenotypic.schema.INTENSITY attribute) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL attribute) (phenotypic.schema.LOG_GROWTH_MODEL attribute) (phenotypic.schema.MeasurementInfo attribute), [1] (phenotypic.schema.METADATA attribute) (phenotypic.schema.MODEL_METRICS attribute) (phenotypic.schema.OBJECT attribute) (phenotypic.schema.PLATE_METADATA attribute) (phenotypic.schema.QUALITY_CHECK attribute) (phenotypic.schema.QUALITY_COUNT attribute) (phenotypic.schema.QUALITY_ICC attribute) (phenotypic.schema.QUALITY_MAD attribute) (phenotypic.schema.QUALITY_SE attribute) (phenotypic.schema.QUALITY_TUKEY attribute) (phenotypic.schema.QUALITY_ZMAX attribute) (phenotypic.schema.RADIAL_EXPANSION attribute) (phenotypic.schema.SAMPLE_METADATA attribute) (phenotypic.schema.SHAPE attribute) (phenotypic.schema.SIZE attribute) (phenotypic.schema.SYMMETRIC_ZONES attribute) (phenotypic.schema.TEXTURE attribute) (phenotypic.sdk_.constants_.ConstantLabels attribute), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS attribute), [1] (phenotypic.sdk_.constants_.PIPE_STATUS attribute), [1] desc_value (phenotypic.abc_.PrefabPipeline attribute), [1] (phenotypic.prefab.FilamentousFungiPipeline attribute), [1] (phenotypic.prefab.GridSectionPipeline attribute), [1] (phenotypic.prefab.HeavyOtsuPipeline attribute), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] (phenotypic.prefab.HeavyWatershedPipeline attribute), [1] (phenotypic.prefab.RoundPeaksPipeline attribute), [1] (phenotypic.prefab.SpImagerPipeline attribute), [1] description (phenotypic.abc_.FigureSpec attribute), [1], [2], [3] (phenotypic.tune.Knob attribute), [1] (phenotypic.tune.targets.TunableParam attribute) DET_EPS (phenotypic.grid.CenteredAutoGridFinder attribute), [1] detail (phenotypic.gui.builder._validation.Issue attribute), [1] detect_mat (phenotypic.Image property) detect_modes() (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) DETECTED (phenotypic.schema.QUALITY_COUNT attribute) DetectionMode (class in phenotypic.abc_), [1] DetectMatAccessor (class in phenotypic._core._image_parts.accessors._detect_mat_accessor) detector_edge_refinement (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] detector_footprint_width (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] detector_min_peak_distance (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] detector_noise_radius (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] detector_peak_prominence (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] detector_remove_noise (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] detector_selection_mode (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] detector_smoothing_sigma (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] detector_split_merged (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] detector_subtract_background (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] detector_thresh_method (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] detectors (phenotypic.detect.CompositeDetector attribute), [1] diagnostics (phenotypic.correction.ColorCheckerProfile attribute), [1], [2], [3] diagnostics() (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) dict() (phenotypic.abc_.BackgroundSubtraction method), [1] (phenotypic.abc_.BaseOperation method), [1] (phenotypic.abc_.ContrastAdjustment method), [1] (phenotypic.abc_.FocusBlob method), [1] (phenotypic.abc_.FocusEdge method), [1] (phenotypic.abc_.GpuDetector method), [1] (phenotypic.abc_.GridCorrector method), [1] (phenotypic.abc_.GridFinder method), [1] (phenotypic.abc_.GridMeasureFeatures method), [1] (phenotypic.abc_.GridObjectDetector method), [1] (phenotypic.abc_.GridObjectRefiner method), [1] (phenotypic.abc_.GridOperation method), [1] (phenotypic.abc_.ImageCorrector method), [1] (phenotypic.abc_.ImageDenoiser method), [1] (phenotypic.abc_.ImageEnhancer method), [1] (phenotypic.abc_.ImageOperation method), [1] (phenotypic.abc_.MeasureFeatures method), [1] (phenotypic.abc_.MorphologicalFiltering method), [1] (phenotypic.abc_.ObjectDetector method), [1] (phenotypic.abc_.ObjectRefiner method), [1] (phenotypic.abc_.PostMeasurement method), [1] (phenotypic.abc_.PrefabPipeline method), [1] (phenotypic.abc_.Smoothing method), [1] (phenotypic.abc_.ThresholdDetector method), [1] (phenotypic.analysis.abc_.ModelFitter method) (phenotypic.analysis.abc_.QualityCheck method) (phenotypic.analysis.abc_.SetAnalyzer method) (phenotypic.analysis.DoubleSoftplus method), [1] (phenotypic.analysis.EdgeCorrector method), [1] (phenotypic.analysis.ErrorCutoffFinder method), [1] (phenotypic.analysis.ExpectedVsDetectedCount method), [1] (phenotypic.analysis.ICC method), [1] (phenotypic.analysis.LinearSoftplus method), [1] (phenotypic.analysis.LogGrowthModel method), [1] (phenotypic.analysis.MADOutlierRemover method), [1] (phenotypic.analysis.MaxModifiedZScore method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount method) (phenotypic.analysis.qc.ICC method) (phenotypic.analysis.qc.MaxModifiedZScore method) (phenotypic.analysis.qc.RelativeMAD method) (phenotypic.analysis.qc.ReplicateAgreement method) (phenotypic.analysis.qc.TukeyOutlierFraction method) (phenotypic.analysis.RelativeMAD method), [1] (phenotypic.analysis.ReplicateAgreement method), [1] (phenotypic.analysis.TukeyOutlierFraction method), [1] (phenotypic.analysis.TukeyOutlierRemover method), [1] (phenotypic.correction.BayesShrinkCorrector method), [1] (phenotypic.correction.CaptureMetadata method), [1] (phenotypic.correction.ColorCheckerProfile method), [1] (phenotypic.correction.ColorCorrector method), [1] (phenotypic.correction.ColorDenoise method), [1] (phenotypic.correction.DenoiseBlockMatch method), [1] (phenotypic.correction.GridAligner method), [1] (phenotypic.correction.ImageCropper method), [1] (phenotypic.correction.ImagePadder method), [1] (phenotypic.correction.VisuShrinkCorrector method), [1] (phenotypic.detect.CannyDetector method), [1] (phenotypic.detect.ChanVeseDetector method), [1] (phenotypic.detect.CompositeDetector method), [1] (phenotypic.detect.FilamentousFungiDetector method), [1] (phenotypic.detect.HysteresisDetector method), [1] (phenotypic.detect.InoculumDetector method), [1] (phenotypic.detect.IsodataDetector method), [1] (phenotypic.detect.LiDetector method), [1] (phenotypic.detect.MadHysteresisDetector method), [1] (phenotypic.detect.ManualGridPointDetector method), [1] (phenotypic.detect.ManualPointDetector method), [1] (phenotypic.detect.MeanDetector method), [1] (phenotypic.detect.MinimumDetector method), [1] (phenotypic.detect.OtsuDetector method), [1] (phenotypic.detect.RankOtsuDetector method), [1] (phenotypic.detect.RoundPeaksDetector method), [1] (phenotypic.detect.SecondaryOtsuDetector method), [1] (phenotypic.detect.SinePeakDetector method), [1] (phenotypic.detect.TriangleDetector method), [1] (phenotypic.detect.UserThreshold method), [1] (phenotypic.detect.WatershedDetector method), [1] (phenotypic.detect.YenDetector method), [1] (phenotypic.enhance.BayesShrinkEnhancer method), [1] (phenotypic.enhance.ContrastStretching method), [1] (phenotypic.enhance.EnhanceBlockMatch method), [1] (phenotypic.enhance.EnhanceLocalContrast method), [1] (phenotypic.enhance.FlattenIllumination method), [1] (phenotypic.enhance.FocusBlobLoG method), [1] (phenotypic.enhance.FocusEdgeFrangi method), [1] (phenotypic.enhance.FocusEdgeHessian method), [1] (phenotypic.enhance.FocusEdgeLaplace method), [1] (phenotypic.enhance.FocusEdgeMeijering method), [1] (phenotypic.enhance.FocusEdgePhase method), [1] (phenotypic.enhance.FocusEdgeSato method), [1] (phenotypic.enhance.FocusEdgeSobel method), [1] (phenotypic.enhance.GaussianBlur method), [1] (phenotypic.enhance.GrayOpening method), [1] (phenotypic.enhance.ImageInverter method), [1] (phenotypic.enhance.LocalEdgeDenoise method), [1] (phenotypic.enhance.MedianFilter method), [1] (phenotypic.enhance.NonLocalMeansDenoiser method), [1] (phenotypic.enhance.RankMedianEnhancer method), [1] (phenotypic.enhance.SetDetectMode method), [1] (phenotypic.enhance.SharpenEdgeGauss method), [1] (phenotypic.enhance.StructureSmoothing method), [1] (phenotypic.enhance.SubtractGaussian method), [1] (phenotypic.enhance.SubtractOpening method), [1] (phenotypic.enhance.SubtractRollingBall method), [1] (phenotypic.enhance.SubtractWhiteTophat method), [1] (phenotypic.enhance.VisuShrinkEnhancer method), [1] (phenotypic.enhance.WhiteTophatEnhance method), [1] (phenotypic.grid.AutoGridFinder method), [1] (phenotypic.grid.CenteredAutoGridFinder method), [1] (phenotypic.grid.GridApply method), [1] (phenotypic.grid.ManualGridFinder method), [1] (phenotypic.measure.MeasureBounds method), [1] (phenotypic.measure.MeasureColor method), [1] (phenotypic.measure.MeasureGridLinRegStats method), [1] (phenotypic.measure.MeasureGridSpatial method), [1] (phenotypic.measure.MeasureGridSpread method), [1] (phenotypic.measure.MeasureIntensity method), [1] (phenotypic.measure.MeasureShape method), [1] (phenotypic.measure.MeasureSize method), [1] (phenotypic.measure.MeasureSymmetricZones method), [1] (phenotypic.measure.MeasureTexture method), [1] (phenotypic.post.AppendString method) (phenotypic.post.ExpandMetadata method) (phenotypic.post.MergeMetadata method) (phenotypic.post.PrependString method) (phenotypic.prefab.FilamentousFungiPipeline method), [1] (phenotypic.prefab.GridSectionPipeline method), [1] (phenotypic.prefab.HeavyOtsuPipeline method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1] (phenotypic.prefab.HeavyWatershedPipeline method), [1] (phenotypic.prefab.RoundPeaksPipeline method), [1] (phenotypic.prefab.SpImagerPipeline method), [1] (phenotypic.refine.ExtractColonyCore method), [1] (phenotypic.refine.GridAlignmentRefiner method), [1] (phenotypic.refine.GridOversizedObjectRemover method), [1] (phenotypic.refine.KeepNearestCenter method), [1] (phenotypic.refine.KeepSectionLargest method), [1] (phenotypic.refine.ManualRefine method), [1] (phenotypic.refine.MaskClosing method), [1] (phenotypic.refine.MaskDilation method), [1] (phenotypic.refine.MaskErosion method), [1] (phenotypic.refine.MaskFill method), [1] (phenotypic.refine.MaskGradient method), [1] (phenotypic.refine.MaskOpening method), [1] (phenotypic.refine.MaskWhiteTophat method), [1] (phenotypic.refine.MergeFragmentChains method), [1] (phenotypic.refine.NearestNeighborMerger method), [1] (phenotypic.refine.ReduceSectionsByLine method), [1] (phenotypic.refine.RefineBySineFit method), [1] (phenotypic.refine.RemoveBorderObjects method), [1] (phenotypic.refine.RemoveByFeature method), [1] (phenotypic.refine.RemoveGridOutliers method), [1] (phenotypic.refine.RemoveLowCircularity method), [1] (phenotypic.refine.SeparateObjects method), [1] (phenotypic.refine.Skeletonize method), [1] (phenotypic.refine.SmallObjectRemover method), [1] (phenotypic.refine.SmallToLargeMerger method), [1] (phenotypic.refine.Thinning method), [1] (phenotypic.refine.TrimAsymmetry method), [1] (phenotypic.tune.Budget method), [1] (phenotypic.tune.Categorical method), [1] (phenotypic.tune.CompositeScorer method), [1] (phenotypic.tune.EvaluationResult method), [1] (phenotypic.tune.Evaluator method), [1] (phenotypic.tune.Excluded method), [1] (phenotypic.tune.Fixed method), [1] (phenotypic.tune.FloatRange method), [1] (phenotypic.tune.GridConfig method), [1] (phenotypic.tune.GroundTruthMasks method), [1] (phenotypic.tune.HeldOutConfig method), [1] (phenotypic.tune.ImportanceReport method), [1] (phenotypic.tune.InferredSearchSpace method), [1] (phenotypic.tune.IntRange method), [1] (phenotypic.tune.Knob method), [1] (phenotypic.tune.OptunaConfig method), [1] (phenotypic.tune.QCScorer method), [1] (phenotypic.tune.RandomConfig method), [1] (phenotypic.tune.ReferenceFreeScorer method), [1] (phenotypic.tune.Scorer method), [1] (phenotypic.tune.SearchSpace method), [1] (phenotypic.tune.StrategyConfig method), [1] (phenotypic.tune.SupervisedScorer method), [1] (phenotypic.tune.targets.Nested method) (phenotypic.tune.targets.Param method) (phenotypic.tune.targets.Presence method) (phenotypic.tune.targets.TunableParam method) (phenotypic.tune.Trial method), [1] (phenotypic.tune.TuningSpec method), [1]

DIFFERENCE_ENTROPY (phenotypic.schema.TEXTURE attribute) DIFFERENCE_VARIANCE (phenotypic.schema.TEXTURE attribute) DijkstraResult (class in phenotypic.sdk_.branch_pathfinding) DinoSize (in module phenotypic.sdk_.typing_) DinoVersion (in module phenotypic.sdk_.typing_) directions (phenotypic.gui.tune.TuneRunRoot attribute) discover() (phenotypic.gui.tune.TuneRunRoot class method) DIST_WEIGHTED_CENTER_CC (phenotypic.schema.BBOX attribute) DIST_WEIGHTED_CENTER_RR (phenotypic.schema.BBOX attribute) distance_threshold (phenotypic.refine.MergeFragmentChains attribute), [1] (phenotypic.refine.NearestNeighborMerger attribute), [1] (phenotypic.refine.SmallToLargeMerger attribute), [1] domain (phenotypic.tune.Knob attribute), [1] domain() (phenotypic.tune.SearchSpace method), [1] DOSE (phenotypic.schema.CONDITION_METADATA attribute) DOUBLE_SOFTPLUS_MODEL (class in phenotypic.schema) DoubleSoftplus (class in phenotypic.analysis), [1] draw() (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap method) (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask method) dt (phenotypic.detect.ChanVeseDetector attribute), [1] (phenotypic.enhance.StructureSmoothing attribute), [1] dtype (phenotypic._core._image_parts.accessors._detect_mat_accessor.DetectMatAccessor property) (phenotypic._core._image_parts.accessors._grayscale_accessor.Grayscale property) (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap property) (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask property) (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor property) (phenotypic._core._image_parts.accessors._rgb_accessor.ImageRGB property) dynamic_range (phenotypic.util.ContrastMetrics attribute), [1] (phenotypic.util.image_metrics.ContrastMetrics attribute)

E

ECCENTRICITY (phenotypic.schema.SHAPE attribute) Edge (class in phenotypic.gui.builder._state) EDGE_CORRECTION (class in phenotypic.schema) edge_id (phenotypic.gui.builder._state.Edge attribute), [1] edge_noise_threshold (phenotypic.detect.FilamentousFungiDetector attribute), [1] edge_refinement (phenotypic.detect.RoundPeaksDetector attribute), [1] (phenotypic.detect.SinePeakDetector attribute), [1] (phenotypic.refine.GridAlignmentRefiner attribute), [1] (phenotypic.refine.RefineBySineFit attribute), [1] EdgeCorrector (class in phenotypic.analysis), [1] edges (phenotypic.gui.builder._state._DagBuilderScope attribute), [1] EmptyImageError, [1] enable_gmm (phenotypic.detect.InoculumDetector attribute), [1] encode() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] encode_srgb() (in module phenotypic.sdk_.colourspace), [1] endswith() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1]

enhance (phenotypic.measure.MeasureTexture attribute), [1] EnhanceBlockMatch (class in phenotypic.enhance), [1] EnhanceLocalContrast (class in phenotypic.enhance), [1] enough_data() (phenotypic.analysis.ErrorCutoffFinder method), [1] ensure_typed_json_suffix() (in module phenotypic.sdk_), [1] ENTROPY (phenotypic.schema.TEXTURE attribute) Entry (class in phenotypic.schema) EnvVar (class in phenotypic.sdk_), [1] eps (phenotypic.analysis.qc.RelativeMAD attribute) (phenotypic.analysis.qc.ReplicateAgreement attribute) (phenotypic.analysis.RelativeMAD attribute), [1] (phenotypic.analysis.ReplicateAgreement attribute), [1] (phenotypic.enhance.FlattenIllumination attribute), [1] error_analysis_csv_path() (in module phenotypic.sdk_), [1] error_analysis_html_path() (in module phenotypic.sdk_), [1] error_analysis_parquet_path() (in module phenotypic.sdk_), [1] ERROR_CATEGORY (phenotypic.schema.CURATION attribute) error_category_parquet_path() (in module phenotypic.sdk_), [1] error_exit() (in module phenotypic.phenotypicCLI) ErrorCategory (class in phenotypic.schema) ErrorCutoffFinder (class in phenotypic.analysis), [1] ERRORS (phenotypic.sdk_.ProcessingStateKey attribute), [1] errors_dir() (in module phenotypic.sdk_), [1] estimate (phenotypic.tune.GeneralizationReport attribute), [1] estimate_concurrent_capacity() (in module phenotypic.sdk_.slurm), [1] euclidean_voronoi_assign() (in module phenotypic.sdk_.branch_pathfinding) evaluate() (phenotypic.tune.Evaluator method), [1] EvaluationResult (class in phenotypic.tune), [1] Evaluator (class in phenotypic.tune), [1] evaluator (phenotypic.tune.TuningSpec attribute), [1] event_log_path() (in module phenotypic.sdk_), [1] Excluded (class in phenotypic.tune), [1] excluded (phenotypic.tune.InferredSearchSpace attribute), [1] EXECUTION_MODE (phenotypic.sdk_.DashboardManifestKey attribute), [1] (phenotypic.sdk_.JobMetadataKey attribute), [1] (phenotypic.sdk_.ProcessingStateKey attribute), [1] ExecutionMode (in module phenotypic.sdk_.typing_) ExpandMetadata (class in phenotypic.post) expandtabs() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] EXPECTED (phenotypic.schema.QUALITY_COUNT attribute) ExpectedVsDetectedCount (class in phenotypic.analysis), [1] (class in phenotypic.analysis.qc) EXPERIMENT_ID (phenotypic.schema.EXPERIMENT_METADATA attribute) EXPERIMENT_METADATA (class in phenotypic.schema) EXPERIMENTER (phenotypic.schema.ACQUISITION_METADATA attribute) exposure_time (phenotypic.correction.CaptureMetadata attribute), [1], [2], [3] EXPOSURE_TIME (phenotypic.schema.ACQUISITION_METADATA attribute) EXT (phenotypic.sdk_.HDF attribute), [1], [2], [3] (phenotypic.sdk_.hdf_.HDF attribute), [1] EXTENT (phenotypic.schema.SHAPE attribute) extent_margin (phenotypic.measure.MeasureSymmetricZones attribute), [1] extract_calibration_branches() (in module phenotypic.sdk_.branch_pathfinding) extract_fragment_paths() (in module phenotypic.sdk_.branch_pathfinding) ExtractColonyCore (class in phenotypic.refine), [1]

F

f_number (phenotypic.correction.CaptureMetadata attribute), [1], [2], [3] f_scale (phenotypic.analysis.abc_.ModelFitter attribute), [1] (phenotypic.analysis.DoubleSoftplus attribute), [1] (phenotypic.analysis.LinearSoftplus attribute), [1] (phenotypic.analysis.LogGrowthModel attribute), [1] fail_threshold (phenotypic.analysis.abc_.QualityCheck attribute), [1] (phenotypic.analysis.ExpectedVsDetectedCount attribute), [1] (phenotypic.analysis.ICC attribute), [1] (phenotypic.analysis.MaxModifiedZScore attribute), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount attribute) (phenotypic.analysis.qc.ICC attribute) (phenotypic.analysis.qc.MaxModifiedZScore attribute) (phenotypic.analysis.qc.RelativeMAD attribute) (phenotypic.analysis.qc.ReplicateAgreement attribute) (phenotypic.analysis.qc.TukeyOutlierFraction attribute) (phenotypic.analysis.RelativeMAD attribute), [1] (phenotypic.analysis.ReplicateAgreement attribute), [1] (phenotypic.analysis.TukeyOutlierFraction attribute), [1] FAILED (phenotypic.sdk_.DashboardManifestKey attribute), [1] (phenotypic.sdk_.ProcessingStateKey attribute), [1] failed (phenotypic.tune.EvaluationResult attribute), [1] (phenotypic.tune.Trial attribute), [1] FAILURE_CATEGORIES (phenotypic.sdk_.DashboardManifestKey attribute), [1] failure_score (phenotypic.tune.Evaluator attribute), [1] failures_jsonl_path() (in module phenotypic.sdk_), [1] FailureSource (in module phenotypic.sdk_.typing_) fast_mode (phenotypic.enhance.NonLocalMeansDenoiser attribute), [1] feature (phenotypic.refine.RemoveByFeature attribute), [1] field (phenotypic.tune.targets.Nested attribute) (phenotypic.tune.targets.Param attribute) field_type (phenotypic.tune.Excluded attribute), [1] FIGSIZE (phenotypic.settings_.MPL attribute) figure() (in module phenotypic.abc_), [1] FigureProvider (class in phenotypic.abc_), [1] figures() (phenotypic.abc_.FigureProvider method), [1] (phenotypic.measure.MeasureSymmetricZones method), [1] FigureSpec (class in phenotypic.abc_), [1] FilamentousFungiDetector (class in phenotypic.detect), [1] FilamentousFungiPipeline (class in phenotypic.prefab), [1] filepath (phenotypic.sdk_.HDF attribute), [1], [2], [3] (phenotypic.sdk_.hdf_.HDF attribute), [1] filter_paths() (in module phenotypic.sdk_.branch_pathfinding) filter_spec_json() (in module phenotypic.analysis), [1] filter_spec_query() (in module phenotypic.analysis), [1] FilterResult (class in phenotypic.sdk_.branch_pathfinding) filters (phenotypic.abc_.PrefabPipeline attribute), [1] (phenotypic.prefab.FilamentousFungiPipeline attribute), [1] (phenotypic.prefab.GridSectionPipeline attribute), [1] (phenotypic.prefab.HeavyOtsuPipeline attribute), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] (phenotypic.prefab.HeavyWatershedPipeline attribute), [1] (phenotypic.prefab.RoundPeaksPipeline attribute), [1] (phenotypic.prefab.SpImagerPipeline attribute), [1] FilterThresholds (class in phenotypic.sdk_.branch_pathfinding) finalize() (phenotypic.tune.CompositeScorer method), [1] (phenotypic.tune.QCScorer method), [1] (phenotypic.tune.ReferenceFreeScorer method), [1] (phenotypic.tune.Scorer method), [1] (phenotypic.tune.SupervisedScorer method), [1] find() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] fit() (phenotypic.correction.ColorCheckerProfile method), [1] Fixed (class in phenotypic.tune), [1] FLAG (phenotypic.schema.QUALITY_CHECK attribute) flag_col() (phenotypic.analysis.abc_.QualityCheck class method) (phenotypic.analysis.ExpectedVsDetectedCount class method), [1] (phenotypic.analysis.ICC class method), [1] (phenotypic.analysis.MaxModifiedZScore class method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount class method) (phenotypic.analysis.qc.ICC class method) (phenotypic.analysis.qc.MaxModifiedZScore class method) (phenotypic.analysis.qc.RelativeMAD class method) (phenotypic.analysis.qc.ReplicateAgreement class method) (phenotypic.analysis.qc.TukeyOutlierFraction class method) (phenotypic.analysis.RelativeMAD class method), [1] (phenotypic.analysis.ReplicateAgreement class method), [1] (phenotypic.analysis.TukeyOutlierFraction class method), [1] flagged (phenotypic.tune.GeneralizationReport attribute), [1] flagged_keys() (phenotypic.analysis.abc_.QualityCheck method) (phenotypic.analysis.ExpectedVsDetectedCount method), [1] (phenotypic.analysis.ICC method), [1] (phenotypic.analysis.MaxModifiedZScore method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount method) (phenotypic.analysis.qc.ICC method) (phenotypic.analysis.qc.MaxModifiedZScore method) (phenotypic.analysis.qc.RelativeMAD method) (phenotypic.analysis.qc.ReplicateAgreement method) (phenotypic.analysis.qc.TukeyOutlierFraction method) (phenotypic.analysis.RelativeMAD method), [1] (phenotypic.analysis.ReplicateAgreement method), [1] (phenotypic.analysis.TukeyOutlierFraction method), [1] FlattenIllumination (class in phenotypic.enhance), [1] FloatRange (class in phenotypic.tune), [1] focal_length (phenotypic.correction.CaptureMetadata attribute), [1], [2], [3] FocusBlob (class in phenotypic.abc_), [1] FocusBlobLoG (class in phenotypic.enhance), [1] FocusEdge (class in phenotypic.abc_), [1] FocusEdgeFrangi (class in phenotypic.enhance), [1] FocusEdgeHessian (class in phenotypic.enhance), [1] FocusEdgeLaplace (class in phenotypic.enhance), [1] FocusEdgeMeijering (class in phenotypic.enhance), [1] FocusEdgePhase (class in phenotypic.enhance), [1] FocusEdgeSato (class in phenotypic.enhance), [1] FocusEdgeSobel (class in phenotypic.enhance), [1] footprint (phenotypic.detect.WatershedDetector attribute), [1] footprint_width (phenotypic.detect.RoundPeaksDetector attribute), [1] (phenotypic.detect.SinePeakDetector attribute), [1] FootprintMixin (class in phenotypic.abc_), [1] (class in phenotypic.sdk_), [1] (class in phenotypic.sdk_.mixin) foreground() (phenotypic._core._image_parts.accessors._detect_mat_accessor.DetectMatAccessor method) (phenotypic._core._image_parts.accessors._grayscale_accessor.Grayscale method) (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap method) (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask method) (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) (phenotypic._core._image_parts.accessors._rgb_accessor.ImageRGB method) format() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] format_map() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] format_sbatch_directives() (in module phenotypic.sdk_.slurm), [1] frag_reach_px (phenotypic.detect.FilamentousFungiDetector attribute), [1] fragment_id (phenotypic.sdk_.branch_pathfinding.FragmentAssignment attribute), [1] (phenotypic.sdk_.branch_pathfinding.FragmentPath attribute), [1] FragmentAssignment (class in phenotypic.sdk_.branch_pathfinding) FragmentPath (class in phenotypic.sdk_.branch_pathfinding) free_param_floor (phenotypic.tune.ScreeningConfig attribute), [1] freeze_epsilon (phenotypic.tune.ScreeningConfig attribute), [1] freeze_flagged (phenotypic.tune.ScreeningResult attribute), [1] freeze_value() (in module phenotypic.tune), [1] from_image() (phenotypic.correction.CaptureMetadata class method), [1] from_json() (phenotypic.abc_.BackgroundSubtraction class method), [1] (phenotypic.abc_.BaseOperation class method), [1] (phenotypic.abc_.ContrastAdjustment class method), [1] (phenotypic.abc_.FocusBlob class method), [1] (phenotypic.abc_.FocusEdge class method), [1] (phenotypic.abc_.GpuDetector class method), [1] (phenotypic.abc_.GridCorrector class method), [1] (phenotypic.abc_.GridFinder class method), [1] (phenotypic.abc_.GridMeasureFeatures class method), [1] (phenotypic.abc_.GridObjectDetector class method), [1] (phenotypic.abc_.GridObjectRefiner class method), [1] (phenotypic.abc_.GridOperation class method), [1] (phenotypic.abc_.ImageCorrector class method), [1] (phenotypic.abc_.ImageDenoiser class method), [1] (phenotypic.abc_.ImageEnhancer class method), [1] (phenotypic.abc_.ImageOperation class method), [1] (phenotypic.abc_.MeasureFeatures class method), [1] (phenotypic.abc_.MorphologicalFiltering class method), [1] (phenotypic.abc_.ObjectDetector class method), [1] (phenotypic.abc_.ObjectRefiner class method), [1] (phenotypic.abc_.PostMeasurement class method), [1] (phenotypic.abc_.PrefabPipeline class method), [1] (phenotypic.abc_.Smoothing class method), [1] (phenotypic.abc_.ThresholdDetector class method), [1] (phenotypic.correction.BayesShrinkCorrector class method), [1] (phenotypic.correction.ColorCheckerProfile class method), [1] (phenotypic.correction.ColorCorrector class method), [1] (phenotypic.correction.ColorDenoise class method), [1] (phenotypic.correction.DenoiseBlockMatch class method), [1] (phenotypic.correction.GridAligner class method), [1] (phenotypic.correction.ImageCropper class method), [1] (phenotypic.correction.ImagePadder class method), [1] (phenotypic.correction.VisuShrinkCorrector class method), [1] (phenotypic.detect.CannyDetector class method), [1] (phenotypic.detect.ChanVeseDetector class method), [1] (phenotypic.detect.CompositeDetector class method), [1] (phenotypic.detect.FilamentousFungiDetector class method), [1] (phenotypic.detect.HysteresisDetector class method), [1] (phenotypic.detect.InoculumDetector class method), [1] (phenotypic.detect.IsodataDetector class method), [1] (phenotypic.detect.LiDetector class method), [1] (phenotypic.detect.MadHysteresisDetector class method), [1] (phenotypic.detect.ManualGridPointDetector class method), [1] (phenotypic.detect.ManualPointDetector class method), [1] (phenotypic.detect.MeanDetector class method), [1] (phenotypic.detect.MinimumDetector class method), [1] (phenotypic.detect.OtsuDetector class method), [1] (phenotypic.detect.RankOtsuDetector class method), [1] (phenotypic.detect.RoundPeaksDetector class method), [1] (phenotypic.detect.SecondaryOtsuDetector class method), [1] (phenotypic.detect.SinePeakDetector class method), [1] (phenotypic.detect.TriangleDetector class method), [1] (phenotypic.detect.UserThreshold class method), [1] (phenotypic.detect.WatershedDetector class method), [1] (phenotypic.detect.YenDetector class method), [1] (phenotypic.enhance.BayesShrinkEnhancer class method), [1] (phenotypic.enhance.ContrastStretching class method), [1] (phenotypic.enhance.EnhanceBlockMatch class method), [1] (phenotypic.enhance.EnhanceLocalContrast class method), [1] (phenotypic.enhance.FlattenIllumination class method), [1] (phenotypic.enhance.FocusBlobLoG class method), [1] (phenotypic.enhance.FocusEdgeFrangi class method), [1] (phenotypic.enhance.FocusEdgeHessian class method), [1] (phenotypic.enhance.FocusEdgeLaplace class method), [1] (phenotypic.enhance.FocusEdgeMeijering class method), [1] (phenotypic.enhance.FocusEdgePhase class method), [1] (phenotypic.enhance.FocusEdgeSato class method), [1] (phenotypic.enhance.FocusEdgeSobel class method), [1] (phenotypic.enhance.GaussianBlur class method), [1] (phenotypic.enhance.GrayOpening class method), [1] (phenotypic.enhance.ImageInverter class method), [1] (phenotypic.enhance.LocalEdgeDenoise class method), [1] (phenotypic.enhance.MedianFilter class method), [1] (phenotypic.enhance.NonLocalMeansDenoiser class method), [1] (phenotypic.enhance.RankMedianEnhancer class method), [1] (phenotypic.enhance.SetDetectMode class method), [1] (phenotypic.enhance.SharpenEdgeGauss class method), [1] (phenotypic.enhance.StructureSmoothing class method), [1] (phenotypic.enhance.SubtractGaussian class method), [1] (phenotypic.enhance.SubtractOpening class method), [1] (phenotypic.enhance.SubtractRollingBall class method), [1] (phenotypic.enhance.SubtractWhiteTophat class method), [1] (phenotypic.enhance.VisuShrinkEnhancer class method), [1] (phenotypic.enhance.WhiteTophatEnhance class method), [1] (phenotypic.grid.AutoGridFinder class method), [1] (phenotypic.grid.CenteredAutoGridFinder class method), [1] (phenotypic.grid.GridApply class method), [1] (phenotypic.grid.ManualGridFinder class method), [1] (phenotypic.ImagePipeline class method) (phenotypic.measure.MeasureBounds class method), [1] (phenotypic.measure.MeasureColor class method), [1] (phenotypic.measure.MeasureGridLinRegStats class method), [1] (phenotypic.measure.MeasureGridSpatial class method), [1] (phenotypic.measure.MeasureGridSpread class method), [1] (phenotypic.measure.MeasureIntensity class method), [1] (phenotypic.measure.MeasureShape class method), [1] (phenotypic.measure.MeasureSize class method), [1] (phenotypic.measure.MeasureSymmetricZones class method), [1] (phenotypic.measure.MeasureTexture class method), [1] (phenotypic.post.AppendString class method) (phenotypic.post.ExpandMetadata class method) (phenotypic.post.MergeMetadata class method) (phenotypic.post.PrependString class method) (phenotypic.prefab.FilamentousFungiPipeline class method), [1] (phenotypic.prefab.GridSectionPipeline class method), [1] (phenotypic.prefab.HeavyOtsuPipeline class method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline class method), [1] (phenotypic.prefab.HeavyWatershedPipeline class method), [1] (phenotypic.prefab.RoundPeaksPipeline class method), [1] (phenotypic.prefab.SpImagerPipeline class method), [1] (phenotypic.refine.ExtractColonyCore class method), [1] (phenotypic.refine.GridAlignmentRefiner class method), [1] (phenotypic.refine.GridOversizedObjectRemover class method), [1] (phenotypic.refine.KeepNearestCenter class method), [1] (phenotypic.refine.KeepSectionLargest class method), [1] (phenotypic.refine.ManualRefine class method), [1] (phenotypic.refine.MaskClosing class method), [1] (phenotypic.refine.MaskDilation class method), [1] (phenotypic.refine.MaskErosion class method), [1] (phenotypic.refine.MaskFill class method), [1] (phenotypic.refine.MaskGradient class method), [1] (phenotypic.refine.MaskOpening class method), [1] (phenotypic.refine.MaskWhiteTophat class method), [1] (phenotypic.refine.MergeFragmentChains class method), [1] (phenotypic.refine.NearestNeighborMerger class method), [1] (phenotypic.refine.ReduceSectionsByLine class method), [1] (phenotypic.refine.RefineBySineFit class method), [1] (phenotypic.refine.RemoveBorderObjects class method), [1] (phenotypic.refine.RemoveByFeature class method), [1] (phenotypic.refine.RemoveGridOutliers class method), [1] (phenotypic.refine.RemoveLowCircularity class method), [1] (phenotypic.refine.SeparateObjects class method), [1] (phenotypic.refine.Skeletonize class method), [1] (phenotypic.refine.SmallObjectRemover class method), [1] (phenotypic.refine.SmallToLargeMerger class method), [1] (phenotypic.refine.Thinning class method), [1] (phenotypic.refine.TrimAsymmetry class method), [1]

from_label() (phenotypic.schema.ErrorCategory class method) from_orm() (phenotypic.abc_.BackgroundSubtraction class method), [1] (phenotypic.abc_.BaseOperation class method), [1] (phenotypic.abc_.ContrastAdjustment class method), [1] (phenotypic.abc_.FocusBlob class method), [1] (phenotypic.abc_.FocusEdge class method), [1] (phenotypic.abc_.GpuDetector class method), [1] (phenotypic.abc_.GridCorrector class method), [1] (phenotypic.abc_.GridFinder class method), [1] (phenotypic.abc_.GridMeasureFeatures class method), [1] (phenotypic.abc_.GridObjectDetector class method), [1] (phenotypic.abc_.GridObjectRefiner class method), [1] (phenotypic.abc_.GridOperation class method), [1] (phenotypic.abc_.ImageCorrector class method), [1] (phenotypic.abc_.ImageDenoiser class method), [1] (phenotypic.abc_.ImageEnhancer class method), [1] (phenotypic.abc_.ImageOperation class method), [1] (phenotypic.abc_.MeasureFeatures class method), [1] (phenotypic.abc_.MorphologicalFiltering class method), [1] (phenotypic.abc_.ObjectDetector class method), [1] (phenotypic.abc_.ObjectRefiner class method), [1] (phenotypic.abc_.PostMeasurement class method), [1] (phenotypic.abc_.PrefabPipeline class method), [1] (phenotypic.abc_.Smoothing class method), [1] (phenotypic.abc_.ThresholdDetector class method), [1] (phenotypic.analysis.abc_.ModelFitter class method) (phenotypic.analysis.abc_.QualityCheck class method) (phenotypic.analysis.abc_.SetAnalyzer class method) (phenotypic.analysis.DoubleSoftplus class method), [1] (phenotypic.analysis.EdgeCorrector class method), [1] (phenotypic.analysis.ErrorCutoffFinder class method), [1] (phenotypic.analysis.ExpectedVsDetectedCount class method), [1] (phenotypic.analysis.ICC class method), [1] (phenotypic.analysis.LinearSoftplus class method), [1] (phenotypic.analysis.LogGrowthModel class method), [1] (phenotypic.analysis.MADOutlierRemover class method), [1] (phenotypic.analysis.MaxModifiedZScore class method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount class method) (phenotypic.analysis.qc.ICC class method) (phenotypic.analysis.qc.MaxModifiedZScore class method) (phenotypic.analysis.qc.RelativeMAD class method) (phenotypic.analysis.qc.ReplicateAgreement class method) (phenotypic.analysis.qc.TukeyOutlierFraction class method) (phenotypic.analysis.RelativeMAD class method), [1] (phenotypic.analysis.ReplicateAgreement class method), [1] (phenotypic.analysis.TukeyOutlierFraction class method), [1] (phenotypic.analysis.TukeyOutlierRemover class method), [1] (phenotypic.correction.BayesShrinkCorrector class method), [1] (phenotypic.correction.CaptureMetadata class method), [1] (phenotypic.correction.ColorCheckerProfile class method), [1] (phenotypic.correction.ColorCorrector class method), [1] (phenotypic.correction.ColorDenoise class method), [1] (phenotypic.correction.DenoiseBlockMatch class method), [1] (phenotypic.correction.GridAligner class method), [1] (phenotypic.correction.ImageCropper class method), [1] (phenotypic.correction.ImagePadder class method), [1] (phenotypic.correction.VisuShrinkCorrector class method), [1] (phenotypic.detect.CannyDetector class method), [1] (phenotypic.detect.ChanVeseDetector class method), [1] (phenotypic.detect.CompositeDetector class method), [1] (phenotypic.detect.FilamentousFungiDetector class method), [1] (phenotypic.detect.HysteresisDetector class method), [1] (phenotypic.detect.InoculumDetector class method), [1] (phenotypic.detect.IsodataDetector class method), [1] (phenotypic.detect.LiDetector class method), [1] (phenotypic.detect.MadHysteresisDetector class method), [1] (phenotypic.detect.ManualGridPointDetector class method), [1] (phenotypic.detect.ManualPointDetector class method), [1] (phenotypic.detect.MeanDetector class method), [1] (phenotypic.detect.MinimumDetector class method), [1] (phenotypic.detect.OtsuDetector class method), [1] (phenotypic.detect.RankOtsuDetector class method), [1] (phenotypic.detect.RoundPeaksDetector class method), [1] (phenotypic.detect.SecondaryOtsuDetector class method), [1] (phenotypic.detect.SinePeakDetector class method), [1] (phenotypic.detect.TriangleDetector class method), [1] (phenotypic.detect.UserThreshold class method), [1] (phenotypic.detect.WatershedDetector class method), [1] (phenotypic.detect.YenDetector class method), [1] (phenotypic.enhance.BayesShrinkEnhancer class method), [1] (phenotypic.enhance.ContrastStretching class method), [1] (phenotypic.enhance.EnhanceBlockMatch class method), [1] (phenotypic.enhance.EnhanceLocalContrast class method), [1] (phenotypic.enhance.FlattenIllumination class method), [1] (phenotypic.enhance.FocusBlobLoG class method), [1] (phenotypic.enhance.FocusEdgeFrangi class method), [1] (phenotypic.enhance.FocusEdgeHessian class method), [1] (phenotypic.enhance.FocusEdgeLaplace class method), [1] (phenotypic.enhance.FocusEdgeMeijering class method), [1] (phenotypic.enhance.FocusEdgePhase class method), [1] (phenotypic.enhance.FocusEdgeSato class method), [1] (phenotypic.enhance.FocusEdgeSobel class method), [1] (phenotypic.enhance.GaussianBlur class method), [1] (phenotypic.enhance.GrayOpening class method), [1] (phenotypic.enhance.ImageInverter class method), [1] (phenotypic.enhance.LocalEdgeDenoise class method), [1] (phenotypic.enhance.MedianFilter class method), [1] (phenotypic.enhance.NonLocalMeansDenoiser class method), [1] (phenotypic.enhance.RankMedianEnhancer class method), [1] (phenotypic.enhance.SetDetectMode class method), [1] (phenotypic.enhance.SharpenEdgeGauss class method), [1] (phenotypic.enhance.StructureSmoothing class method), [1] (phenotypic.enhance.SubtractGaussian class method), [1] (phenotypic.enhance.SubtractOpening class method), [1] (phenotypic.enhance.SubtractRollingBall class method), [1] (phenotypic.enhance.SubtractWhiteTophat class method), [1] (phenotypic.enhance.VisuShrinkEnhancer class method), [1] (phenotypic.enhance.WhiteTophatEnhance class method), [1] (phenotypic.grid.AutoGridFinder class method), [1] (phenotypic.grid.CenteredAutoGridFinder class method), [1] (phenotypic.grid.GridApply class method), [1] (phenotypic.grid.ManualGridFinder class method), [1] (phenotypic.measure.MeasureBounds class method), [1] (phenotypic.measure.MeasureColor class method), [1] (phenotypic.measure.MeasureGridLinRegStats class method), [1] (phenotypic.measure.MeasureGridSpatial class method), [1] (phenotypic.measure.MeasureGridSpread class method), [1] (phenotypic.measure.MeasureIntensity class method), [1] (phenotypic.measure.MeasureShape class method), [1] (phenotypic.measure.MeasureSize class method), [1] (phenotypic.measure.MeasureSymmetricZones class method), [1] (phenotypic.measure.MeasureTexture class method), [1] (phenotypic.post.AppendString class method) (phenotypic.post.ExpandMetadata class method) (phenotypic.post.MergeMetadata class method) (phenotypic.post.PrependString class method) (phenotypic.prefab.FilamentousFungiPipeline class method), [1] (phenotypic.prefab.GridSectionPipeline class method), [1] (phenotypic.prefab.HeavyOtsuPipeline class method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline class method), [1] (phenotypic.prefab.HeavyWatershedPipeline class method), [1] (phenotypic.prefab.RoundPeaksPipeline class method), [1] (phenotypic.prefab.SpImagerPipeline class method), [1] (phenotypic.refine.ExtractColonyCore class method), [1] (phenotypic.refine.GridAlignmentRefiner class method), [1] (phenotypic.refine.GridOversizedObjectRemover class method), [1] (phenotypic.refine.KeepNearestCenter class method), [1] (phenotypic.refine.KeepSectionLargest class method), [1] (phenotypic.refine.ManualRefine class method), [1] (phenotypic.refine.MaskClosing class method), [1] (phenotypic.refine.MaskDilation class method), [1] (phenotypic.refine.MaskErosion class method), [1] (phenotypic.refine.MaskFill class method), [1] (phenotypic.refine.MaskGradient class method), [1] (phenotypic.refine.MaskOpening class method), [1] (phenotypic.refine.MaskWhiteTophat class method), [1] (phenotypic.refine.MergeFragmentChains class method), [1] (phenotypic.refine.NearestNeighborMerger class method), [1] (phenotypic.refine.ReduceSectionsByLine class method), [1] (phenotypic.refine.RefineBySineFit class method), [1] (phenotypic.refine.RemoveBorderObjects class method), [1] (phenotypic.refine.RemoveByFeature class method), [1] (phenotypic.refine.RemoveGridOutliers class method), [1] (phenotypic.refine.RemoveLowCircularity class method), [1] (phenotypic.refine.SeparateObjects class method), [1] (phenotypic.refine.Skeletonize class method), [1] (phenotypic.refine.SmallObjectRemover class method), [1] (phenotypic.refine.SmallToLargeMerger class method), [1] (phenotypic.refine.Thinning class method), [1] (phenotypic.refine.TrimAsymmetry class method), [1] (phenotypic.tune.Budget class method), [1] (phenotypic.tune.Categorical class method), [1] (phenotypic.tune.CompositeScorer class method), [1] (phenotypic.tune.EvaluationResult class method), [1] (phenotypic.tune.Evaluator class method), [1] (phenotypic.tune.Excluded class method), [1] (phenotypic.tune.Fixed class method), [1] (phenotypic.tune.FloatRange class method), [1] (phenotypic.tune.GridConfig class method), [1] (phenotypic.tune.GroundTruthMasks class method), [1] (phenotypic.tune.HeldOutConfig class method), [1] (phenotypic.tune.ImportanceReport class method), [1] (phenotypic.tune.InferredSearchSpace class method), [1] (phenotypic.tune.IntRange class method), [1] (phenotypic.tune.Knob class method), [1] (phenotypic.tune.OptunaConfig class method), [1] (phenotypic.tune.QCScorer class method), [1] (phenotypic.tune.RandomConfig class method), [1] (phenotypic.tune.ReferenceFreeScorer class method), [1] (phenotypic.tune.Scorer class method), [1] (phenotypic.tune.SearchSpace class method), [1] (phenotypic.tune.StrategyConfig class method), [1] (phenotypic.tune.SupervisedScorer class method), [1] (phenotypic.tune.targets.Nested class method) (phenotypic.tune.targets.Param class method) (phenotypic.tune.targets.Presence class method) (phenotypic.tune.targets.TunableParam class method) (phenotypic.tune.Trial class method), [1] (phenotypic.tune.TuningSpec class method), [1] from_parquet() (phenotypic.tune.JournalStudyStore class method), [1] from_path() (phenotypic.gui.shell.SandboxRoot class method) from_pipeline_dag() (in module phenotypic.gui.builder._conversion_dag) fromkeys() (phenotypic.util.BackgroundMetrics class method), [1] (phenotypic.util.ContrastMetrics class method), [1] (phenotypic.util.image_metrics.BackgroundMetrics class method) (phenotypic.util.image_metrics.ContrastMetrics class method) (phenotypic.util.image_metrics.NoiseMetrics class method) (phenotypic.util.image_metrics.QualityScores class method) (phenotypic.util.image_metrics.StructureMetrics class method) (phenotypic.util.NoiseMetrics class method), [1] (phenotypic.util.QualityScores class method), [1] (phenotypic.util.StructureMetrics class method), [1] frozen (phenotypic.tune.ScreeningResult attribute), [1]

G

g (phenotypic.enhance.FocusEdgePhase attribute), [1] gain (phenotypic.correction.DenoiseBlockMatch attribute), [1] gamma (phenotypic.detect.FilamentousFungiDetector attribute), [1] (phenotypic.enhance.FocusEdgeFrangi attribute), [1] (phenotypic.enhance.FocusEdgeHessian attribute), [1] GAMMA_ENCODINGS (class in phenotypic.sdk_.constants_), [1] gamma_high (phenotypic.enhance.FlattenIllumination attribute), [1] gamma_low (phenotypic.enhance.FlattenIllumination attribute), [1] gap (phenotypic.tune.EvaluationResult attribute), [1] (phenotypic.tune.GeneralizationReport attribute), [1] (phenotypic.tune.Trial attribute), [1] gap_crossing_penalty (phenotypic.detect.FilamentousFungiDetector attribute), [1] gap_margin_absolute (phenotypic.tune.GeneralizationReport attribute), [1] (phenotypic.tune.HeldOutConfig attribute), [1] gap_margin_relative (phenotypic.tune.GeneralizationReport attribute), [1] (phenotypic.tune.HeldOutConfig attribute), [1] gat_gain (phenotypic.correction.BayesShrinkCorrector attribute), [1] (phenotypic.correction.ColorDenoise attribute), [1] (phenotypic.correction.VisuShrinkCorrector attribute), [1] (phenotypic.enhance.BayesShrinkEnhancer attribute), [1] (phenotypic.enhance.EnhanceBlockMatch attribute), [1] (phenotypic.enhance.LocalEdgeDenoise attribute), [1] (phenotypic.enhance.NonLocalMeansDenoiser attribute), [1] (phenotypic.enhance.VisuShrinkEnhancer attribute), [1] gat_mu (phenotypic.correction.BayesShrinkCorrector attribute), [1] (phenotypic.correction.ColorDenoise attribute), [1] (phenotypic.correction.VisuShrinkCorrector attribute), [1] (phenotypic.enhance.BayesShrinkEnhancer attribute), [1] (phenotypic.enhance.EnhanceBlockMatch attribute), [1] (phenotypic.enhance.LocalEdgeDenoise attribute), [1] (phenotypic.enhance.NonLocalMeansDenoiser attribute), [1] (phenotypic.enhance.VisuShrinkEnhancer attribute), [1] gat_read_sigma (phenotypic.correction.BayesShrinkCorrector attribute), [1] (phenotypic.correction.ColorDenoise attribute), [1] (phenotypic.correction.VisuShrinkCorrector attribute), [1] (phenotypic.enhance.BayesShrinkEnhancer attribute), [1] (phenotypic.enhance.EnhanceBlockMatch attribute), [1] (phenotypic.enhance.LocalEdgeDenoise attribute), [1] (phenotypic.enhance.NonLocalMeansDenoiser attribute), [1] (phenotypic.enhance.VisuShrinkEnhancer attribute), [1] gat_scale_factor (phenotypic.correction.BayesShrinkCorrector attribute), [1] (phenotypic.correction.ColorDenoise attribute), [1] (phenotypic.correction.VisuShrinkCorrector attribute), [1] (phenotypic.enhance.BayesShrinkEnhancer attribute), [1] (phenotypic.enhance.EnhanceBlockMatch attribute), [1] (phenotypic.enhance.LocalEdgeDenoise attribute), [1] (phenotypic.enhance.NonLocalMeansDenoiser attribute), [1] (phenotypic.enhance.VisuShrinkEnhancer attribute), [1] gauss_n_iter (phenotypic.detect.FilamentousFungiDetector attribute), [1] gauss_sigma (phenotypic.detect.FilamentousFungiDetector attribute), [1] GaussianBlur (class in phenotypic.enhance), [1] generalization_path() (in module phenotypic.sdk_), [1] GeneralizationReport (class in phenotypic.tune), [1] generate_dispatcher_chain() (in module phenotypic.sdk_.slurm), [1] generate_dispatcher_script() (in module phenotypic.sdk_.slurm), [1] generate_interpretation() (phenotypic.util.image_metrics.ImageMetricsCalculator static method) (phenotypic.util.ImageMetricsCalculator static method), [1] generate_output_key() (in module phenotypic.util), [1] generate_recommendations() (phenotypic.util.image_metrics.ImageMetricsCalculator static method) (phenotypic.util.ImageMetricsCalculator static method), [1] GENERATION (phenotypic.schema.INCUBATION_METADATA attribute) GENETIC_METADATA (class in phenotypic.schema) GENOTYPE (phenotypic.schema.GENETIC_METADATA attribute) geomedian_max_iter (phenotypic.measure.MeasureColor attribute), [1] geomedian_tol (phenotypic.measure.MeasureColor attribute), [1] geometric_median() (in module phenotypic.util), [1] get() (phenotypic._core._image_parts.accessors._metadata_accessor.MetadataAccessor method) (phenotypic.gui.shell.ToolSession method) (phenotypic.sdk_.register.AnalysisPluginRegistry class method), [1] (phenotypic.sdk_.register.BaseRegistry class method), [1] (phenotypic.sdk_.register.PlotterRegistry class method), [1] (phenotypic.util.BackgroundMetrics method), [1] (phenotypic.util.ContrastMetrics method), [1] (phenotypic.util.image_metrics.BackgroundMetrics method) (phenotypic.util.image_metrics.ContrastMetrics method) (phenotypic.util.image_metrics.NoiseMetrics method) (phenotypic.util.image_metrics.QualityScores method) (phenotypic.util.image_metrics.StructureMetrics method) (phenotypic.util.NoiseMetrics method), [1] (phenotypic.util.QualityScores method), [1] (phenotypic.util.StructureMetrics method), [1] get_analysis_plugin() (in module phenotypic.sdk_.register), [1] get_col_edges() (phenotypic.abc_.GridFinder method), [1] (phenotypic.grid.AutoGridFinder method), [1] (phenotypic.grid.CenteredAutoGridFinder method), [1] (phenotypic.grid.ManualGridFinder method), [1] get_data_group() (phenotypic.sdk_.HDF method), [1] (phenotypic.sdk_.hdf_.HDF method) get_filters() (phenotypic.abc_.PrefabPipeline method), [1] (phenotypic.prefab.FilamentousFungiPipeline method), [1] (phenotypic.prefab.GridSectionPipeline method), [1] (phenotypic.prefab.HeavyOtsuPipeline method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1] (phenotypic.prefab.HeavyWatershedPipeline method), [1] (phenotypic.prefab.RoundPeaksPipeline method), [1] (phenotypic.prefab.SpImagerPipeline method), [1] get_group() (phenotypic.sdk_.HDF static method), [1] (phenotypic.sdk_.hdf_.HDF static method) get_headers() (phenotypic.abc_.MeasurementInfo class method), [1] (phenotypic.schema.ACQUISITION_METADATA class method) (phenotypic.schema.BBOX class method) (phenotypic.schema.ColorComposition class method) (phenotypic.schema.ColorHSV class method) (phenotypic.schema.ColorLab class method) (phenotypic.schema.Colorxy class method) (phenotypic.schema.ColorXYZ class method) (phenotypic.schema.CONDITION_METADATA class method) (phenotypic.schema.CURATION class method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL class method) (phenotypic.schema.EDGE_CORRECTION class method) (phenotypic.schema.ErrorCategory class method) (phenotypic.schema.EXPERIMENT_METADATA class method) (phenotypic.schema.GENETIC_METADATA class method) (phenotypic.schema.GRID class method) (phenotypic.schema.GRID_LINREG_STATS class method) (phenotypic.schema.GRID_SPATIAL class method) (phenotypic.schema.GRID_SPREAD class method) (phenotypic.schema.INCUBATION_METADATA class method) (phenotypic.schema.INTENSITY class method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL class method) (phenotypic.schema.LOG_GROWTH_MODEL class method) (phenotypic.schema.MeasurementInfo class method) (phenotypic.schema.METADATA class method) (phenotypic.schema.MODEL_METRICS class method) (phenotypic.schema.OBJECT class method) (phenotypic.schema.PLATE_METADATA class method) (phenotypic.schema.QUALITY_CHECK class method) (phenotypic.schema.QUALITY_COUNT class method) (phenotypic.schema.QUALITY_ICC class method) (phenotypic.schema.QUALITY_MAD class method) (phenotypic.schema.QUALITY_SE class method) (phenotypic.schema.QUALITY_TUKEY class method) (phenotypic.schema.QUALITY_ZMAX class method) (phenotypic.schema.RADIAL_EXPANSION class method) (phenotypic.schema.SAMPLE_METADATA class method) (phenotypic.schema.SHAPE class method) (phenotypic.schema.SIZE class method) (phenotypic.schema.SYMMETRIC_ZONES class method) (phenotypic.schema.TEXTURE class method) (phenotypic.sdk_.constants_.ConstantLabels class method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS class method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS class method), [1] get_home() (phenotypic.sdk_.HDF method), [1] (phenotypic.sdk_.hdf_.HDF method) get_image_group() (phenotypic.sdk_.HDF method), [1] (phenotypic.sdk_.hdf_.HDF method) get_image_measurement_subgroup() (phenotypic.sdk_.HDF method), [1] (phenotypic.sdk_.hdf_.HDF method) get_label_idx() (phenotypic._core._image_parts.accessors._objects_accessor.ObjectsAccessor method) get_labels() (phenotypic.abc_.MeasurementInfo class method), [1] (phenotypic.schema.ACQUISITION_METADATA class method) (phenotypic.schema.BBOX class method) (phenotypic.schema.ColorComposition class method) (phenotypic.schema.ColorHSV class method) (phenotypic.schema.ColorLab class method) (phenotypic.schema.Colorxy class method) (phenotypic.schema.ColorXYZ class method) (phenotypic.schema.CONDITION_METADATA class method) (phenotypic.schema.CURATION class method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL class method) (phenotypic.schema.EDGE_CORRECTION class method) (phenotypic.schema.ErrorCategory class method) (phenotypic.schema.EXPERIMENT_METADATA class method) (phenotypic.schema.GENETIC_METADATA class method) (phenotypic.schema.GRID class method) (phenotypic.schema.GRID_LINREG_STATS class method) (phenotypic.schema.GRID_SPATIAL class method) (phenotypic.schema.GRID_SPREAD class method) (phenotypic.schema.INCUBATION_METADATA class method) (phenotypic.schema.INTENSITY class method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL class method) (phenotypic.schema.LOG_GROWTH_MODEL class method) (phenotypic.schema.MeasurementInfo class method) (phenotypic.schema.METADATA class method) (phenotypic.schema.MODEL_METRICS class method) (phenotypic.schema.OBJECT class method) (phenotypic.schema.PLATE_METADATA class method) (phenotypic.schema.QUALITY_CHECK class method) (phenotypic.schema.QUALITY_COUNT class method) (phenotypic.schema.QUALITY_ICC class method) (phenotypic.schema.QUALITY_MAD class method) (phenotypic.schema.QUALITY_SE class method) (phenotypic.schema.QUALITY_TUKEY class method) (phenotypic.schema.QUALITY_ZMAX class method) (phenotypic.schema.RADIAL_EXPANSION class method) (phenotypic.schema.SAMPLE_METADATA class method) (phenotypic.schema.SHAPE class method) (phenotypic.schema.SIZE class method) (phenotypic.schema.SYMMETRIC_ZONES class method) (phenotypic.schema.TEXTURE class method) (phenotypic.sdk_.constants_.ConstantLabels class method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS class method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS class method), [1]

get_meas() (phenotypic.abc_.PrefabPipeline method), [1] (phenotypic.prefab.FilamentousFungiPipeline method), [1] (phenotypic.prefab.GridSectionPipeline method), [1] (phenotypic.prefab.HeavyOtsuPipeline method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1] (phenotypic.prefab.HeavyWatershedPipeline method), [1] (phenotypic.prefab.RoundPeaksPipeline method), [1] (phenotypic.prefab.SpImagerPipeline method), [1] get_model() (phenotypic.abc_.PrefabPipeline method), [1] (phenotypic.prefab.FilamentousFungiPipeline method), [1] (phenotypic.prefab.GridSectionPipeline method), [1] (phenotypic.prefab.HeavyOtsuPipeline method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1] (phenotypic.prefab.HeavyWatershedPipeline method), [1] (phenotypic.prefab.RoundPeaksPipeline method), [1] (phenotypic.prefab.SpImagerPipeline method), [1] get_ops() (phenotypic.abc_.PrefabPipeline method), [1] (phenotypic.prefab.FilamentousFungiPipeline method), [1] (phenotypic.prefab.GridSectionPipeline method), [1] (phenotypic.prefab.HeavyOtsuPipeline method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1] (phenotypic.prefab.HeavyWatershedPipeline method), [1] (phenotypic.prefab.RoundPeaksPipeline method), [1] (phenotypic.prefab.SpImagerPipeline method), [1] get_plotter() (in module phenotypic.sdk_.register), [1] get_post() (phenotypic.abc_.PrefabPipeline method), [1] (phenotypic.prefab.FilamentousFungiPipeline method), [1] (phenotypic.prefab.GridSectionPipeline method), [1] (phenotypic.prefab.HeavyOtsuPipeline method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1] (phenotypic.prefab.HeavyWatershedPipeline method), [1] (phenotypic.prefab.RoundPeaksPipeline method), [1] (phenotypic.prefab.SpImagerPipeline method), [1] get_protected_metadata_subgroup() (phenotypic.sdk_.HDF method), [1] (phenotypic.sdk_.hdf_.HDF method) get_public_metadata_subgroup() (phenotypic.sdk_.HDF method), [1] (phenotypic.sdk_.hdf_.HDF method) get_qc() (phenotypic.abc_.PrefabPipeline method), [1] (phenotypic.prefab.FilamentousFungiPipeline method), [1] (phenotypic.prefab.GridSectionPipeline method), [1] (phenotypic.prefab.HeavyOtsuPipeline method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1] (phenotypic.prefab.HeavyWatershedPipeline method), [1] (phenotypic.prefab.RoundPeaksPipeline method), [1] (phenotypic.prefab.SpImagerPipeline method), [1] get_root_group() (phenotypic.sdk_.HDF method), [1] (phenotypic.sdk_.hdf_.HDF method) get_row_edges() (phenotypic.abc_.GridFinder method), [1] (phenotypic.grid.AutoGridFinder method), [1] (phenotypic.grid.CenteredAutoGridFinder method), [1] (phenotypic.grid.ManualGridFinder method), [1] get_slurm_array_limit() (in module phenotypic.sdk_.slurm), [1] get_slurm_max_submit_jobs() (in module phenotypic.sdk_.slurm), [1] get_status_subgroup() (phenotypic.sdk_.HDF method), [1] (phenotypic.sdk_.hdf_.HDF method) get_uncompressed_sizes_for_group() (phenotypic.sdk_.HDF static method), [1] (phenotypic.sdk_.hdf_.HDF static method) gmm_n_components (phenotypic.detect.InoculumDetector attribute), [1] gmm_separation_threshold (phenotypic.detect.InoculumDetector attribute), [1] GpuDetector (class in phenotypic.abc_), [1] GpuInputLayer (in module phenotypic.sdk_.typing_) GpuOutputKind (in module phenotypic.sdk_.typing_) gray (phenotypic.Image property) gray_band_snr (phenotypic.sdk_.branch_pathfinding.PathMetrics attribute), [1] GRAY_PCT (phenotypic.schema.ColorComposition attribute) gray_snr_values (phenotypic.sdk_.branch_pathfinding.CalibrationData attribute), [1] GrayOpening (class in phenotypic.enhance), [1] Grayscale (class in phenotypic._core._image_parts.accessors._grayscale_accessor) GRAYSCALE (phenotypic.sdk_.constants_.IMAGE_MODE attribute), [1] GRAYSCALE_SINGLE_CHANNEL (phenotypic.sdk_.constants_.IMAGE_MODE attribute), [1] GrayscaleOutOfRangeError, [1] GREEN_PCT (phenotypic.schema.ColorComposition attribute) GRID (class in phenotypic.schema) grid (phenotypic.GridImage property) GRID (phenotypic.sdk_.constants_.IMAGE_TYPES attribute), [1] grid section grid_aligner_axis (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] grid_aligner_mode (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] GRID_LINREG_STATS (class in phenotypic.schema) GRID_LINREG_STATS_EXTRACTOR (class in phenotypic.sdk_.constants_), [1] GRID_SECTION (phenotypic.sdk_.constants_.IMAGE_TYPES attribute), [1] GRID_SPATIAL (class in phenotypic.schema) GRID_SPREAD (class in phenotypic.schema) GridAligner (class in phenotypic.correction), [1] GridAlignmentRefiner (class in phenotypic.refine), [1] GridApply (class in phenotypic.grid), [1] GridConfig (class in phenotypic.tune), [1] GridCorrector (class in phenotypic.abc_), [1] GridFinder (class in phenotypic.abc_), [1] GridImage GridImageInputError, [1] GridInferenceMixin (class in phenotypic.sdk_), [1] (class in phenotypic.sdk_.mixin) GridMeasureFeatures (class in phenotypic.abc_), [1] GridObjectDetector (class in phenotypic.abc_), [1] GridObjectRefiner (class in phenotypic.abc_), [1] GridOperation (class in phenotypic.abc_), [1] GridOversizedObjectRemover (class in phenotypic.refine), [1] GridSectionPipeline (class in phenotypic.prefab), [1] GroundTruthMasks (class in phenotypic.tune), [1] group_key (phenotypic.tune.HeldOutConfig attribute), [1] group_members() (phenotypic.analysis.abc_.QualityCheck method) (phenotypic.analysis.ExpectedVsDetectedCount method), [1] (phenotypic.analysis.ICC method), [1] (phenotypic.analysis.MaxModifiedZScore method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount method) (phenotypic.analysis.qc.ICC method) (phenotypic.analysis.qc.MaxModifiedZScore method) (phenotypic.analysis.qc.RelativeMAD method) (phenotypic.analysis.qc.ReplicateAgreement method) (phenotypic.analysis.qc.TukeyOutlierFraction method) (phenotypic.analysis.RelativeMAD method), [1] (phenotypic.analysis.ReplicateAgreement method), [1] (phenotypic.analysis.TukeyOutlierFraction method), [1] groupby (phenotypic.analysis.abc_.ModelFitter attribute) (phenotypic.analysis.abc_.QualityCheck attribute) (phenotypic.analysis.abc_.SetAnalyzer attribute) (phenotypic.analysis.DoubleSoftplus attribute), [1] (phenotypic.analysis.EdgeCorrector attribute), [1] (phenotypic.analysis.ExpectedVsDetectedCount attribute), [1] (phenotypic.analysis.ICC attribute), [1] (phenotypic.analysis.LinearSoftplus attribute), [1] (phenotypic.analysis.LogGrowthModel attribute), [1] (phenotypic.analysis.MADOutlierRemover attribute), [1], [2], [3] (phenotypic.analysis.MaxModifiedZScore attribute), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount attribute) (phenotypic.analysis.qc.ICC attribute) (phenotypic.analysis.qc.MaxModifiedZScore attribute) (phenotypic.analysis.qc.RelativeMAD attribute) (phenotypic.analysis.qc.ReplicateAgreement attribute) (phenotypic.analysis.qc.TukeyOutlierFraction attribute) (phenotypic.analysis.RelativeMAD attribute), [1] (phenotypic.analysis.ReplicateAgreement attribute), [1] (phenotypic.analysis.TukeyOutlierFraction attribute), [1] (phenotypic.analysis.TukeyOutlierRemover attribute), [1], [2], [3] GROWTH_RATE (phenotypic.schema.LOG_GROWTH_MODEL attribute) gt (phenotypic.tune.SupervisedScorer attribute), [1] gt_format (phenotypic.tune.GroundTruthMasks attribute), [1] gt_masks_source (phenotypic.tune.GroundTruthMasks attribute), [1] (phenotypic.tune.ReferenceFreeScorer attribute), [1]

H

h (phenotypic.enhance.NonLocalMeansDenoiser attribute), [1] has_config_suffix() (in module phenotypic.sdk_), [1] HDF (class in phenotypic.sdk_), [1] (class in phenotypic.sdk_.hdf_) HdfAttr (class in phenotypic.sdk_), [1] HeavyOtsuPipeline (class in phenotypic.prefab), [1] HeavyRoundPeaksPipeline (class in phenotypic.prefab), [1] HeavyWatershedPipeline (class in phenotypic.prefab), [1] held_out (phenotypic.tune.TuningSpec attribute), [1] held_out_fraction (phenotypic.tune.HeldOutConfig attribute), [1] heldout_score (phenotypic.tune.GeneralizationReport attribute), [1] HeldOutConfig (class in phenotypic.tune), [1] help (phenotypic.abc_.Control attribute), [1] high (phenotypic.detect.HysteresisDetector attribute), [1] (phenotypic.sdk_.typing_.TuneSpec attribute) (phenotypic.tune.FloatRange attribute), [1] (phenotypic.tune.IntRange attribute), [1] (phenotypic.tune.TuneSpec attribute), [1]

high_threshold (phenotypic.detect.CannyDetector attribute), [1] histogram() (phenotypic._core._image_parts.accessors._detect_mat_accessor.DetectMatAccessor method) (phenotypic._core._image_parts.accessors._grayscale_accessor.Grayscale method) (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap method) (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask method) (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) (phenotypic._core._image_parts.accessors._rgb_accessor.ImageRGB method) home_posix (phenotypic.sdk_.HDF attribute), [1], [2], [3] (phenotypic.sdk_.hdf_.HDF attribute), [1] hsv (phenotypic._core._image_parts.accessors._color_accessor.ColorAccessor property) HSV (phenotypic.sdk_.constants_.IMAGE_MODE attribute), [1] HSV_CONE_VARIANCE (phenotypic.schema.ColorHSV attribute) hsv_to_cone() (in module phenotypic.util), [1] HUE_ROBUST_MEAN (phenotypic.schema.ColorHSV attribute) HUMIDITY (phenotypic.schema.INCUBATION_METADATA attribute) hyphae HysteresisDetector (class in phenotypic.detect), [1]

I

ICC (class in phenotypic.analysis), [1] (class in phenotypic.analysis.qc) idle_seconds() (phenotypic.gui.shell.ToolSession method) ignore_borders (phenotypic.detect.FilamentousFungiDetector attribute), [1] (phenotypic.detect.HysteresisDetector attribute), [1] (phenotypic.detect.IsodataDetector attribute), [1] (phenotypic.detect.LiDetector attribute), [1] (phenotypic.detect.MadHysteresisDetector attribute), [1] (phenotypic.detect.MeanDetector attribute), [1] (phenotypic.detect.MinimumDetector attribute), [1] (phenotypic.detect.OtsuDetector attribute), [1] (phenotypic.detect.UserThreshold attribute), [1] (phenotypic.detect.YenDetector attribute), [1] ignore_zeros (phenotypic.detect.HysteresisDetector attribute), [1] (phenotypic.detect.IsodataDetector attribute), [1] (phenotypic.detect.LiDetector attribute), [1] (phenotypic.detect.MadHysteresisDetector attribute), [1] (phenotypic.detect.MeanDetector attribute), [1] (phenotypic.detect.MinimumDetector attribute), [1] (phenotypic.detect.OtsuDetector attribute), [1] (phenotypic.detect.RankOtsuDetector attribute), [1] (phenotypic.detect.UserThreshold attribute), [1] (phenotypic.detect.WatershedDetector attribute), [1] (phenotypic.detect.YenDetector attribute), [1] IllegalAssignmentError, [1] IllegalElementAssignmentError, [1] iloc() (phenotypic._core._image_parts.accessors._objects_accessor.ObjectsAccessor method) Image (in module phenotypic.sdk_.funcs_) image (phenotypic.abc_.MeasurementInfo attribute), [1], [2], [3] (phenotypic.schema.ACQUISITION_METADATA attribute) (phenotypic.schema.BBOX attribute) (phenotypic.schema.ColorComposition attribute) (phenotypic.schema.ColorHSV attribute) (phenotypic.schema.ColorLab attribute) (phenotypic.schema.Colorxy attribute) (phenotypic.schema.ColorXYZ attribute) (phenotypic.schema.CONDITION_METADATA attribute) (phenotypic.schema.CURATION attribute) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL attribute) (phenotypic.schema.EDGE_CORRECTION attribute) (phenotypic.schema.Entry attribute) (phenotypic.schema.ErrorCategory attribute) (phenotypic.schema.EXPERIMENT_METADATA attribute) (phenotypic.schema.GENETIC_METADATA attribute) (phenotypic.schema.GRID attribute) (phenotypic.schema.GRID_LINREG_STATS attribute) (phenotypic.schema.GRID_SPATIAL attribute) (phenotypic.schema.GRID_SPREAD attribute) (phenotypic.schema.INCUBATION_METADATA attribute) (phenotypic.schema.INTENSITY attribute) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL attribute) (phenotypic.schema.LOG_GROWTH_MODEL attribute) (phenotypic.schema.MeasurementInfo attribute), [1] (phenotypic.schema.METADATA attribute) (phenotypic.schema.MODEL_METRICS attribute) (phenotypic.schema.OBJECT attribute) (phenotypic.schema.PLATE_METADATA attribute) (phenotypic.schema.QUALITY_CHECK attribute) (phenotypic.schema.QUALITY_COUNT attribute) (phenotypic.schema.QUALITY_ICC attribute) (phenotypic.schema.QUALITY_MAD attribute) (phenotypic.schema.QUALITY_SE attribute) (phenotypic.schema.QUALITY_TUKEY attribute) (phenotypic.schema.QUALITY_ZMAX attribute) (phenotypic.schema.RADIAL_EXPANSION attribute) (phenotypic.schema.SAMPLE_METADATA attribute) (phenotypic.schema.SHAPE attribute) (phenotypic.schema.SIZE attribute) (phenotypic.schema.SYMMETRIC_ZONES attribute) (phenotypic.schema.TEXTURE attribute) (phenotypic.sdk_.constants_.ConstantLabels attribute), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS attribute), [1] (phenotypic.sdk_.constants_.PIPE_STATUS attribute), [1] IMAGE_MEASUREMENT_IMAGE_SUBGROUP_KEY (phenotypic.sdk_.constants_.IO attribute), [1] IMAGE_MEASUREMENT_SUBGROUP_KEY (phenotypic.sdk_.HDF attribute), [1], [2], [3] (phenotypic.sdk_.hdf_.HDF attribute), [1] IMAGE_MODE (class in phenotypic.sdk_.constants_), [1] IMAGE_NAME (phenotypic.schema.METADATA attribute) image_op (phenotypic.grid.GridApply attribute), [1] IMAGE_SET_DATA_POSIX (phenotypic.sdk_.HDF attribute), [1], [2], [3] (phenotypic.sdk_.hdf_.HDF attribute), [1] IMAGE_SET_HDF5_PARENT_GROUP (phenotypic.sdk_.constants_.IO attribute), [1] IMAGE_SET_ROOT_POSIX (phenotypic.sdk_.HDF attribute), [1], [2], [3] (phenotypic.sdk_.hdf_.HDF attribute), [1] IMAGE_STATUS_SUBGROUP_KEY (phenotypic.sdk_.constants_.IO attribute), [1] (phenotypic.sdk_.HDF attribute), [1], [2], [3] (phenotypic.sdk_.hdf_.HDF attribute), [1] IMAGE_TASK_MAPPING (phenotypic.sdk_.JobMetadataKey attribute), [1] IMAGE_TYPE (phenotypic.schema.METADATA attribute) IMAGE_TYPES (class in phenotypic.sdk_.constants_), [1] ImageCorrector (class in phenotypic.abc_), [1] ImageCropper (class in phenotypic.correction), [1] ImageDenoiser (class in phenotypic.abc_), [1] ImageEnhancer (class in phenotypic.abc_), [1] ImageInverter (class in phenotypic.enhance), [1] ImageMetricsCalculator (class in phenotypic.util), [1] (class in phenotypic.util.image_metrics) ImageOperation (class in phenotypic.abc_), [1] ImageOperationError, [1] ImagePadder (class in phenotypic.correction), [1] ImagePipeline ImageRGB (class in phenotypic._core._image_parts.accessors._rgb_accessor) images_dir (phenotypic.gui.tune.TuneRunRoot attribute) ImageTypeName (in module phenotypic.sdk_.typing_) IMAGING_DATE (phenotypic.schema.ACQUISITION_METADATA attribute) IMC1 (phenotypic.schema.TEXTURE attribute) IMC2 (phenotypic.schema.TEXTURE attribute) IMFORMAT (phenotypic.schema.METADATA attribute) ImmutableComponentError, [1] ImportanceReport (class in phenotypic.tune), [1] importances (phenotypic.tune.ImportanceReport attribute), [1] imread() (phenotypic.Image class method) imsave() (phenotypic._core._image_parts.accessors._detect_mat_accessor.DetectMatAccessor method) (phenotypic._core._image_parts.accessors._grayscale_accessor.Grayscale method) (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap method) (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask method) (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) (phenotypic._core._image_parts.accessors._rgb_accessor.ImageRGB method) INCLUDE_DATASET_COLUMN (phenotypic.sdk_.JobMetadataKey attribute), [1] include_xy (phenotypic.measure.MeasureColor attribute), [1] include_XYZ (phenotypic.measure.MeasureColor attribute), [1] INCUBATION_METADATA (class in phenotypic.schema) INCUBATOR_POSITION (phenotypic.schema.PLATE_METADATA attribute) index (phenotypic.tune.targets.Nested attribute) index() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] INDUCER (phenotypic.schema.CONDITION_METADATA attribute) infer_batch() (phenotypic.abc_.GpuDetector method), [1] infer_group_key() (in module phenotypic.tune), [1] infer_search_space() (in module phenotypic.tune), [1] InferredSearchSpace (class in phenotypic.tune), [1] info() (phenotypic._core._image_parts.accessors._objects_accessor.ObjectsAccessor method) init_level_set (phenotypic.detect.ChanVeseDetector attribute), [1] INITIAL_IMAGES (phenotypic.sdk_.ProcessingStateKey attribute), [1] inoculum inoculum_detector (phenotypic.detect.FilamentousFungiDetector attribute), [1] InoculumDetector (class in phenotypic.detect), [1] INPUT_IMAGE_CLASS_NAME (in module phenotypic.gui.builder._state) input_layer (phenotypic.abc_.GpuDetector attribute), [1] INPUT_PATH (phenotypic.sdk_.DashboardManifestKey attribute), [1] (phenotypic.sdk_.JobMetadataKey attribute), [1] (phenotypic.sdk_.ProcessingStateKey attribute), [1] InputShapeMismatchError, [1] insert_metadata() (phenotypic._core._image_parts.accessors._metadata_accessor.MetadataAccessor method) inspect() (phenotypic.abc_.FigureProvider method), [1] (phenotypic.measure.MeasureSymmetricZones method), [1] INSTRUMENT (phenotypic.schema.ACQUISITION_METADATA attribute) INTEGRATED_INTENSITY (phenotypic.schema.INTENSITY attribute) (phenotypic.schema.SIZE attribute) INTENSITY (class in phenotypic.schema) intensity_source (phenotypic.measure.MeasureSymmetricZones attribute), [1] INTENSITY_WEIGHTED_CENTER_CC (phenotypic.schema.BBOX attribute) INTENSITY_WEIGHTED_CENTER_RR (phenotypic.schema.BBOX attribute) interactions_estimated (phenotypic.tune.ImportanceReport attribute), [1] (phenotypic.tune.ScreeningResult attribute), [1] InterfaceError, [1] IntRange (class in phenotypic.tune), [1] InvalidHsvSchemaError, [1] InvalidMapValueError, [1] InvalidMaskScalarValueError, [1] InvalidMaskValueError, [1] InvalidShapeError, [1] INVERSE_DIFFERENCE_MOMENT (phenotypic.schema.TEXTURE attribute) invert_edges (phenotypic.detect.CannyDetector attribute), [1] IO (class in phenotypic.sdk_.constants_), [1] iou_tau (phenotypic.tune.SupervisedScorer attribute), [1] IQR_INTENSITY (phenotypic.schema.INTENSITY attribute) is_active() (phenotypic.tune.Knob method), [1] is_ambiguous() (phenotypic.sdk_.constants_.IMAGE_MODE method), [1] is_array() (phenotypic.sdk_.constants_.IMAGE_MODE method), [1] is_binary_mask() (in module phenotypic.sdk_), [1] (in module phenotypic.sdk_.funcs_) is_bridge (phenotypic.sdk_.branch_pathfinding.FragmentAssignment attribute), [1] is_built() (phenotypic.gui.shell.ToolSession method) IS_COMPLETE (phenotypic.sdk_.DashboardManifestKey attribute), [1] is_fitted (phenotypic.correction.ColorCheckerProfile attribute), [1], [2], [3] is_matrix() (phenotypic.sdk_.constants_.IMAGE_MODE method), [1] is_none() (phenotypic.sdk_.constants_.IMAGE_MODE method), [1] is_resumable_in_place() (phenotypic.tune.JournalStudyStore method), [1] is_static_method() (in module phenotypic.sdk_.funcs_) is_unattended_safe() (phenotypic.tune.ReferenceFreeScorer method), [1] isalnum() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] isalpha() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] isascii() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] isdecimal() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1]

isdigit() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] isempty() (phenotypic._core._image_parts.accessors._detect_mat_accessor.DetectMatAccessor method) (phenotypic._core._image_parts.accessors._grayscale_accessor.Grayscale method) (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap method) (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask method) (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) (phenotypic._core._image_parts.accessors._rgb_accessor.ImageRGB method) isidentifier() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] islower() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] isnumeric() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] iso (phenotypic.correction.CaptureMetadata attribute), [1], [2], [3] IsodataDetector (class in phenotypic.detect), [1] isprintable() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] isspace() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] Issue (class in phenotypic.gui.builder._validation) istitle() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] isupper() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] items() (phenotypic._core._image_parts.accessors._metadata_accessor.MetadataAccessor method) (phenotypic.util.BackgroundMetrics method), [1] (phenotypic.util.ContrastMetrics method), [1] (phenotypic.util.image_metrics.BackgroundMetrics method) (phenotypic.util.image_metrics.ContrastMetrics method) (phenotypic.util.image_metrics.NoiseMetrics method) (phenotypic.util.image_metrics.QualityScores method) (phenotypic.util.image_metrics.StructureMetrics method) (phenotypic.util.NoiseMetrics method), [1] (phenotypic.util.QualityScores method), [1] (phenotypic.util.StructureMetrics method), [1] iter_figures() (phenotypic.abc_.FigureProvider method), [1] (phenotypic.measure.MeasureSymmetricZones method), [1]

J

job_metadata_path() (in module phenotypic.sdk_), [1] JobMetadataKey (class in phenotypic.sdk_), [1] join() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] JournalStudyStore (class in phenotypic.tune), [1] JPEG_FILE_EXTENSIONS (phenotypic.sdk_.constants_.IO attribute), [1] json() (phenotypic.abc_.BackgroundSubtraction method), [1] (phenotypic.abc_.BaseOperation method), [1] (phenotypic.abc_.ContrastAdjustment method), [1] (phenotypic.abc_.FocusBlob method), [1] (phenotypic.abc_.FocusEdge method), [1] (phenotypic.abc_.GpuDetector method), [1] (phenotypic.abc_.GridCorrector method), [1] (phenotypic.abc_.GridFinder method), [1] (phenotypic.abc_.GridMeasureFeatures method), [1] (phenotypic.abc_.GridObjectDetector method), [1] (phenotypic.abc_.GridObjectRefiner method), [1] (phenotypic.abc_.GridOperation method), [1] (phenotypic.abc_.ImageCorrector method), [1] (phenotypic.abc_.ImageDenoiser method), [1] (phenotypic.abc_.ImageEnhancer method), [1] (phenotypic.abc_.ImageOperation method), [1] (phenotypic.abc_.MeasureFeatures method), [1] (phenotypic.abc_.MorphologicalFiltering method), [1] (phenotypic.abc_.ObjectDetector method), [1] (phenotypic.abc_.ObjectRefiner method), [1] (phenotypic.abc_.PostMeasurement method), [1] (phenotypic.abc_.PrefabPipeline method), [1] (phenotypic.abc_.Smoothing method), [1] (phenotypic.abc_.ThresholdDetector method), [1] (phenotypic.analysis.abc_.ModelFitter method) (phenotypic.analysis.abc_.QualityCheck method) (phenotypic.analysis.abc_.SetAnalyzer method) (phenotypic.analysis.DoubleSoftplus method), [1] (phenotypic.analysis.EdgeCorrector method), [1] (phenotypic.analysis.ErrorCutoffFinder method), [1] (phenotypic.analysis.ExpectedVsDetectedCount method), [1] (phenotypic.analysis.ICC method), [1] (phenotypic.analysis.LinearSoftplus method), [1] (phenotypic.analysis.LogGrowthModel method), [1] (phenotypic.analysis.MADOutlierRemover method), [1] (phenotypic.analysis.MaxModifiedZScore method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount method) (phenotypic.analysis.qc.ICC method) (phenotypic.analysis.qc.MaxModifiedZScore method) (phenotypic.analysis.qc.RelativeMAD method) (phenotypic.analysis.qc.ReplicateAgreement method) (phenotypic.analysis.qc.TukeyOutlierFraction method) (phenotypic.analysis.RelativeMAD method), [1] (phenotypic.analysis.ReplicateAgreement method), [1] (phenotypic.analysis.TukeyOutlierFraction method), [1] (phenotypic.analysis.TukeyOutlierRemover method), [1] (phenotypic.correction.BayesShrinkCorrector method), [1] (phenotypic.correction.CaptureMetadata method), [1] (phenotypic.correction.ColorCheckerProfile method), [1] (phenotypic.correction.ColorCorrector method), [1] (phenotypic.correction.ColorDenoise method), [1] (phenotypic.correction.DenoiseBlockMatch method), [1] (phenotypic.correction.GridAligner method), [1] (phenotypic.correction.ImageCropper method), [1] (phenotypic.correction.ImagePadder method), [1] (phenotypic.correction.VisuShrinkCorrector method), [1] (phenotypic.detect.CannyDetector method), [1] (phenotypic.detect.ChanVeseDetector method), [1] (phenotypic.detect.CompositeDetector method), [1] (phenotypic.detect.FilamentousFungiDetector method), [1] (phenotypic.detect.HysteresisDetector method), [1] (phenotypic.detect.InoculumDetector method), [1] (phenotypic.detect.IsodataDetector method), [1] (phenotypic.detect.LiDetector method), [1] (phenotypic.detect.MadHysteresisDetector method), [1] (phenotypic.detect.ManualGridPointDetector method), [1] (phenotypic.detect.ManualPointDetector method), [1] (phenotypic.detect.MeanDetector method), [1] (phenotypic.detect.MinimumDetector method), [1] (phenotypic.detect.OtsuDetector method), [1] (phenotypic.detect.RankOtsuDetector method), [1] (phenotypic.detect.RoundPeaksDetector method), [1] (phenotypic.detect.SecondaryOtsuDetector method), [1] (phenotypic.detect.SinePeakDetector method), [1] (phenotypic.detect.TriangleDetector method), [1] (phenotypic.detect.UserThreshold method), [1] (phenotypic.detect.WatershedDetector method), [1] (phenotypic.detect.YenDetector method), [1] (phenotypic.enhance.BayesShrinkEnhancer method), [1] (phenotypic.enhance.ContrastStretching method), [1] (phenotypic.enhance.EnhanceBlockMatch method), [1] (phenotypic.enhance.EnhanceLocalContrast method), [1] (phenotypic.enhance.FlattenIllumination method), [1] (phenotypic.enhance.FocusBlobLoG method), [1] (phenotypic.enhance.FocusEdgeFrangi method), [1] (phenotypic.enhance.FocusEdgeHessian method), [1] (phenotypic.enhance.FocusEdgeLaplace method), [1] (phenotypic.enhance.FocusEdgeMeijering method), [1] (phenotypic.enhance.FocusEdgePhase method), [1] (phenotypic.enhance.FocusEdgeSato method), [1] (phenotypic.enhance.FocusEdgeSobel method), [1] (phenotypic.enhance.GaussianBlur method), [1] (phenotypic.enhance.GrayOpening method), [1] (phenotypic.enhance.ImageInverter method), [1] (phenotypic.enhance.LocalEdgeDenoise method), [1] (phenotypic.enhance.MedianFilter method), [1] (phenotypic.enhance.NonLocalMeansDenoiser method), [1] (phenotypic.enhance.RankMedianEnhancer method), [1] (phenotypic.enhance.SetDetectMode method), [1] (phenotypic.enhance.SharpenEdgeGauss method), [1] (phenotypic.enhance.StructureSmoothing method), [1] (phenotypic.enhance.SubtractGaussian method), [1] (phenotypic.enhance.SubtractOpening method), [1] (phenotypic.enhance.SubtractRollingBall method), [1] (phenotypic.enhance.SubtractWhiteTophat method), [1] (phenotypic.enhance.VisuShrinkEnhancer method), [1] (phenotypic.enhance.WhiteTophatEnhance method), [1] (phenotypic.grid.AutoGridFinder method), [1] (phenotypic.grid.CenteredAutoGridFinder method), [1] (phenotypic.grid.GridApply method), [1] (phenotypic.grid.ManualGridFinder method), [1] (phenotypic.measure.MeasureBounds method), [1] (phenotypic.measure.MeasureColor method), [1] (phenotypic.measure.MeasureGridLinRegStats method), [1] (phenotypic.measure.MeasureGridSpatial method), [1] (phenotypic.measure.MeasureGridSpread method), [1] (phenotypic.measure.MeasureIntensity method), [1] (phenotypic.measure.MeasureShape method), [1] (phenotypic.measure.MeasureSize method), [1] (phenotypic.measure.MeasureSymmetricZones method), [1] (phenotypic.measure.MeasureTexture method), [1] (phenotypic.post.AppendString method) (phenotypic.post.ExpandMetadata method) (phenotypic.post.MergeMetadata method) (phenotypic.post.PrependString method) (phenotypic.prefab.FilamentousFungiPipeline method), [1] (phenotypic.prefab.GridSectionPipeline method), [1] (phenotypic.prefab.HeavyOtsuPipeline method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1] (phenotypic.prefab.HeavyWatershedPipeline method), [1] (phenotypic.prefab.RoundPeaksPipeline method), [1] (phenotypic.prefab.SpImagerPipeline method), [1] (phenotypic.refine.ExtractColonyCore method), [1] (phenotypic.refine.GridAlignmentRefiner method), [1] (phenotypic.refine.GridOversizedObjectRemover method), [1] (phenotypic.refine.KeepNearestCenter method), [1] (phenotypic.refine.KeepSectionLargest method), [1] (phenotypic.refine.ManualRefine method), [1] (phenotypic.refine.MaskClosing method), [1] (phenotypic.refine.MaskDilation method), [1] (phenotypic.refine.MaskErosion method), [1] (phenotypic.refine.MaskFill method), [1] (phenotypic.refine.MaskGradient method), [1] (phenotypic.refine.MaskOpening method), [1] (phenotypic.refine.MaskWhiteTophat method), [1] (phenotypic.refine.MergeFragmentChains method), [1] (phenotypic.refine.NearestNeighborMerger method), [1] (phenotypic.refine.ReduceSectionsByLine method), [1] (phenotypic.refine.RefineBySineFit method), [1] (phenotypic.refine.RemoveBorderObjects method), [1] (phenotypic.refine.RemoveByFeature method), [1] (phenotypic.refine.RemoveGridOutliers method), [1] (phenotypic.refine.RemoveLowCircularity method), [1] (phenotypic.refine.SeparateObjects method), [1] (phenotypic.refine.Skeletonize method), [1] (phenotypic.refine.SmallObjectRemover method), [1] (phenotypic.refine.SmallToLargeMerger method), [1] (phenotypic.refine.Thinning method), [1] (phenotypic.refine.TrimAsymmetry method), [1] (phenotypic.tune.Budget method), [1] (phenotypic.tune.Categorical method), [1] (phenotypic.tune.CompositeScorer method), [1] (phenotypic.tune.EvaluationResult method), [1] (phenotypic.tune.Evaluator method), [1] (phenotypic.tune.Excluded method), [1] (phenotypic.tune.Fixed method), [1] (phenotypic.tune.FloatRange method), [1] (phenotypic.tune.GridConfig method), [1] (phenotypic.tune.GroundTruthMasks method), [1] (phenotypic.tune.HeldOutConfig method), [1] (phenotypic.tune.ImportanceReport method), [1] (phenotypic.tune.InferredSearchSpace method), [1] (phenotypic.tune.IntRange method), [1] (phenotypic.tune.Knob method), [1] (phenotypic.tune.OptunaConfig method), [1] (phenotypic.tune.QCScorer method), [1] (phenotypic.tune.RandomConfig method), [1] (phenotypic.tune.ReferenceFreeScorer method), [1] (phenotypic.tune.Scorer method), [1] (phenotypic.tune.SearchSpace method), [1] (phenotypic.tune.StrategyConfig method), [1] (phenotypic.tune.SupervisedScorer method), [1] (phenotypic.tune.targets.Nested method) (phenotypic.tune.targets.Param method) (phenotypic.tune.targets.Presence method) (phenotypic.tune.targets.TunableParam method) (phenotypic.tune.Trial method), [1] (phenotypic.tune.TuningSpec method), [1]

K

k (phenotypic.analysis.qc.TukeyOutlierFraction attribute) (phenotypic.analysis.TukeyOutlierFraction attribute), [1] (phenotypic.analysis.TukeyOutlierRemover attribute), [1], [2], [3] (phenotypic.enhance.FocusEdgePhase attribute), [1] K_FIT (phenotypic.schema.LOG_GROWTH_MODEL attribute) k_high (phenotypic.detect.MadHysteresisDetector attribute), [1] k_iqr (phenotypic.sdk_.branch_pathfinding.FilterThresholds attribute), [1] k_low (phenotypic.detect.MadHysteresisDetector attribute), [1] K_MAX (phenotypic.schema.LOG_GROWTH_MODEL attribute) KeepNearestCenter (class in phenotypic.refine), [1] KeepSectionLargest (class in phenotypic.refine), [1] kernel (phenotypic.enhance.SubtractRollingBall attribute), [1] kernel_size (phenotypic.enhance.EnhanceLocalContrast attribute), [1] (phenotypic.enhance.FocusEdgeLaplace attribute), [1] key (phenotypic.tune.Excluded attribute), [1] (phenotypic.tune.Knob property), [1] (phenotypic.tune.targets.Nested property) (phenotypic.tune.targets.Param property) (phenotypic.tune.targets.Presence property) keys() (phenotypic._core._image_parts.accessors._metadata_accessor.MetadataAccessor method) (phenotypic.tune.SearchSpace method), [1] (phenotypic.util.BackgroundMetrics method), [1] (phenotypic.util.ContrastMetrics method), [1] (phenotypic.util.image_metrics.BackgroundMetrics method) (phenotypic.util.image_metrics.ContrastMetrics method) (phenotypic.util.image_metrics.NoiseMetrics method) (phenotypic.util.image_metrics.QualityScores method) (phenotypic.util.image_metrics.StructureMetrics method) (phenotypic.util.NoiseMetrics method), [1] (phenotypic.util.QualityScores method), [1] (phenotypic.util.StructureMetrics method), [1]

kind (phenotypic.abc_.Control attribute), [1] (phenotypic.gui.builder._state.Edge attribute), [1] (phenotypic.gui.builder._validation.Issue attribute), [1] (phenotypic.tune.Categorical attribute), [1] (phenotypic.tune.Fixed attribute), [1] (phenotypic.tune.FloatRange attribute), [1] (phenotypic.tune.GeneralizationReport attribute), [1] (phenotypic.tune.GridConfig attribute), [1] (phenotypic.tune.IntRange attribute), [1] (phenotypic.tune.OptunaConfig attribute), [1] (phenotypic.tune.RandomConfig attribute), [1] (phenotypic.tune.targets.Nested attribute) (phenotypic.tune.targets.Param attribute) (phenotypic.tune.targets.Presence attribute) Kmax_label (phenotypic.analysis.LogGrowthModel attribute), [1] knee_point() (phenotypic.tune.JournalStudyStore method), [1] Knob (class in phenotypic.tune), [1] knobs (phenotypic.tune.InferredSearchSpace attribute), [1] (phenotypic.tune.SearchSpace attribute), [1]

L

L_STAR_GEOMEDIAN (phenotypic.schema.ColorLab attribute) L_STAR_MEDOID (phenotypic.schema.ColorLab attribute) Lab (phenotypic._core._image_parts.accessors._color_accessor.ColorAccessor property) lab_to_srgb_hex() (in module phenotypic.util), [1] LAB_TOTAL_VARIANCE (phenotypic.schema.ColorLab attribute) label (phenotypic.abc_.Control attribute), [1] (phenotypic.abc_.MeasurementInfo attribute), [1], [2], [3] (phenotypic.gui.builder._state.BlockNode attribute), [1] (phenotypic.post.MergeMetadata attribute) (phenotypic.schema.ACQUISITION_METADATA attribute) (phenotypic.schema.BBOX attribute) (phenotypic.schema.ColorComposition attribute) (phenotypic.schema.ColorHSV attribute) (phenotypic.schema.ColorLab attribute) (phenotypic.schema.Colorxy attribute) (phenotypic.schema.ColorXYZ attribute) (phenotypic.schema.CONDITION_METADATA attribute) (phenotypic.schema.CURATION attribute) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL attribute) (phenotypic.schema.EDGE_CORRECTION attribute) (phenotypic.schema.Entry attribute) (phenotypic.schema.ErrorCategory attribute) (phenotypic.schema.EXPERIMENT_METADATA attribute) (phenotypic.schema.GENETIC_METADATA attribute) (phenotypic.schema.GRID attribute) (phenotypic.schema.GRID_LINREG_STATS attribute) (phenotypic.schema.GRID_SPATIAL attribute) (phenotypic.schema.GRID_SPREAD attribute) (phenotypic.schema.INCUBATION_METADATA attribute) (phenotypic.schema.INTENSITY attribute) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL attribute) (phenotypic.schema.LOG_GROWTH_MODEL attribute) (phenotypic.schema.MeasurementInfo attribute), [1] (phenotypic.schema.METADATA attribute) (phenotypic.schema.MODEL_METRICS attribute) LABEL (phenotypic.schema.OBJECT attribute) label (phenotypic.schema.OBJECT attribute) (phenotypic.schema.PLATE_METADATA attribute) (phenotypic.schema.QUALITY_CHECK attribute) (phenotypic.schema.QUALITY_COUNT attribute) (phenotypic.schema.QUALITY_ICC attribute) (phenotypic.schema.QUALITY_MAD attribute) (phenotypic.schema.QUALITY_SE attribute) (phenotypic.schema.QUALITY_TUKEY attribute) (phenotypic.schema.QUALITY_ZMAX attribute) (phenotypic.schema.RADIAL_EXPANSION attribute) (phenotypic.schema.SAMPLE_METADATA attribute) (phenotypic.schema.SHAPE attribute) (phenotypic.schema.SIZE attribute) (phenotypic.schema.SYMMETRIC_ZONES attribute) (phenotypic.schema.TEXTURE attribute) (phenotypic.sdk_.constants_.ConstantLabels attribute), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS attribute), [1] (phenotypic.sdk_.constants_.PIPE_STATUS attribute), [1] LabelEditorWidget (class in phenotypic.sdk_.napari_), [1] labels (phenotypic._core._image_parts.accessors._objects_accessor.ObjectsAccessor property) (phenotypic.post.ExpandMetadata attribute) labels() (phenotypic.schema.ErrorCategory class method) labels2series() (phenotypic._core._image_parts.accessors._objects_accessor.ObjectsAccessor method) lam (phenotypic.analysis.LogGrowthModel attribute), [1] (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL attribute) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL attribute) LAM (phenotypic.schema.LOG_GROWTH_MODEL attribute) lambda1 (phenotypic.detect.ChanVeseDetector attribute), [1] lambda2 (phenotypic.detect.ChanVeseDetector attribute), [1] LAST_UPDATED (phenotypic.sdk_.DashboardManifestKey attribute), [1] (phenotypic.sdk_.ProcessingStateKey attribute), [1] launch_gui() (in module phenotypic.gui.shell) launch_results_viewer() (in module phenotypic.gui.results_viewer) LazyWidgetMixin (class in phenotypic.sdk_), [1] (class in phenotypic.sdk_.mixin) leaf (phenotypic.tune.targets.Nested attribute) left (phenotypic.correction.ImageCropper attribute), [1] (phenotypic.correction.ImagePadder attribute), [1] LEFT_DISTANCE (phenotypic.schema.GRID_SPATIAL attribute) LEFT_NEIGHBOR_OBJ_LABEL (phenotypic.schema.GRID_SPATIAL attribute) lens_model (phenotypic.correction.CaptureMetadata attribute), [1], [2], [3] LIBRARY_ID (phenotypic.schema.SAMPLE_METADATA attribute) LiDetector (class in phenotypic.detect), [1] LINEAR (phenotypic.sdk_.constants_.GAMMA_ENCODINGS attribute), [1] LINEAR_RGB (phenotypic.sdk_.constants_.IMAGE_MODE attribute), [1] LINEAR_SOFTPLUS_MODEL (class in phenotypic.schema) LinearSoftplus (class in phenotypic.analysis), [1] list_children() (phenotypic.gui.shell.SandboxRoot method) list_slot_counts (phenotypic.gui.builder._state.BlockNode attribute), [1] ljust() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] load() (phenotypic._core._image_parts.accessors._detect_mat_accessor.DetectMatAccessor class method) (phenotypic._core._image_parts.accessors._grayscale_accessor.Grayscale class method) (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap class method) (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask class method) (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor class method) (phenotypic._core._image_parts.accessors._rgb_accessor.ImageRGB class method)

load_colony() (in module phenotypic.data), [1] load_early_colony() (in module phenotypic.data), [1] load_faint_early_colony() (in module phenotypic.data), [1] load_frame() (phenotypic.sdk_.HDF static method), [1] (phenotypic.sdk_.hdf_.HDF static method) load_fungi_plate() (in module phenotypic.data), [1] load_fungi_plate_full() (in module phenotypic.data), [1] load_hdf5() (phenotypic.Image class method) load_image_from_hdf() (in module phenotypic.sdk_), [1] load_master_measurements() (in module phenotypic.sdk_), [1] load_plate_12hr() (in module phenotypic.data), [1] load_plate_72hr() (in module phenotypic.data), [1] load_series() (phenotypic.sdk_.HDF static method), [1] (phenotypic.sdk_.hdf_.HDF static method) load_synth_yeast_plate() (in module phenotypic.data), [1] load_yeast_plate() (in module phenotypic.data), [1] load_yeast_plate_full() (in module phenotypic.data), [1] loc() (phenotypic._core._image_parts.accessors._objects_accessor.ObjectsAccessor method) LocalEdgeDenoise (class in phenotypic.enhance), [1] log (phenotypic.sdk_.typing_.TuneSpec attribute) (phenotypic.tune.FloatRange attribute), [1] (phenotypic.tune.IntRange attribute), [1] (phenotypic.tune.TuneSpec attribute), [1] LOG_GROWTH_MODEL (class in phenotypic.schema) LogGrowthModel (class in phenotypic.analysis), [1] logs_dir() (in module phenotypic.sdk_), [1] loss (phenotypic.analysis.abc_.ModelFitter attribute), [1] (phenotypic.analysis.DoubleSoftplus attribute), [1] (phenotypic.analysis.LinearSoftplus attribute), [1] (phenotypic.analysis.LogGrowthModel attribute), [1] LOSS (phenotypic.schema.MODEL_METRICS attribute) low (phenotypic.detect.HysteresisDetector attribute), [1] (phenotypic.sdk_.typing_.TuneSpec attribute) (phenotypic.tune.FloatRange attribute), [1] (phenotypic.tune.IntRange attribute), [1] (phenotypic.tune.TuneSpec attribute), [1] low_threshold (phenotypic.detect.CannyDetector attribute), [1] lower() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] LOWER_FENCE (phenotypic.schema.QUALITY_TUKEY attribute) lower_percentile (phenotypic.enhance.ContrastStretching attribute), [1] lstrip() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1]

M

MAD (phenotypic.schema.QUALITY_MAD attribute) (phenotypic.schema.QUALITY_ZMAX attribute) mad_window (phenotypic.detect.FilamentousFungiDetector attribute), [1] MadHysteresisDetector (class in phenotypic.detect), [1] MADOutlierRemover (class in phenotypic.analysis), [1] MAE (phenotypic.schema.MODEL_METRICS attribute) main() (in module phenotypic.gui.shell) MAJOR_AXIS_LENGTH (phenotypic.schema.SHAPE attribute) majority_fraction (phenotypic.sdk_.branch_pathfinding.FragmentAssignment attribute), [1] make_synthetic_colony() (in module phenotypic.data), [1] make_synthetic_filamentous_plate() (in module phenotypic.data), [1] make_synthetic_plate() (in module phenotypic.data), [1] maketrans() (phenotypic.abc_.MeasurementInfo static method), [1] (phenotypic.schema.ACQUISITION_METADATA static method) (phenotypic.schema.BBOX static method) (phenotypic.schema.ColorComposition static method) (phenotypic.schema.ColorHSV static method) (phenotypic.schema.ColorLab static method) (phenotypic.schema.Colorxy static method) (phenotypic.schema.ColorXYZ static method) (phenotypic.schema.CONDITION_METADATA static method) (phenotypic.schema.CURATION static method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL static method) (phenotypic.schema.EDGE_CORRECTION static method) (phenotypic.schema.ErrorCategory static method) (phenotypic.schema.EXPERIMENT_METADATA static method) (phenotypic.schema.GENETIC_METADATA static method) (phenotypic.schema.GRID static method) (phenotypic.schema.GRID_LINREG_STATS static method) (phenotypic.schema.GRID_SPATIAL static method) (phenotypic.schema.GRID_SPREAD static method) (phenotypic.schema.INCUBATION_METADATA static method) (phenotypic.schema.INTENSITY static method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL static method) (phenotypic.schema.LOG_GROWTH_MODEL static method) (phenotypic.schema.MeasurementInfo static method) (phenotypic.schema.METADATA static method) (phenotypic.schema.MODEL_METRICS static method) (phenotypic.schema.OBJECT static method) (phenotypic.schema.PLATE_METADATA static method) (phenotypic.schema.QUALITY_CHECK static method) (phenotypic.schema.QUALITY_COUNT static method) (phenotypic.schema.QUALITY_ICC static method) (phenotypic.schema.QUALITY_MAD static method) (phenotypic.schema.QUALITY_SE static method) (phenotypic.schema.QUALITY_TUKEY static method) (phenotypic.schema.QUALITY_ZMAX static method) (phenotypic.schema.RADIAL_EXPANSION static method) (phenotypic.schema.SAMPLE_METADATA static method) (phenotypic.schema.SHAPE static method) (phenotypic.schema.SIZE static method) (phenotypic.schema.SYMMETRIC_ZONES static method) (phenotypic.schema.TEXTURE static method) (phenotypic.sdk_.constants_.ConstantLabels static method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS static method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS static method), [1] manifest_json_path() (in module phenotypic.sdk_), [1] ManualGridFinder (class in phenotypic.grid), [1] ManualGridPointDetector (class in phenotypic.detect), [1] ManualPointDetector (class in phenotypic.detect), [1] ManualRefine (class in phenotypic.refine), [1] mask (phenotypic.enhance.FocusEdgeLaplace attribute), [1] mask_fill_origin (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] mask_fill_structure (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] mask_opener_footprint (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] mask_opener_n_iter (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] mask_opener_width (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] MaskClosing (class in phenotypic.refine), [1] MaskDilation (class in phenotypic.refine), [1] MaskErosion (class in phenotypic.refine), [1] MaskFill (class in phenotypic.refine), [1] MaskGradient (class in phenotypic.refine), [1] MaskOpening (class in phenotypic.refine), [1] masks_for() (phenotypic.tune.GroundTruthMasks method), [1] MaskWhiteTophat (class in phenotypic.refine), [1] master_measurements_csv_path() (in module phenotypic.sdk_), [1] master_measurements_parquet_path() (in module phenotypic.sdk_), [1] match_strategy (phenotypic.tune.SupervisedScorer attribute), [1] matches_any_suffix() (in module phenotypic.sdk_), [1] MATING_TYPE (phenotypic.schema.GENETIC_METADATA attribute) MATRIX_FORMATS (phenotypic.sdk_.constants_.IMAGE_MODE attribute), [1] MAX_BRANCH_LENGTH (phenotypic.schema.RADIAL_EXPANSION attribute) MAX_CC (phenotypic.schema.BBOX attribute) max_coeff_variance (phenotypic.refine.RemoveGridOutliers attribute), [1] max_colony_radius_px (phenotypic.detect.FilamentousFungiDetector attribute), [1] max_diameter (phenotypic.detect.InoculumDetector attribute), [1] MAX_EXPANSION (phenotypic.schema.SYMMETRIC_ZONES attribute) max_failures (phenotypic.tune.Budget attribute), [1] MAX_FERET_DIAMETER (phenotypic.schema.SHAPE attribute) max_gap_length (phenotypic.detect.FilamentousFungiDetector attribute), [1] max_intensity (phenotypic.util.image_metrics.ImageMetricsCalculator property) (phenotypic.util.ImageMetricsCalculator property), [1] max_iter (phenotypic.grid.AutoGridFinder attribute), [1] (phenotypic.grid.CenteredAutoGridFinder attribute), [1] max_num_iter (phenotypic.detect.ChanVeseDetector attribute), [1] (phenotypic.refine.Thinning attribute), [1] max_radius (phenotypic.enhance.FocusBlobLoG attribute), [1] MAX_RADIUS (phenotypic.schema.SHAPE attribute) MAX_RR (phenotypic.schema.BBOX attribute) max_value (phenotypic.refine.RemoveByFeature attribute), [1] max_window_cost (phenotypic.sdk_.branch_pathfinding.PathMetrics attribute), [1] max_window_cost_values (phenotypic.sdk_.branch_pathfinding.CalibrationData attribute), [1] MAXIMUM_INTENSITY (phenotypic.schema.INTENSITY attribute) MaxModifiedZScore (class in phenotypic.analysis), [1] (class in phenotypic.analysis.qc) MEAN (phenotypic.schema.QUALITY_SE attribute) mean_coherence (phenotypic.util.image_metrics.StructureMetrics attribute) (phenotypic.util.StructureMetrics attribute), [1] mean_cost (phenotypic.sdk_.branch_pathfinding.FragmentAssignment attribute), [1] MEAN_EXPANSION (phenotypic.schema.SYMMETRIC_ZONES attribute) mean_gradient (phenotypic.util.BackgroundMetrics attribute), [1] (phenotypic.util.image_metrics.BackgroundMetrics attribute) MEAN_INTENSITY (phenotypic.schema.INTENSITY attribute) MEAN_RADIUS (phenotypic.schema.RADIAL_EXPANSION attribute) (phenotypic.schema.SHAPE attribute) MeanDetector (class in phenotypic.detect), [1] meas (phenotypic.abc_.PrefabPipeline attribute), [1] (phenotypic.prefab.FilamentousFungiPipeline attribute), [1] (phenotypic.prefab.GridSectionPipeline attribute), [1] (phenotypic.prefab.HeavyOtsuPipeline attribute), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] (phenotypic.prefab.HeavyWatershedPipeline attribute), [1] (phenotypic.prefab.RoundPeaksPipeline attribute), [1] (phenotypic.prefab.SpImagerPipeline attribute), [1] measure() (phenotypic.abc_.GridFinder method), [1] (phenotypic.abc_.GridMeasureFeatures method), [1] (phenotypic.abc_.MeasureFeatures method), [1] (phenotypic.abc_.PrefabPipeline method), [1] (phenotypic.grid.AutoGridFinder method), [1] (phenotypic.grid.CenteredAutoGridFinder method), [1] (phenotypic.grid.ManualGridFinder method), [1] (phenotypic.ImagePipeline method) (phenotypic.measure.MeasureBounds method), [1] (phenotypic.measure.MeasureColor method), [1] (phenotypic.measure.MeasureGridLinRegStats method), [1] (phenotypic.measure.MeasureGridSpatial method), [1] (phenotypic.measure.MeasureGridSpread method), [1] (phenotypic.measure.MeasureIntensity method), [1] (phenotypic.measure.MeasureShape method), [1] (phenotypic.measure.MeasureSize method), [1] (phenotypic.measure.MeasureSymmetricZones method), [1] (phenotypic.measure.MeasureTexture method), [1] (phenotypic.prefab.FilamentousFungiPipeline method), [1] (phenotypic.prefab.GridSectionPipeline method), [1] (phenotypic.prefab.HeavyOtsuPipeline method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1] (phenotypic.prefab.HeavyWatershedPipeline method), [1] (phenotypic.prefab.RoundPeaksPipeline method), [1] (phenotypic.prefab.SpImagerPipeline method), [1] measure_kwargs (phenotypic.refine.RemoveByFeature attribute), [1] MeasureBounds (class in phenotypic.measure), [1] MeasureColor (class in phenotypic.measure), [1] MEASURED (phenotypic.sdk_.constants_.PIPE_STATUS attribute), [1] MeasureFeatures (class in phenotypic.abc_), [1] MeasureGridLinRegStats (class in phenotypic.measure), [1] MeasureGridSpatial (class in phenotypic.measure), [1] MeasureGridSpread (class in phenotypic.measure), [1] MeasureIntensity (class in phenotypic.measure), [1] measurement_columns() (phenotypic.analysis.ErrorCutoffFinder method), [1] measurement_prefixes (phenotypic.analysis.ErrorCutoffFinder attribute), [1] MeasurementInfo (class in phenotypic.abc_), [1] (class in phenotypic.schema) measurements_by_feature_dir() (in module phenotypic.sdk_), [1] measurements_csv_path() (in module phenotypic.sdk_), [1] measurements_parquet_path() (in module phenotypic.sdk_), [1] MeasureShape (class in phenotypic.measure), [1] MeasureSize (class in phenotypic.measure), [1] MeasureSymmetricZones (class in phenotypic.measure), [1] MeasureTexture (class in phenotypic.measure), [1] MEDIA (phenotypic.schema.CONDITION_METADATA attribute) MEDIAN (phenotypic.schema.QUALITY_MAD attribute) (phenotypic.schema.QUALITY_ZMAX attribute) median_cost_values (phenotypic.sdk_.branch_pathfinding.CalibrationData attribute), [1] median_cval (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] median_filter_size (phenotypic.correction.ColorCheckerProfile attribute), [1] MEDIAN_INTENSITY (phenotypic.schema.INTENSITY attribute) median_mode (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] median_radius (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] MEDIAN_RADIUS (phenotypic.schema.RADIAL_EXPANSION attribute) (phenotypic.schema.SHAPE attribute) median_raw_cost (phenotypic.sdk_.branch_pathfinding.PathMetrics attribute), [1] median_shape (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] MedianFilter (class in phenotypic.enhance), [1] medoid_ciede2000() (in module phenotypic.util), [1] MEDOID_COLOR_HEX (phenotypic.schema.ColorLab attribute) medoid_max_pixels (phenotypic.measure.MeasureColor attribute), [1] MERGED (phenotypic.schema.ErrorCategory attribute) MergeFragmentChains (class in phenotypic.refine), [1] MergeMetadata (class in phenotypic.post) meta_validate() (phenotypic.tune.ReferenceFreeScorer method), [1] METADATA (class in phenotypic.schema) metadata (phenotypic.analysis.ExpectedVsDetectedCount attribute), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount attribute) (phenotypic.Image property) METADATA_CSV (phenotypic.sdk_.JobMetadataKey attribute), [1] metadata_source (phenotypic.analysis.ExpectedVsDetectedCount attribute), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount attribute) MetadataAccessor (class in phenotypic._core._image_parts.accessors._metadata_accessor) MetadataKeySpacesError, [1] MetadataKeyValueError, [1] MetadataValueNonScalarError, [1] method (phenotypic.abc_.FigureSpec attribute), [1], [2], [3] (phenotypic.measure.MeasureSymmetricZones attribute), [1] (phenotypic.refine.Skeletonize attribute), [1] (phenotypic.refine.TrimAsymmetry attribute), [1] (phenotypic.tune.ImportanceReport attribute), [1] (phenotypic.tune.ScreeningResult attribute), [1] METRIC (phenotypic.schema.QUALITY_CHECK attribute) metric_col() (phenotypic.analysis.abc_.QualityCheck class method) (phenotypic.analysis.ExpectedVsDetectedCount class method), [1] (phenotypic.analysis.ICC class method), [1] (phenotypic.analysis.MaxModifiedZScore class method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount class method) (phenotypic.analysis.qc.ICC class method) (phenotypic.analysis.qc.MaxModifiedZScore class method) (phenotypic.analysis.qc.RelativeMAD class method) (phenotypic.analysis.qc.ReplicateAgreement class method) (phenotypic.analysis.qc.TukeyOutlierFraction class method) (phenotypic.analysis.RelativeMAD class method), [1] (phenotypic.analysis.ReplicateAgreement class method), [1] (phenotypic.analysis.TukeyOutlierFraction class method), [1] metrics (phenotypic.sdk_.branch_pathfinding.FilterResult attribute), [1] michelson (phenotypic.util.ContrastMetrics attribute), [1] (phenotypic.util.image_metrics.ContrastMetrics attribute) migrate_legacy_machine_state() (in module phenotypic.sdk_), [1] min_area (phenotypic.tune.ReferenceFreeScorer attribute), [1] min_branch_width_px (phenotypic.detect.FilamentousFungiDetector attribute), [1] MIN_CC (phenotypic.schema.BBOX attribute) min_cc_area (phenotypic.refine.TrimAsymmetry attribute), [1] min_core_area (phenotypic.refine.ExtractColonyCore attribute), [1] min_diameter (phenotypic.detect.InoculumDetector attribute), [1] min_distance (phenotypic.refine.SeparateObjects attribute), [1] min_error_n (phenotypic.analysis.ErrorCutoffFinder attribute), [1] MIN_FERET_DIAMETER (phenotypic.schema.SHAPE attribute) min_fit_objects (phenotypic.grid.CenteredAutoGridFinder attribute), [1] min_good_n (phenotypic.analysis.ErrorCutoffFinder attribute), [1] min_heldout_plates (phenotypic.tune.HeldOutConfig attribute), [1] min_object_area (phenotypic.refine.TrimAsymmetry attribute), [1] min_overlap_ratio (phenotypic.detect.CompositeDetector attribute), [1] min_peak_distance (phenotypic.detect.RoundPeaksDetector attribute), [1] (phenotypic.detect.SinePeakDetector attribute), [1] (phenotypic.refine.GridAlignmentRefiner attribute), [1] (phenotypic.refine.RefineBySineFit attribute), [1] min_radius (phenotypic.enhance.FocusBlobLoG attribute), [1] min_replicates (phenotypic.analysis.MaxModifiedZScore attribute), [1] (phenotypic.analysis.qc.MaxModifiedZScore attribute) (phenotypic.analysis.qc.RelativeMAD attribute) (phenotypic.analysis.qc.ReplicateAgreement attribute) (phenotypic.analysis.qc.TukeyOutlierFraction attribute) (phenotypic.analysis.RelativeMAD attribute), [1] (phenotypic.analysis.ReplicateAgreement attribute), [1] (phenotypic.analysis.TukeyOutlierFraction attribute), [1] MIN_RR (phenotypic.schema.BBOX attribute) min_rungs (phenotypic.tune.Evaluator attribute), [1] min_samples_per_ring (phenotypic.measure.MeasureSymmetricZones attribute), [1] min_size (phenotypic.detect.CannyDetector attribute), [1] (phenotypic.detect.ChanVeseDetector attribute), [1] (phenotypic.detect.MadHysteresisDetector attribute), [1] (phenotypic.detect.WatershedDetector attribute), [1] (phenotypic.refine.NearestNeighborMerger attribute), [1] (phenotypic.refine.SmallObjectRemover attribute), [1] min_stability_n (phenotypic.tune.Evaluator attribute), [1] min_swatch_area_frac (phenotypic.correction.ColorCheckerProfile attribute), [1] min_value (phenotypic.refine.RemoveByFeature attribute), [1] min_wavelength (phenotypic.enhance.FocusEdgePhase attribute), [1] MINIMUM_INTENSITY (phenotypic.schema.INTENSITY attribute) MinimumDetector (class in phenotypic.detect), [1] MINOR_AXIS_LENGTH (phenotypic.schema.SHAPE attribute) modality() (phenotypic.tune.GroundTruthMasks method), [1] mode (phenotypic.correction.BayesShrinkCorrector attribute), [1] (phenotypic.correction.GridAligner attribute), [1] (phenotypic.correction.ImagePadder attribute), [1] (phenotypic.correction.VisuShrinkCorrector attribute), [1] (phenotypic.detect.CompositeDetector attribute), [1] (phenotypic.enhance.BayesShrinkEnhancer attribute), [1] (phenotypic.enhance.FocusEdgeHessian attribute), [1] (phenotypic.enhance.FocusEdgeMeijering attribute), [1] (phenotypic.enhance.FocusEdgeSato attribute), [1] (phenotypic.enhance.GaussianBlur attribute), [1] (phenotypic.enhance.LocalEdgeDenoise attribute), [1] (phenotypic.enhance.MedianFilter attribute), [1] (phenotypic.enhance.SetDetectMode attribute), [1] (phenotypic.enhance.SubtractGaussian attribute), [1] (phenotypic.enhance.VisuShrinkEnhancer attribute), [1] (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL attribute) (phenotypic.sdk_.HDF attribute), [1], [2], [3] (phenotypic.sdk_.hdf_.HDF attribute), [1] model (phenotypic.abc_.PrefabPipeline attribute), [1] (phenotypic.prefab.FilamentousFungiPipeline attribute), [1] (phenotypic.prefab.GridSectionPipeline attribute), [1] (phenotypic.prefab.HeavyOtsuPipeline attribute), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] (phenotypic.prefab.HeavyWatershedPipeline attribute), [1] (phenotypic.prefab.RoundPeaksPipeline attribute), [1] (phenotypic.prefab.SpImagerPipeline attribute), [1] model_computed_fields (phenotypic.abc_.BackgroundSubtraction attribute), [1] (phenotypic.abc_.BaseOperation attribute), [1] (phenotypic.abc_.ContrastAdjustment attribute), [1] (phenotypic.abc_.FocusBlob attribute), [1] (phenotypic.abc_.FocusEdge attribute), [1] (phenotypic.abc_.GpuDetector attribute), [1] (phenotypic.abc_.GridCorrector attribute), [1] (phenotypic.abc_.GridFinder attribute), [1] (phenotypic.abc_.GridMeasureFeatures attribute), [1] (phenotypic.abc_.GridObjectDetector attribute), [1] (phenotypic.abc_.GridObjectRefiner attribute), [1] (phenotypic.abc_.GridOperation attribute), [1] (phenotypic.abc_.ImageCorrector attribute), [1] (phenotypic.abc_.ImageDenoiser attribute), [1] (phenotypic.abc_.ImageEnhancer attribute), [1] (phenotypic.abc_.ImageOperation attribute), [1] (phenotypic.abc_.MeasureFeatures attribute), [1] (phenotypic.abc_.MorphologicalFiltering attribute), [1] (phenotypic.abc_.ObjectDetector attribute), [1] (phenotypic.abc_.ObjectRefiner attribute), [1] (phenotypic.abc_.PostMeasurement attribute), [1] (phenotypic.abc_.PrefabPipeline attribute), [1] (phenotypic.abc_.Smoothing attribute), [1] (phenotypic.abc_.ThresholdDetector attribute), [1] (phenotypic.analysis.abc_.ModelFitter attribute) (phenotypic.analysis.abc_.QualityCheck attribute) (phenotypic.analysis.abc_.SetAnalyzer attribute) (phenotypic.analysis.DoubleSoftplus attribute), [1] (phenotypic.analysis.EdgeCorrector attribute), [1] (phenotypic.analysis.ErrorCutoffFinder attribute), [1] (phenotypic.analysis.ExpectedVsDetectedCount attribute), [1] (phenotypic.analysis.ICC attribute), [1] (phenotypic.analysis.LinearSoftplus attribute), [1] (phenotypic.analysis.LogGrowthModel attribute), [1] (phenotypic.analysis.MADOutlierRemover attribute), [1] (phenotypic.analysis.MaxModifiedZScore attribute), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount attribute) (phenotypic.analysis.qc.ICC attribute) (phenotypic.analysis.qc.MaxModifiedZScore attribute) (phenotypic.analysis.qc.RelativeMAD attribute) (phenotypic.analysis.qc.ReplicateAgreement attribute) (phenotypic.analysis.qc.TukeyOutlierFraction attribute) (phenotypic.analysis.RelativeMAD attribute), [1] (phenotypic.analysis.ReplicateAgreement attribute), [1] (phenotypic.analysis.TukeyOutlierFraction attribute), [1] (phenotypic.analysis.TukeyOutlierRemover attribute), [1] (phenotypic.correction.BayesShrinkCorrector attribute), [1] (phenotypic.correction.CaptureMetadata attribute), [1] (phenotypic.correction.ColorCheckerProfile attribute), [1] (phenotypic.correction.ColorCorrector attribute), [1] (phenotypic.correction.ColorDenoise attribute), [1] (phenotypic.correction.DenoiseBlockMatch attribute), [1] (phenotypic.correction.GridAligner attribute), [1] (phenotypic.correction.ImageCropper attribute), [1] (phenotypic.correction.ImagePadder attribute), [1] (phenotypic.correction.VisuShrinkCorrector attribute), [1] (phenotypic.detect.CannyDetector attribute), [1] (phenotypic.detect.ChanVeseDetector attribute), [1] (phenotypic.detect.CompositeDetector attribute), [1] (phenotypic.detect.FilamentousFungiDetector attribute), [1] (phenotypic.detect.HysteresisDetector attribute), [1] (phenotypic.detect.InoculumDetector attribute), [1] (phenotypic.detect.IsodataDetector attribute), [1] (phenotypic.detect.LiDetector attribute), [1] (phenotypic.detect.MadHysteresisDetector attribute), [1] (phenotypic.detect.ManualGridPointDetector attribute), [1] (phenotypic.detect.ManualPointDetector attribute), [1] (phenotypic.detect.MeanDetector attribute), [1] (phenotypic.detect.MinimumDetector attribute), [1] (phenotypic.detect.OtsuDetector attribute), [1] (phenotypic.detect.RankOtsuDetector attribute), [1] (phenotypic.detect.RoundPeaksDetector attribute), [1] (phenotypic.detect.SecondaryOtsuDetector attribute), [1] (phenotypic.detect.SinePeakDetector attribute), [1] (phenotypic.detect.TriangleDetector attribute), [1] (phenotypic.detect.UserThreshold attribute), [1] (phenotypic.detect.WatershedDetector attribute), [1] (phenotypic.detect.YenDetector attribute), [1] (phenotypic.enhance.BayesShrinkEnhancer attribute), [1] (phenotypic.enhance.ContrastStretching attribute), [1] (phenotypic.enhance.EnhanceBlockMatch attribute), [1] (phenotypic.enhance.EnhanceLocalContrast attribute), [1] (phenotypic.enhance.FlattenIllumination attribute), [1] (phenotypic.enhance.FocusBlobLoG attribute), [1] (phenotypic.enhance.FocusEdgeFrangi attribute), [1] (phenotypic.enhance.FocusEdgeHessian attribute), [1] (phenotypic.enhance.FocusEdgeLaplace attribute), [1] (phenotypic.enhance.FocusEdgeMeijering attribute), [1] (phenotypic.enhance.FocusEdgePhase attribute), [1] (phenotypic.enhance.FocusEdgeSato attribute), [1] (phenotypic.enhance.FocusEdgeSobel attribute), [1] (phenotypic.enhance.GaussianBlur attribute), [1] (phenotypic.enhance.GrayOpening attribute), [1] (phenotypic.enhance.ImageInverter attribute), [1] (phenotypic.enhance.LocalEdgeDenoise attribute), [1] (phenotypic.enhance.MedianFilter attribute), [1] (phenotypic.enhance.NonLocalMeansDenoiser attribute), [1] (phenotypic.enhance.RankMedianEnhancer attribute), [1] (phenotypic.enhance.SetDetectMode attribute), [1] (phenotypic.enhance.SharpenEdgeGauss attribute), [1] (phenotypic.enhance.StructureSmoothing attribute), [1] (phenotypic.enhance.SubtractGaussian attribute), [1] (phenotypic.enhance.SubtractOpening attribute), [1] (phenotypic.enhance.SubtractRollingBall attribute), [1] (phenotypic.enhance.SubtractWhiteTophat attribute), [1] (phenotypic.enhance.VisuShrinkEnhancer attribute), [1] (phenotypic.enhance.WhiteTophatEnhance attribute), [1] (phenotypic.grid.AutoGridFinder attribute), [1] (phenotypic.grid.CenteredAutoGridFinder attribute), [1] (phenotypic.grid.GridApply attribute), [1] (phenotypic.grid.ManualGridFinder attribute), [1] (phenotypic.measure.MeasureBounds attribute), [1] (phenotypic.measure.MeasureColor attribute), [1] (phenotypic.measure.MeasureGridLinRegStats attribute), [1] (phenotypic.measure.MeasureGridSpatial attribute), [1] (phenotypic.measure.MeasureGridSpread attribute), [1] (phenotypic.measure.MeasureIntensity attribute), [1] (phenotypic.measure.MeasureShape attribute), [1] (phenotypic.measure.MeasureSize attribute), [1] (phenotypic.measure.MeasureSymmetricZones attribute), [1] (phenotypic.measure.MeasureTexture attribute), [1] (phenotypic.post.AppendString attribute) (phenotypic.post.ExpandMetadata attribute) (phenotypic.post.MergeMetadata attribute) (phenotypic.post.PrependString attribute) (phenotypic.prefab.FilamentousFungiPipeline attribute), [1] (phenotypic.prefab.GridSectionPipeline attribute), [1] (phenotypic.prefab.HeavyOtsuPipeline attribute), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] (phenotypic.prefab.HeavyWatershedPipeline attribute), [1] (phenotypic.prefab.RoundPeaksPipeline attribute), [1] (phenotypic.prefab.SpImagerPipeline attribute), [1] (phenotypic.refine.ExtractColonyCore attribute), [1] (phenotypic.refine.GridAlignmentRefiner attribute), [1] (phenotypic.refine.GridOversizedObjectRemover attribute), [1] (phenotypic.refine.KeepNearestCenter attribute), [1] (phenotypic.refine.KeepSectionLargest attribute), [1] (phenotypic.refine.ManualRefine attribute), [1] (phenotypic.refine.MaskClosing attribute), [1] (phenotypic.refine.MaskDilation attribute), [1] (phenotypic.refine.MaskErosion attribute), [1] (phenotypic.refine.MaskFill attribute), [1] (phenotypic.refine.MaskGradient attribute), [1] (phenotypic.refine.MaskOpening attribute), [1] (phenotypic.refine.MaskWhiteTophat attribute), [1] (phenotypic.refine.MergeFragmentChains attribute), [1] (phenotypic.refine.NearestNeighborMerger attribute), [1] (phenotypic.refine.ReduceSectionsByLine attribute), [1] (phenotypic.refine.RefineBySineFit attribute), [1] (phenotypic.refine.RemoveBorderObjects attribute), [1] (phenotypic.refine.RemoveByFeature attribute), [1] (phenotypic.refine.RemoveGridOutliers attribute), [1] (phenotypic.refine.RemoveLowCircularity attribute), [1] (phenotypic.refine.SeparateObjects attribute), [1] (phenotypic.refine.Skeletonize attribute), [1] (phenotypic.refine.SmallObjectRemover attribute), [1] (phenotypic.refine.SmallToLargeMerger attribute), [1] (phenotypic.refine.Thinning attribute), [1] (phenotypic.refine.TrimAsymmetry attribute), [1] (phenotypic.tune.Budget attribute), [1] (phenotypic.tune.Categorical attribute), [1] (phenotypic.tune.CompositeScorer attribute), [1] (phenotypic.tune.EvaluationResult attribute), [1] (phenotypic.tune.Evaluator attribute), [1] (phenotypic.tune.Excluded attribute), [1] (phenotypic.tune.Fixed attribute), [1] (phenotypic.tune.FloatRange attribute), [1] (phenotypic.tune.GridConfig attribute), [1] (phenotypic.tune.GroundTruthMasks attribute), [1] (phenotypic.tune.HeldOutConfig attribute), [1] (phenotypic.tune.ImportanceReport attribute), [1] (phenotypic.tune.InferredSearchSpace attribute), [1] (phenotypic.tune.IntRange attribute), [1] (phenotypic.tune.Knob attribute), [1] (phenotypic.tune.OptunaConfig attribute), [1] (phenotypic.tune.QCScorer attribute), [1] (phenotypic.tune.RandomConfig attribute), [1] (phenotypic.tune.ReferenceFreeScorer attribute), [1] (phenotypic.tune.Scorer attribute), [1] (phenotypic.tune.SearchSpace attribute), [1] (phenotypic.tune.StrategyConfig attribute), [1] (phenotypic.tune.SupervisedScorer attribute), [1] (phenotypic.tune.targets.Nested attribute) (phenotypic.tune.targets.Param attribute) (phenotypic.tune.targets.Presence attribute) (phenotypic.tune.targets.TunableParam attribute) (phenotypic.tune.Trial attribute), [1] (phenotypic.tune.TuningSpec attribute), [1] model_config (phenotypic.abc_.BackgroundSubtraction attribute), [1] (phenotypic.abc_.BaseOperation attribute), [1] (phenotypic.abc_.ContrastAdjustment attribute), [1] (phenotypic.abc_.FocusBlob attribute), [1] (phenotypic.abc_.FocusEdge attribute), [1] (phenotypic.abc_.GpuDetector attribute), [1] (phenotypic.abc_.GridCorrector attribute), [1] (phenotypic.abc_.GridFinder attribute), [1] (phenotypic.abc_.GridMeasureFeatures attribute), [1] (phenotypic.abc_.GridObjectDetector attribute), [1] (phenotypic.abc_.GridObjectRefiner attribute), [1] (phenotypic.abc_.GridOperation attribute), [1] (phenotypic.abc_.ImageCorrector attribute), [1] (phenotypic.abc_.ImageDenoiser attribute), [1] (phenotypic.abc_.ImageEnhancer attribute), [1] (phenotypic.abc_.ImageOperation attribute), [1] (phenotypic.abc_.MeasureFeatures attribute), [1] (phenotypic.abc_.MorphologicalFiltering attribute), [1] (phenotypic.abc_.ObjectDetector attribute), [1] (phenotypic.abc_.ObjectRefiner attribute), [1] (phenotypic.abc_.PostMeasurement attribute), [1] (phenotypic.abc_.PrefabPipeline attribute), [1] (phenotypic.abc_.Smoothing attribute), [1] (phenotypic.abc_.ThresholdDetector attribute), [1] (phenotypic.analysis.abc_.ModelFitter attribute) (phenotypic.analysis.abc_.QualityCheck attribute) (phenotypic.analysis.abc_.SetAnalyzer attribute) (phenotypic.analysis.DoubleSoftplus attribute), [1] (phenotypic.analysis.EdgeCorrector attribute), [1] (phenotypic.analysis.ErrorCutoffFinder attribute), [1] (phenotypic.analysis.ExpectedVsDetectedCount attribute), [1] (phenotypic.analysis.ICC attribute), [1] (phenotypic.analysis.LinearSoftplus attribute), [1] (phenotypic.analysis.LogGrowthModel attribute), [1] (phenotypic.analysis.MADOutlierRemover attribute), [1] (phenotypic.analysis.MaxModifiedZScore attribute), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount attribute) (phenotypic.analysis.qc.ICC attribute) (phenotypic.analysis.qc.MaxModifiedZScore attribute) (phenotypic.analysis.qc.RelativeMAD attribute) (phenotypic.analysis.qc.ReplicateAgreement attribute) (phenotypic.analysis.qc.TukeyOutlierFraction attribute) (phenotypic.analysis.RelativeMAD attribute), [1] (phenotypic.analysis.ReplicateAgreement attribute), [1] (phenotypic.analysis.TukeyOutlierFraction attribute), [1] (phenotypic.analysis.TukeyOutlierRemover attribute), [1] (phenotypic.correction.BayesShrinkCorrector attribute), [1] (phenotypic.correction.CaptureMetadata attribute), [1] (phenotypic.correction.ColorCheckerProfile attribute), [1] (phenotypic.correction.ColorCorrector attribute), [1] (phenotypic.correction.ColorDenoise attribute), [1] (phenotypic.correction.DenoiseBlockMatch attribute), [1] (phenotypic.correction.GridAligner attribute), [1] (phenotypic.correction.ImageCropper attribute), [1] (phenotypic.correction.ImagePadder attribute), [1] (phenotypic.correction.VisuShrinkCorrector attribute), [1] (phenotypic.detect.CannyDetector attribute), [1] (phenotypic.detect.ChanVeseDetector attribute), [1] (phenotypic.detect.CompositeDetector attribute), [1] (phenotypic.detect.FilamentousFungiDetector attribute), [1] (phenotypic.detect.HysteresisDetector attribute), [1] (phenotypic.detect.InoculumDetector attribute), [1] (phenotypic.detect.IsodataDetector attribute), [1] (phenotypic.detect.LiDetector attribute), [1] (phenotypic.detect.MadHysteresisDetector attribute), [1] (phenotypic.detect.ManualGridPointDetector attribute), [1] (phenotypic.detect.ManualPointDetector attribute), [1] (phenotypic.detect.MeanDetector attribute), [1] (phenotypic.detect.MinimumDetector attribute), [1] (phenotypic.detect.OtsuDetector attribute), [1] (phenotypic.detect.RankOtsuDetector attribute), [1] (phenotypic.detect.RoundPeaksDetector attribute), [1] (phenotypic.detect.SecondaryOtsuDetector attribute), [1] (phenotypic.detect.SinePeakDetector attribute), [1] (phenotypic.detect.TriangleDetector attribute), [1] (phenotypic.detect.UserThreshold attribute), [1] (phenotypic.detect.WatershedDetector attribute), [1] (phenotypic.detect.YenDetector attribute), [1] (phenotypic.enhance.BayesShrinkEnhancer attribute), [1] (phenotypic.enhance.ContrastStretching attribute), [1] (phenotypic.enhance.EnhanceBlockMatch attribute), [1] (phenotypic.enhance.EnhanceLocalContrast attribute), [1] (phenotypic.enhance.FlattenIllumination attribute), [1] (phenotypic.enhance.FocusBlobLoG attribute), [1] (phenotypic.enhance.FocusEdgeFrangi attribute), [1] (phenotypic.enhance.FocusEdgeHessian attribute), [1] (phenotypic.enhance.FocusEdgeLaplace attribute), [1] (phenotypic.enhance.FocusEdgeMeijering attribute), [1] (phenotypic.enhance.FocusEdgePhase attribute), [1] (phenotypic.enhance.FocusEdgeSato attribute), [1] (phenotypic.enhance.FocusEdgeSobel attribute), [1] (phenotypic.enhance.GaussianBlur attribute), [1] (phenotypic.enhance.GrayOpening attribute), [1] (phenotypic.enhance.ImageInverter attribute), [1] (phenotypic.enhance.LocalEdgeDenoise attribute), [1] (phenotypic.enhance.MedianFilter attribute), [1] (phenotypic.enhance.NonLocalMeansDenoiser attribute), [1] (phenotypic.enhance.RankMedianEnhancer attribute), [1] (phenotypic.enhance.SetDetectMode attribute), [1] (phenotypic.enhance.SharpenEdgeGauss attribute), [1] (phenotypic.enhance.StructureSmoothing attribute), [1] (phenotypic.enhance.SubtractGaussian attribute), [1] (phenotypic.enhance.SubtractOpening attribute), [1] (phenotypic.enhance.SubtractRollingBall attribute), [1] (phenotypic.enhance.SubtractWhiteTophat attribute), [1] (phenotypic.enhance.VisuShrinkEnhancer attribute), [1] (phenotypic.enhance.WhiteTophatEnhance attribute), [1] (phenotypic.grid.AutoGridFinder attribute), [1] (phenotypic.grid.CenteredAutoGridFinder attribute), [1] (phenotypic.grid.GridApply attribute), [1] (phenotypic.grid.ManualGridFinder attribute), [1] (phenotypic.measure.MeasureBounds attribute), [1] (phenotypic.measure.MeasureColor attribute), [1] (phenotypic.measure.MeasureGridLinRegStats attribute), [1] (phenotypic.measure.MeasureGridSpatial attribute), [1] (phenotypic.measure.MeasureGridSpread attribute), [1] (phenotypic.measure.MeasureIntensity attribute), [1] (phenotypic.measure.MeasureShape attribute), [1] (phenotypic.measure.MeasureSize attribute), [1] (phenotypic.measure.MeasureSymmetricZones attribute), [1] (phenotypic.measure.MeasureTexture attribute), [1] (phenotypic.post.AppendString attribute) (phenotypic.post.ExpandMetadata attribute) (phenotypic.post.MergeMetadata attribute) (phenotypic.post.PrependString attribute) (phenotypic.prefab.FilamentousFungiPipeline attribute), [1] (phenotypic.prefab.GridSectionPipeline attribute), [1] (phenotypic.prefab.HeavyOtsuPipeline attribute), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] (phenotypic.prefab.HeavyWatershedPipeline attribute), [1] (phenotypic.prefab.RoundPeaksPipeline attribute), [1] (phenotypic.prefab.SpImagerPipeline attribute), [1] (phenotypic.refine.ExtractColonyCore attribute), [1] (phenotypic.refine.GridAlignmentRefiner attribute), [1] (phenotypic.refine.GridOversizedObjectRemover attribute), [1] (phenotypic.refine.KeepNearestCenter attribute), [1] (phenotypic.refine.KeepSectionLargest attribute), [1] (phenotypic.refine.ManualRefine attribute), [1] (phenotypic.refine.MaskClosing attribute), [1] (phenotypic.refine.MaskDilation attribute), [1] (phenotypic.refine.MaskErosion attribute), [1] (phenotypic.refine.MaskFill attribute), [1] (phenotypic.refine.MaskGradient attribute), [1] (phenotypic.refine.MaskOpening attribute), [1] (phenotypic.refine.MaskWhiteTophat attribute), [1] (phenotypic.refine.MergeFragmentChains attribute), [1] (phenotypic.refine.NearestNeighborMerger attribute), [1] (phenotypic.refine.ReduceSectionsByLine attribute), [1] (phenotypic.refine.RefineBySineFit attribute), [1] (phenotypic.refine.RemoveBorderObjects attribute), [1] (phenotypic.refine.RemoveByFeature attribute), [1] (phenotypic.refine.RemoveGridOutliers attribute), [1] (phenotypic.refine.RemoveLowCircularity attribute), [1] (phenotypic.refine.SeparateObjects attribute), [1] (phenotypic.refine.Skeletonize attribute), [1] (phenotypic.refine.SmallObjectRemover attribute), [1] (phenotypic.refine.SmallToLargeMerger attribute), [1] (phenotypic.refine.Thinning attribute), [1] (phenotypic.refine.TrimAsymmetry attribute), [1] (phenotypic.tune.Budget attribute), [1] (phenotypic.tune.Categorical attribute), [1] (phenotypic.tune.CompositeScorer attribute), [1] (phenotypic.tune.EvaluationResult attribute), [1] (phenotypic.tune.Evaluator attribute), [1] (phenotypic.tune.Excluded attribute), [1] (phenotypic.tune.Fixed attribute), [1] (phenotypic.tune.FloatRange attribute), [1] (phenotypic.tune.GridConfig attribute), [1] (phenotypic.tune.GroundTruthMasks attribute), [1] (phenotypic.tune.HeldOutConfig attribute), [1] (phenotypic.tune.ImportanceReport attribute), [1] (phenotypic.tune.InferredSearchSpace attribute), [1] (phenotypic.tune.IntRange attribute), [1] (phenotypic.tune.Knob attribute), [1] (phenotypic.tune.OptunaConfig attribute), [1] (phenotypic.tune.QCScorer attribute), [1] (phenotypic.tune.RandomConfig attribute), [1] (phenotypic.tune.ReferenceFreeScorer attribute), [1] (phenotypic.tune.Scorer attribute), [1] (phenotypic.tune.SearchSpace attribute), [1] (phenotypic.tune.StrategyConfig attribute), [1] (phenotypic.tune.SupervisedScorer attribute), [1] (phenotypic.tune.targets.Nested attribute) (phenotypic.tune.targets.Param attribute) (phenotypic.tune.targets.Presence attribute) (phenotypic.tune.targets.TunableParam attribute) (phenotypic.tune.Trial attribute), [1] (phenotypic.tune.TuningSpec attribute), [1] model_construct() (phenotypic.abc_.BackgroundSubtraction class method), [1] (phenotypic.abc_.BaseOperation class method), [1] (phenotypic.abc_.ContrastAdjustment class method), [1] (phenotypic.abc_.FocusBlob class method), [1] (phenotypic.abc_.FocusEdge class method), [1] (phenotypic.abc_.GpuDetector class method), [1] (phenotypic.abc_.GridCorrector class method), [1] (phenotypic.abc_.GridFinder class method), [1] (phenotypic.abc_.GridMeasureFeatures class method), [1] (phenotypic.abc_.GridObjectDetector class method), [1] (phenotypic.abc_.GridObjectRefiner class method), [1] (phenotypic.abc_.GridOperation class method), [1] (phenotypic.abc_.ImageCorrector class method), [1] (phenotypic.abc_.ImageDenoiser class method), [1] (phenotypic.abc_.ImageEnhancer class method), [1] (phenotypic.abc_.ImageOperation class method), [1] (phenotypic.abc_.MeasureFeatures class method), [1] (phenotypic.abc_.MorphologicalFiltering class method), [1] (phenotypic.abc_.ObjectDetector class method), [1] (phenotypic.abc_.ObjectRefiner class method), [1] (phenotypic.abc_.PostMeasurement class method), [1] (phenotypic.abc_.PrefabPipeline class method), [1] (phenotypic.abc_.Smoothing class method), [1] (phenotypic.abc_.ThresholdDetector class method), [1] (phenotypic.analysis.abc_.ModelFitter class method) (phenotypic.analysis.abc_.QualityCheck class method) (phenotypic.analysis.abc_.SetAnalyzer class method) (phenotypic.analysis.DoubleSoftplus class method), [1] (phenotypic.analysis.EdgeCorrector class method), [1] (phenotypic.analysis.ErrorCutoffFinder class method), [1] (phenotypic.analysis.ExpectedVsDetectedCount class method), [1] (phenotypic.analysis.ICC class method), [1] (phenotypic.analysis.LinearSoftplus class method), [1] (phenotypic.analysis.LogGrowthModel class method), [1] (phenotypic.analysis.MADOutlierRemover class method), [1] (phenotypic.analysis.MaxModifiedZScore class method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount class method) (phenotypic.analysis.qc.ICC class method) (phenotypic.analysis.qc.MaxModifiedZScore class method) (phenotypic.analysis.qc.RelativeMAD class method) (phenotypic.analysis.qc.ReplicateAgreement class method) (phenotypic.analysis.qc.TukeyOutlierFraction class method) (phenotypic.analysis.RelativeMAD class method), [1] (phenotypic.analysis.ReplicateAgreement class method), [1] (phenotypic.analysis.TukeyOutlierFraction class method), [1] (phenotypic.analysis.TukeyOutlierRemover class method), [1] (phenotypic.correction.BayesShrinkCorrector class method), [1] (phenotypic.correction.CaptureMetadata class method), [1] (phenotypic.correction.ColorCheckerProfile class method), [1] (phenotypic.correction.ColorCorrector class method), [1] (phenotypic.correction.ColorDenoise class method), [1] (phenotypic.correction.DenoiseBlockMatch class method), [1] (phenotypic.correction.GridAligner class method), [1] (phenotypic.correction.ImageCropper class method), [1] (phenotypic.correction.ImagePadder class method), [1] (phenotypic.correction.VisuShrinkCorrector class method), [1] (phenotypic.detect.CannyDetector class method), [1] (phenotypic.detect.ChanVeseDetector class method), [1] (phenotypic.detect.CompositeDetector class method), [1] (phenotypic.detect.FilamentousFungiDetector class method), [1] (phenotypic.detect.HysteresisDetector class method), [1] (phenotypic.detect.InoculumDetector class method), [1] (phenotypic.detect.IsodataDetector class method), [1] (phenotypic.detect.LiDetector class method), [1] (phenotypic.detect.MadHysteresisDetector class method), [1] (phenotypic.detect.ManualGridPointDetector class method), [1] (phenotypic.detect.ManualPointDetector class method), [1] (phenotypic.detect.MeanDetector class method), [1] (phenotypic.detect.MinimumDetector class method), [1] (phenotypic.detect.OtsuDetector class method), [1] (phenotypic.detect.RankOtsuDetector class method), [1] (phenotypic.detect.RoundPeaksDetector class method), [1] (phenotypic.detect.SecondaryOtsuDetector class method), [1] (phenotypic.detect.SinePeakDetector class method), [1] (phenotypic.detect.TriangleDetector class method), [1] (phenotypic.detect.UserThreshold class method), [1] (phenotypic.detect.WatershedDetector class method), [1] (phenotypic.detect.YenDetector class method), [1] (phenotypic.enhance.BayesShrinkEnhancer class method), [1] (phenotypic.enhance.ContrastStretching class method), [1] (phenotypic.enhance.EnhanceBlockMatch class method), [1] (phenotypic.enhance.EnhanceLocalContrast class method), [1] (phenotypic.enhance.FlattenIllumination class method), [1] (phenotypic.enhance.FocusBlobLoG class method), [1] (phenotypic.enhance.FocusEdgeFrangi class method), [1] (phenotypic.enhance.FocusEdgeHessian class method), [1] (phenotypic.enhance.FocusEdgeLaplace class method), [1] (phenotypic.enhance.FocusEdgeMeijering class method), [1] (phenotypic.enhance.FocusEdgePhase class method), [1] (phenotypic.enhance.FocusEdgeSato class method), [1] (phenotypic.enhance.FocusEdgeSobel class method), [1] (phenotypic.enhance.GaussianBlur class method), [1] (phenotypic.enhance.GrayOpening class method), [1] (phenotypic.enhance.ImageInverter class method), [1] (phenotypic.enhance.LocalEdgeDenoise class method), [1] (phenotypic.enhance.MedianFilter class method), [1] (phenotypic.enhance.NonLocalMeansDenoiser class method), [1] (phenotypic.enhance.RankMedianEnhancer class method), [1] (phenotypic.enhance.SetDetectMode class method), [1] (phenotypic.enhance.SharpenEdgeGauss class method), [1] (phenotypic.enhance.StructureSmoothing class method), [1] (phenotypic.enhance.SubtractGaussian class method), [1] (phenotypic.enhance.SubtractOpening class method), [1] (phenotypic.enhance.SubtractRollingBall class method), [1] (phenotypic.enhance.SubtractWhiteTophat class method), [1] (phenotypic.enhance.VisuShrinkEnhancer class method), [1] (phenotypic.enhance.WhiteTophatEnhance class method), [1] (phenotypic.grid.AutoGridFinder class method), [1] (phenotypic.grid.CenteredAutoGridFinder class method), [1] (phenotypic.grid.GridApply class method), [1] (phenotypic.grid.ManualGridFinder class method), [1] (phenotypic.measure.MeasureBounds class method), [1] (phenotypic.measure.MeasureColor class method), [1] (phenotypic.measure.MeasureGridLinRegStats class method), [1] (phenotypic.measure.MeasureGridSpatial class method), [1] (phenotypic.measure.MeasureGridSpread class method), [1] (phenotypic.measure.MeasureIntensity class method), [1] (phenotypic.measure.MeasureShape class method), [1] (phenotypic.measure.MeasureSize class method), [1] (phenotypic.measure.MeasureSymmetricZones class method), [1] (phenotypic.measure.MeasureTexture class method), [1] (phenotypic.post.AppendString class method) (phenotypic.post.ExpandMetadata class method) (phenotypic.post.MergeMetadata class method) (phenotypic.post.PrependString class method) (phenotypic.prefab.FilamentousFungiPipeline class method), [1] (phenotypic.prefab.GridSectionPipeline class method), [1] (phenotypic.prefab.HeavyOtsuPipeline class method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline class method), [1] (phenotypic.prefab.HeavyWatershedPipeline class method), [1] (phenotypic.prefab.RoundPeaksPipeline class method), [1] (phenotypic.prefab.SpImagerPipeline class method), [1] (phenotypic.refine.ExtractColonyCore class method), [1] (phenotypic.refine.GridAlignmentRefiner class method), [1] (phenotypic.refine.GridOversizedObjectRemover class method), [1] (phenotypic.refine.KeepNearestCenter class method), [1] (phenotypic.refine.KeepSectionLargest class method), [1] (phenotypic.refine.ManualRefine class method), [1] (phenotypic.refine.MaskClosing class method), [1] (phenotypic.refine.MaskDilation class method), [1] (phenotypic.refine.MaskErosion class method), [1] (phenotypic.refine.MaskFill class method), [1] (phenotypic.refine.MaskGradient class method), [1] (phenotypic.refine.MaskOpening class method), [1] (phenotypic.refine.MaskWhiteTophat class method), [1] (phenotypic.refine.MergeFragmentChains class method), [1] (phenotypic.refine.NearestNeighborMerger class method), [1] (phenotypic.refine.ReduceSectionsByLine class method), [1] (phenotypic.refine.RefineBySineFit class method), [1] (phenotypic.refine.RemoveBorderObjects class method), [1] (phenotypic.refine.RemoveByFeature class method), [1] (phenotypic.refine.RemoveGridOutliers class method), [1] (phenotypic.refine.RemoveLowCircularity class method), [1] (phenotypic.refine.SeparateObjects class method), [1] (phenotypic.refine.Skeletonize class method), [1] (phenotypic.refine.SmallObjectRemover class method), [1] (phenotypic.refine.SmallToLargeMerger class method), [1] (phenotypic.refine.Thinning class method), [1] (phenotypic.refine.TrimAsymmetry class method), [1] (phenotypic.tune.Budget class method), [1] (phenotypic.tune.Categorical class method), [1] (phenotypic.tune.CompositeScorer class method), [1] (phenotypic.tune.EvaluationResult class method), [1] (phenotypic.tune.Evaluator class method), [1] (phenotypic.tune.Excluded class method), [1] (phenotypic.tune.Fixed class method), [1] (phenotypic.tune.FloatRange class method), [1] (phenotypic.tune.GridConfig class method), [1] (phenotypic.tune.GroundTruthMasks class method), [1] (phenotypic.tune.HeldOutConfig class method), [1] (phenotypic.tune.ImportanceReport class method), [1] (phenotypic.tune.InferredSearchSpace class method), [1] (phenotypic.tune.IntRange class method), [1] (phenotypic.tune.Knob class method), [1] (phenotypic.tune.OptunaConfig class method), [1] (phenotypic.tune.QCScorer class method), [1] (phenotypic.tune.RandomConfig class method), [1] (phenotypic.tune.ReferenceFreeScorer class method), [1] (phenotypic.tune.Scorer class method), [1] (phenotypic.tune.SearchSpace class method), [1] (phenotypic.tune.StrategyConfig class method), [1] (phenotypic.tune.SupervisedScorer class method), [1] (phenotypic.tune.targets.Nested class method) (phenotypic.tune.targets.Param class method) (phenotypic.tune.targets.Presence class method) (phenotypic.tune.targets.TunableParam class method) (phenotypic.tune.Trial class method), [1] (phenotypic.tune.TuningSpec class method), [1] model_copy() (phenotypic.abc_.BackgroundSubtraction method), [1] (phenotypic.abc_.BaseOperation method), [1] (phenotypic.abc_.ContrastAdjustment method), [1] (phenotypic.abc_.FocusBlob method), [1] (phenotypic.abc_.FocusEdge method), [1] (phenotypic.abc_.GpuDetector method), [1] (phenotypic.abc_.GridCorrector method), [1] (phenotypic.abc_.GridFinder method), [1] (phenotypic.abc_.GridMeasureFeatures method), [1] (phenotypic.abc_.GridObjectDetector method), [1] (phenotypic.abc_.GridObjectRefiner method), [1] (phenotypic.abc_.GridOperation method), [1] (phenotypic.abc_.ImageCorrector method), [1] (phenotypic.abc_.ImageDenoiser method), [1] (phenotypic.abc_.ImageEnhancer method), [1] (phenotypic.abc_.ImageOperation method), [1] (phenotypic.abc_.MeasureFeatures method), [1] (phenotypic.abc_.MorphologicalFiltering method), [1] (phenotypic.abc_.ObjectDetector method), [1] (phenotypic.abc_.ObjectRefiner method), [1] (phenotypic.abc_.PostMeasurement method), [1] (phenotypic.abc_.PrefabPipeline method), [1] (phenotypic.abc_.Smoothing method), [1] (phenotypic.abc_.ThresholdDetector method), [1] (phenotypic.analysis.abc_.ModelFitter method) (phenotypic.analysis.abc_.QualityCheck method) (phenotypic.analysis.abc_.SetAnalyzer method) (phenotypic.analysis.DoubleSoftplus method), [1] (phenotypic.analysis.EdgeCorrector method), [1] (phenotypic.analysis.ErrorCutoffFinder method), [1] (phenotypic.analysis.ExpectedVsDetectedCount method), [1] (phenotypic.analysis.ICC method), [1] (phenotypic.analysis.LinearSoftplus method), [1] (phenotypic.analysis.LogGrowthModel method), [1] (phenotypic.analysis.MADOutlierRemover method), [1] (phenotypic.analysis.MaxModifiedZScore method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount method) (phenotypic.analysis.qc.ICC method) (phenotypic.analysis.qc.MaxModifiedZScore method) (phenotypic.analysis.qc.RelativeMAD method) (phenotypic.analysis.qc.ReplicateAgreement method) (phenotypic.analysis.qc.TukeyOutlierFraction method) (phenotypic.analysis.RelativeMAD method), [1] (phenotypic.analysis.ReplicateAgreement method), [1] (phenotypic.analysis.TukeyOutlierFraction method), [1] (phenotypic.analysis.TukeyOutlierRemover method), [1] (phenotypic.correction.BayesShrinkCorrector method), [1] (phenotypic.correction.CaptureMetadata method), [1] (phenotypic.correction.ColorCheckerProfile method), [1] (phenotypic.correction.ColorCorrector method), [1] (phenotypic.correction.ColorDenoise method), [1] (phenotypic.correction.DenoiseBlockMatch method), [1] (phenotypic.correction.GridAligner method), [1] (phenotypic.correction.ImageCropper method), [1] (phenotypic.correction.ImagePadder method), [1] (phenotypic.correction.VisuShrinkCorrector method), [1] (phenotypic.detect.CannyDetector method), [1] (phenotypic.detect.ChanVeseDetector method), [1] 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(phenotypic.measure.MeasureGridSpread method), [1] (phenotypic.measure.MeasureIntensity method), [1] (phenotypic.measure.MeasureShape method), [1] (phenotypic.measure.MeasureSize method), [1] (phenotypic.measure.MeasureSymmetricZones method), [1] (phenotypic.measure.MeasureTexture method), [1] (phenotypic.post.AppendString method) (phenotypic.post.ExpandMetadata method) (phenotypic.post.MergeMetadata method) (phenotypic.post.PrependString method) (phenotypic.prefab.FilamentousFungiPipeline method), [1] (phenotypic.prefab.GridSectionPipeline method), [1] (phenotypic.prefab.HeavyOtsuPipeline method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1] (phenotypic.prefab.HeavyWatershedPipeline method), [1] (phenotypic.prefab.RoundPeaksPipeline method), [1] (phenotypic.prefab.SpImagerPipeline method), [1] (phenotypic.refine.ExtractColonyCore method), [1] (phenotypic.refine.GridAlignmentRefiner method), [1] (phenotypic.refine.GridOversizedObjectRemover method), [1] (phenotypic.refine.KeepNearestCenter method), [1] (phenotypic.refine.KeepSectionLargest method), [1] (phenotypic.refine.ManualRefine method), [1] (phenotypic.refine.MaskClosing method), [1] (phenotypic.refine.MaskDilation method), [1] (phenotypic.refine.MaskErosion method), [1] (phenotypic.refine.MaskFill method), [1] (phenotypic.refine.MaskGradient method), [1] (phenotypic.refine.MaskOpening method), [1] (phenotypic.refine.MaskWhiteTophat method), [1] (phenotypic.refine.MergeFragmentChains method), [1] (phenotypic.refine.NearestNeighborMerger method), [1] (phenotypic.refine.ReduceSectionsByLine method), [1] (phenotypic.refine.RefineBySineFit method), [1] (phenotypic.refine.RemoveBorderObjects method), [1] (phenotypic.refine.RemoveByFeature method), [1] (phenotypic.refine.RemoveGridOutliers method), [1] (phenotypic.refine.RemoveLowCircularity method), [1] (phenotypic.refine.SeparateObjects method), [1] (phenotypic.refine.Skeletonize method), [1] (phenotypic.refine.SmallObjectRemover method), [1] (phenotypic.refine.SmallToLargeMerger method), [1] (phenotypic.refine.Thinning method), [1] (phenotypic.refine.TrimAsymmetry method), [1] (phenotypic.tune.Budget method), [1] (phenotypic.tune.Categorical method), [1] (phenotypic.tune.CompositeScorer method), [1] (phenotypic.tune.EvaluationResult method), [1] (phenotypic.tune.Evaluator method), [1] (phenotypic.tune.Excluded method), [1] (phenotypic.tune.Fixed method), [1] (phenotypic.tune.FloatRange method), [1] (phenotypic.tune.GridConfig method), [1] (phenotypic.tune.GroundTruthMasks method), [1] (phenotypic.tune.HeldOutConfig method), [1] (phenotypic.tune.ImportanceReport method), [1] (phenotypic.tune.InferredSearchSpace method), [1] (phenotypic.tune.IntRange method), [1] (phenotypic.tune.Knob method), [1] (phenotypic.tune.OptunaConfig method), [1] (phenotypic.tune.QCScorer method), [1] (phenotypic.tune.RandomConfig method), [1] (phenotypic.tune.ReferenceFreeScorer method), [1] (phenotypic.tune.Scorer method), [1] (phenotypic.tune.SearchSpace method), [1] (phenotypic.tune.StrategyConfig method), [1] (phenotypic.tune.SupervisedScorer method), [1] (phenotypic.tune.targets.Nested method) (phenotypic.tune.targets.Param method) (phenotypic.tune.targets.Presence method) (phenotypic.tune.targets.TunableParam method) (phenotypic.tune.Trial method), [1] (phenotypic.tune.TuningSpec method), [1] model_extra (phenotypic.abc_.BackgroundSubtraction property), [1] (phenotypic.abc_.BaseOperation property), [1] (phenotypic.abc_.ContrastAdjustment property), [1] (phenotypic.abc_.FocusBlob property), [1] (phenotypic.abc_.FocusEdge property), [1] (phenotypic.abc_.GpuDetector property), [1] (phenotypic.abc_.GridCorrector property), [1] (phenotypic.abc_.GridFinder property), [1] (phenotypic.abc_.GridMeasureFeatures property), [1] (phenotypic.abc_.GridObjectDetector property), [1] (phenotypic.abc_.GridObjectRefiner property), [1] (phenotypic.abc_.GridOperation property), [1] (phenotypic.abc_.ImageCorrector property), [1] (phenotypic.abc_.ImageDenoiser property), [1] (phenotypic.abc_.ImageEnhancer property), [1] (phenotypic.abc_.ImageOperation property), [1] (phenotypic.abc_.MeasureFeatures property), [1] (phenotypic.abc_.MorphologicalFiltering property), [1] (phenotypic.abc_.ObjectDetector property), [1] (phenotypic.abc_.ObjectRefiner property), [1] (phenotypic.abc_.PostMeasurement property), [1] (phenotypic.abc_.PrefabPipeline property), [1] (phenotypic.abc_.Smoothing property), [1] (phenotypic.abc_.ThresholdDetector property), [1] (phenotypic.analysis.abc_.ModelFitter property) (phenotypic.analysis.abc_.QualityCheck property) (phenotypic.analysis.abc_.SetAnalyzer property) (phenotypic.analysis.DoubleSoftplus property), [1] (phenotypic.analysis.EdgeCorrector property), [1] (phenotypic.analysis.ErrorCutoffFinder property), [1] (phenotypic.analysis.ExpectedVsDetectedCount property), [1] (phenotypic.analysis.ICC property), [1] (phenotypic.analysis.LinearSoftplus property), [1] (phenotypic.analysis.LogGrowthModel property), [1] (phenotypic.analysis.MADOutlierRemover property), [1] (phenotypic.analysis.MaxModifiedZScore property), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount property) (phenotypic.analysis.qc.ICC property) (phenotypic.analysis.qc.MaxModifiedZScore property) (phenotypic.analysis.qc.RelativeMAD property) (phenotypic.analysis.qc.ReplicateAgreement property) (phenotypic.analysis.qc.TukeyOutlierFraction property) (phenotypic.analysis.RelativeMAD property), [1] (phenotypic.analysis.ReplicateAgreement property), [1] (phenotypic.analysis.TukeyOutlierFraction property), [1] (phenotypic.analysis.TukeyOutlierRemover property), [1] (phenotypic.correction.BayesShrinkCorrector property), [1] (phenotypic.correction.CaptureMetadata property), [1] (phenotypic.correction.ColorCheckerProfile property), [1] (phenotypic.correction.ColorCorrector property), [1] (phenotypic.correction.ColorDenoise property), [1] (phenotypic.correction.DenoiseBlockMatch property), [1] (phenotypic.correction.GridAligner property), [1] (phenotypic.correction.ImageCropper property), [1] (phenotypic.correction.ImagePadder property), [1] (phenotypic.correction.VisuShrinkCorrector property), [1] (phenotypic.detect.CannyDetector property), [1] (phenotypic.detect.ChanVeseDetector property), [1] (phenotypic.detect.CompositeDetector property), [1] (phenotypic.detect.FilamentousFungiDetector property), [1] (phenotypic.detect.HysteresisDetector property), [1] (phenotypic.detect.InoculumDetector property), [1] (phenotypic.detect.IsodataDetector property), [1] (phenotypic.detect.LiDetector property), [1] (phenotypic.detect.MadHysteresisDetector property), [1] (phenotypic.detect.ManualGridPointDetector property), [1] (phenotypic.detect.ManualPointDetector property), [1] (phenotypic.detect.MeanDetector property), [1] (phenotypic.detect.MinimumDetector property), [1] (phenotypic.detect.OtsuDetector property), [1] (phenotypic.detect.RankOtsuDetector property), [1] (phenotypic.detect.RoundPeaksDetector property), [1] (phenotypic.detect.SecondaryOtsuDetector property), [1] (phenotypic.detect.SinePeakDetector property), [1] (phenotypic.detect.TriangleDetector property), [1] (phenotypic.detect.UserThreshold property), [1] (phenotypic.detect.WatershedDetector property), [1] (phenotypic.detect.YenDetector property), [1] (phenotypic.enhance.BayesShrinkEnhancer property), [1] (phenotypic.enhance.ContrastStretching property), [1] (phenotypic.enhance.EnhanceBlockMatch property), [1] (phenotypic.enhance.EnhanceLocalContrast property), [1] (phenotypic.enhance.FlattenIllumination property), [1] (phenotypic.enhance.FocusBlobLoG property), [1] (phenotypic.enhance.FocusEdgeFrangi property), [1] (phenotypic.enhance.FocusEdgeHessian property), [1] (phenotypic.enhance.FocusEdgeLaplace property), [1] (phenotypic.enhance.FocusEdgeMeijering property), [1] (phenotypic.enhance.FocusEdgePhase property), [1] (phenotypic.enhance.FocusEdgeSato property), [1] (phenotypic.enhance.FocusEdgeSobel property), [1] (phenotypic.enhance.GaussianBlur property), [1] (phenotypic.enhance.GrayOpening property), [1] (phenotypic.enhance.ImageInverter property), [1] (phenotypic.enhance.LocalEdgeDenoise property), [1] (phenotypic.enhance.MedianFilter property), [1] (phenotypic.enhance.NonLocalMeansDenoiser property), [1] (phenotypic.enhance.RankMedianEnhancer property), [1] (phenotypic.enhance.SetDetectMode property), [1] (phenotypic.enhance.SharpenEdgeGauss property), [1] (phenotypic.enhance.StructureSmoothing property), [1] (phenotypic.enhance.SubtractGaussian property), [1] (phenotypic.enhance.SubtractOpening property), [1] (phenotypic.enhance.SubtractRollingBall property), [1] (phenotypic.enhance.SubtractWhiteTophat property), [1] (phenotypic.enhance.VisuShrinkEnhancer property), [1] (phenotypic.enhance.WhiteTophatEnhance property), [1] (phenotypic.grid.AutoGridFinder property), [1] (phenotypic.grid.CenteredAutoGridFinder property), [1] (phenotypic.grid.GridApply property), [1] (phenotypic.grid.ManualGridFinder property), [1] (phenotypic.measure.MeasureBounds property), [1] (phenotypic.measure.MeasureColor property), [1] (phenotypic.measure.MeasureGridLinRegStats property), [1] (phenotypic.measure.MeasureGridSpatial property), [1] (phenotypic.measure.MeasureGridSpread property), [1] (phenotypic.measure.MeasureIntensity property), [1] (phenotypic.measure.MeasureShape property), [1] (phenotypic.measure.MeasureSize property), [1] (phenotypic.measure.MeasureSymmetricZones property), [1] (phenotypic.measure.MeasureTexture property), [1] (phenotypic.post.AppendString property) (phenotypic.post.ExpandMetadata property) (phenotypic.post.MergeMetadata property) (phenotypic.post.PrependString property) (phenotypic.prefab.FilamentousFungiPipeline property), [1] (phenotypic.prefab.GridSectionPipeline property), [1] (phenotypic.prefab.HeavyOtsuPipeline property), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline property), [1] (phenotypic.prefab.HeavyWatershedPipeline property), [1] (phenotypic.prefab.RoundPeaksPipeline property), [1] (phenotypic.prefab.SpImagerPipeline property), [1] (phenotypic.refine.ExtractColonyCore property), [1] (phenotypic.refine.GridAlignmentRefiner property), [1] (phenotypic.refine.GridOversizedObjectRemover property), [1] (phenotypic.refine.KeepNearestCenter property), [1] (phenotypic.refine.KeepSectionLargest property), [1] (phenotypic.refine.ManualRefine property), [1] (phenotypic.refine.MaskClosing property), [1] (phenotypic.refine.MaskDilation property), [1] (phenotypic.refine.MaskErosion property), [1] (phenotypic.refine.MaskFill property), [1] (phenotypic.refine.MaskGradient property), [1] (phenotypic.refine.MaskOpening property), [1] (phenotypic.refine.MaskWhiteTophat property), [1] (phenotypic.refine.MergeFragmentChains property), [1] (phenotypic.refine.NearestNeighborMerger property), [1] (phenotypic.refine.ReduceSectionsByLine property), [1] (phenotypic.refine.RefineBySineFit property), [1] (phenotypic.refine.RemoveBorderObjects property), [1] (phenotypic.refine.RemoveByFeature property), [1] (phenotypic.refine.RemoveGridOutliers property), [1] (phenotypic.refine.RemoveLowCircularity property), [1] (phenotypic.refine.SeparateObjects property), [1] (phenotypic.refine.Skeletonize property), [1] (phenotypic.refine.SmallObjectRemover property), [1] (phenotypic.refine.SmallToLargeMerger property), [1] (phenotypic.refine.Thinning property), [1] (phenotypic.refine.TrimAsymmetry property), [1] (phenotypic.tune.Budget property), [1] (phenotypic.tune.Categorical property), [1] (phenotypic.tune.CompositeScorer property), [1] (phenotypic.tune.EvaluationResult property), [1] (phenotypic.tune.Evaluator property), [1] (phenotypic.tune.Excluded property), [1] (phenotypic.tune.Fixed property), [1] (phenotypic.tune.FloatRange property), [1] (phenotypic.tune.GridConfig property), [1] (phenotypic.tune.GroundTruthMasks property), [1] (phenotypic.tune.HeldOutConfig property), [1] (phenotypic.tune.ImportanceReport property), [1] (phenotypic.tune.InferredSearchSpace property), [1] (phenotypic.tune.IntRange property), [1] (phenotypic.tune.Knob property), [1] (phenotypic.tune.OptunaConfig property), [1] (phenotypic.tune.QCScorer property), [1] (phenotypic.tune.RandomConfig property), [1] (phenotypic.tune.ReferenceFreeScorer property), [1] (phenotypic.tune.Scorer property), [1] (phenotypic.tune.SearchSpace property), [1] (phenotypic.tune.StrategyConfig property), [1] (phenotypic.tune.SupervisedScorer property), [1] (phenotypic.tune.targets.Nested property) (phenotypic.tune.targets.Param property) (phenotypic.tune.targets.Presence property) (phenotypic.tune.targets.TunableParam property) (phenotypic.tune.Trial property), [1] (phenotypic.tune.TuningSpec property), [1] model_fields (phenotypic.abc_.BackgroundSubtraction attribute), [1] (phenotypic.abc_.BaseOperation attribute), [1] (phenotypic.abc_.ContrastAdjustment attribute), [1] (phenotypic.abc_.FocusBlob attribute), [1] (phenotypic.abc_.FocusEdge attribute), [1] (phenotypic.abc_.GpuDetector attribute), [1] (phenotypic.abc_.GridCorrector attribute), [1] (phenotypic.abc_.GridFinder attribute), [1] (phenotypic.abc_.GridMeasureFeatures attribute), [1] (phenotypic.abc_.GridObjectDetector attribute), [1] (phenotypic.abc_.GridObjectRefiner attribute), [1] (phenotypic.abc_.GridOperation attribute), [1] (phenotypic.abc_.ImageCorrector attribute), [1] (phenotypic.abc_.ImageDenoiser attribute), [1] (phenotypic.abc_.ImageEnhancer attribute), [1] (phenotypic.abc_.ImageOperation attribute), [1] (phenotypic.abc_.MeasureFeatures attribute), [1] (phenotypic.abc_.MorphologicalFiltering attribute), [1] (phenotypic.abc_.ObjectDetector attribute), [1] (phenotypic.abc_.ObjectRefiner attribute), [1] (phenotypic.abc_.PostMeasurement attribute), [1] (phenotypic.abc_.PrefabPipeline attribute), [1] (phenotypic.abc_.Smoothing attribute), [1] (phenotypic.abc_.ThresholdDetector attribute), [1] (phenotypic.analysis.abc_.ModelFitter attribute) (phenotypic.analysis.abc_.QualityCheck attribute) (phenotypic.analysis.abc_.SetAnalyzer attribute) (phenotypic.analysis.DoubleSoftplus attribute), [1] (phenotypic.analysis.EdgeCorrector attribute), [1] (phenotypic.analysis.ErrorCutoffFinder attribute), [1] (phenotypic.analysis.ExpectedVsDetectedCount attribute), [1] (phenotypic.analysis.ICC attribute), [1] (phenotypic.analysis.LinearSoftplus attribute), [1] (phenotypic.analysis.LogGrowthModel attribute), [1] (phenotypic.analysis.MADOutlierRemover attribute), [1] (phenotypic.analysis.MaxModifiedZScore attribute), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount attribute) (phenotypic.analysis.qc.ICC attribute) (phenotypic.analysis.qc.MaxModifiedZScore attribute) (phenotypic.analysis.qc.RelativeMAD attribute) (phenotypic.analysis.qc.ReplicateAgreement attribute) (phenotypic.analysis.qc.TukeyOutlierFraction attribute) (phenotypic.analysis.RelativeMAD attribute), [1] (phenotypic.analysis.ReplicateAgreement attribute), [1] (phenotypic.analysis.TukeyOutlierFraction attribute), [1] (phenotypic.analysis.TukeyOutlierRemover attribute), [1] (phenotypic.correction.BayesShrinkCorrector attribute), [1] (phenotypic.correction.CaptureMetadata attribute), [1] (phenotypic.correction.ColorCheckerProfile attribute), [1] (phenotypic.correction.ColorCorrector attribute), [1] (phenotypic.correction.ColorDenoise attribute), [1] (phenotypic.correction.DenoiseBlockMatch attribute), [1] (phenotypic.correction.GridAligner attribute), [1] (phenotypic.correction.ImageCropper attribute), [1] (phenotypic.correction.ImagePadder attribute), [1] (phenotypic.correction.VisuShrinkCorrector attribute), [1] (phenotypic.detect.CannyDetector attribute), [1] (phenotypic.detect.ChanVeseDetector attribute), [1] (phenotypic.detect.CompositeDetector attribute), [1] (phenotypic.detect.FilamentousFungiDetector attribute), [1] (phenotypic.detect.HysteresisDetector attribute), [1] (phenotypic.detect.InoculumDetector attribute), [1] (phenotypic.detect.IsodataDetector attribute), [1] (phenotypic.detect.LiDetector attribute), [1] (phenotypic.detect.MadHysteresisDetector attribute), [1] (phenotypic.detect.ManualGridPointDetector attribute), [1] (phenotypic.detect.ManualPointDetector attribute), [1] (phenotypic.detect.MeanDetector attribute), [1] (phenotypic.detect.MinimumDetector attribute), [1] (phenotypic.detect.OtsuDetector attribute), [1] (phenotypic.detect.RankOtsuDetector attribute), [1] (phenotypic.detect.RoundPeaksDetector attribute), [1] (phenotypic.detect.SecondaryOtsuDetector attribute), [1] (phenotypic.detect.SinePeakDetector attribute), [1] (phenotypic.detect.TriangleDetector attribute), [1] (phenotypic.detect.UserThreshold attribute), [1] (phenotypic.detect.WatershedDetector attribute), [1] (phenotypic.detect.YenDetector attribute), [1] (phenotypic.enhance.BayesShrinkEnhancer attribute), [1] (phenotypic.enhance.ContrastStretching attribute), [1] (phenotypic.enhance.EnhanceBlockMatch attribute), [1] (phenotypic.enhance.EnhanceLocalContrast attribute), [1] (phenotypic.enhance.FlattenIllumination attribute), [1] (phenotypic.enhance.FocusBlobLoG attribute), [1] (phenotypic.enhance.FocusEdgeFrangi attribute), [1] (phenotypic.enhance.FocusEdgeHessian attribute), [1] (phenotypic.enhance.FocusEdgeLaplace attribute), [1] (phenotypic.enhance.FocusEdgeMeijering attribute), [1] (phenotypic.enhance.FocusEdgePhase attribute), [1] (phenotypic.enhance.FocusEdgeSato attribute), [1] (phenotypic.enhance.FocusEdgeSobel attribute), [1] (phenotypic.enhance.GaussianBlur attribute), [1] (phenotypic.enhance.GrayOpening attribute), [1] (phenotypic.enhance.ImageInverter attribute), [1] (phenotypic.enhance.LocalEdgeDenoise attribute), [1] (phenotypic.enhance.MedianFilter attribute), [1] (phenotypic.enhance.NonLocalMeansDenoiser attribute), [1] (phenotypic.enhance.RankMedianEnhancer attribute), [1] (phenotypic.enhance.SetDetectMode attribute), [1] (phenotypic.enhance.SharpenEdgeGauss attribute), [1] (phenotypic.enhance.StructureSmoothing attribute), [1] (phenotypic.enhance.SubtractGaussian attribute), [1] (phenotypic.enhance.SubtractOpening attribute), [1] (phenotypic.enhance.SubtractRollingBall attribute), [1] (phenotypic.enhance.SubtractWhiteTophat attribute), [1] (phenotypic.enhance.VisuShrinkEnhancer attribute), [1] (phenotypic.enhance.WhiteTophatEnhance attribute), [1] (phenotypic.grid.AutoGridFinder attribute), [1] (phenotypic.grid.CenteredAutoGridFinder attribute), [1] (phenotypic.grid.GridApply attribute), [1] (phenotypic.grid.ManualGridFinder attribute), [1] (phenotypic.measure.MeasureBounds attribute), [1] (phenotypic.measure.MeasureColor attribute), [1] (phenotypic.measure.MeasureGridLinRegStats attribute), [1] (phenotypic.measure.MeasureGridSpatial attribute), [1] (phenotypic.measure.MeasureGridSpread attribute), [1] (phenotypic.measure.MeasureIntensity attribute), [1] (phenotypic.measure.MeasureShape attribute), [1] (phenotypic.measure.MeasureSize attribute), [1] (phenotypic.measure.MeasureSymmetricZones attribute), [1] (phenotypic.measure.MeasureTexture attribute), [1] (phenotypic.post.AppendString attribute) (phenotypic.post.ExpandMetadata attribute) (phenotypic.post.MergeMetadata attribute) (phenotypic.post.PrependString attribute) (phenotypic.prefab.FilamentousFungiPipeline attribute), [1] (phenotypic.prefab.GridSectionPipeline attribute), [1] (phenotypic.prefab.HeavyOtsuPipeline attribute), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] (phenotypic.prefab.HeavyWatershedPipeline attribute), [1] (phenotypic.prefab.RoundPeaksPipeline attribute), [1] (phenotypic.prefab.SpImagerPipeline attribute), [1] (phenotypic.refine.ExtractColonyCore attribute), [1] (phenotypic.refine.GridAlignmentRefiner attribute), [1] (phenotypic.refine.GridOversizedObjectRemover attribute), [1] (phenotypic.refine.KeepNearestCenter attribute), [1] (phenotypic.refine.KeepSectionLargest attribute), [1] (phenotypic.refine.ManualRefine attribute), [1] (phenotypic.refine.MaskClosing attribute), [1] (phenotypic.refine.MaskDilation attribute), [1] (phenotypic.refine.MaskErosion attribute), [1] (phenotypic.refine.MaskFill attribute), [1] (phenotypic.refine.MaskGradient attribute), [1] (phenotypic.refine.MaskOpening attribute), [1] (phenotypic.refine.MaskWhiteTophat attribute), [1] (phenotypic.refine.MergeFragmentChains attribute), [1] (phenotypic.refine.NearestNeighborMerger attribute), [1] (phenotypic.refine.ReduceSectionsByLine attribute), [1] (phenotypic.refine.RefineBySineFit attribute), [1] (phenotypic.refine.RemoveBorderObjects attribute), [1] (phenotypic.refine.RemoveByFeature attribute), [1] (phenotypic.refine.RemoveGridOutliers attribute), [1] (phenotypic.refine.RemoveLowCircularity attribute), [1] (phenotypic.refine.SeparateObjects attribute), [1] (phenotypic.refine.Skeletonize attribute), [1] (phenotypic.refine.SmallObjectRemover attribute), [1] (phenotypic.refine.SmallToLargeMerger attribute), [1] (phenotypic.refine.Thinning attribute), [1] (phenotypic.refine.TrimAsymmetry attribute), [1] (phenotypic.tune.Budget attribute), [1] (phenotypic.tune.Categorical attribute), [1] (phenotypic.tune.CompositeScorer attribute), [1] (phenotypic.tune.EvaluationResult attribute), [1] (phenotypic.tune.Evaluator attribute), [1] (phenotypic.tune.Excluded attribute), [1] (phenotypic.tune.Fixed attribute), [1] (phenotypic.tune.FloatRange attribute), [1] (phenotypic.tune.GridConfig attribute), [1] (phenotypic.tune.GroundTruthMasks attribute), [1] (phenotypic.tune.HeldOutConfig attribute), [1] (phenotypic.tune.ImportanceReport attribute), [1] (phenotypic.tune.InferredSearchSpace attribute), [1] (phenotypic.tune.IntRange attribute), [1] (phenotypic.tune.Knob attribute), [1] (phenotypic.tune.OptunaConfig attribute), [1] (phenotypic.tune.QCScorer attribute), [1] (phenotypic.tune.RandomConfig attribute), [1] (phenotypic.tune.ReferenceFreeScorer attribute), [1] (phenotypic.tune.Scorer attribute), [1] (phenotypic.tune.SearchSpace attribute), [1] (phenotypic.tune.StrategyConfig attribute), [1] (phenotypic.tune.SupervisedScorer attribute), [1] (phenotypic.tune.targets.Nested attribute) (phenotypic.tune.targets.Param attribute) (phenotypic.tune.targets.Presence attribute) (phenotypic.tune.targets.TunableParam attribute) (phenotypic.tune.Trial attribute), [1] (phenotypic.tune.TuningSpec attribute), [1]

model_fields_set (phenotypic.abc_.BackgroundSubtraction property), [1] (phenotypic.abc_.BaseOperation property), [1] (phenotypic.abc_.ContrastAdjustment property), [1] (phenotypic.abc_.FocusBlob property), [1] (phenotypic.abc_.FocusEdge property), [1] (phenotypic.abc_.GpuDetector property), [1] (phenotypic.abc_.GridCorrector property), [1] (phenotypic.abc_.GridFinder property), [1] (phenotypic.abc_.GridMeasureFeatures property), [1] (phenotypic.abc_.GridObjectDetector property), [1] (phenotypic.abc_.GridObjectRefiner property), [1] (phenotypic.abc_.GridOperation property), [1] (phenotypic.abc_.ImageCorrector property), [1] (phenotypic.abc_.ImageDenoiser property), [1] (phenotypic.abc_.ImageEnhancer property), [1] (phenotypic.abc_.ImageOperation property), [1] (phenotypic.abc_.MeasureFeatures property), [1] (phenotypic.abc_.MorphologicalFiltering property), [1] (phenotypic.abc_.ObjectDetector property), [1] (phenotypic.abc_.ObjectRefiner property), [1] (phenotypic.abc_.PostMeasurement property), [1] (phenotypic.abc_.PrefabPipeline property), [1] (phenotypic.abc_.Smoothing property), [1] (phenotypic.abc_.ThresholdDetector property), [1] (phenotypic.analysis.abc_.ModelFitter property) (phenotypic.analysis.abc_.QualityCheck property) (phenotypic.analysis.abc_.SetAnalyzer property) (phenotypic.analysis.DoubleSoftplus property), [1] (phenotypic.analysis.EdgeCorrector property), [1] (phenotypic.analysis.ErrorCutoffFinder property), [1] (phenotypic.analysis.ExpectedVsDetectedCount property), [1] (phenotypic.analysis.ICC property), [1] (phenotypic.analysis.LinearSoftplus property), [1] (phenotypic.analysis.LogGrowthModel property), [1] (phenotypic.analysis.MADOutlierRemover property), [1] (phenotypic.analysis.MaxModifiedZScore property), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount property) (phenotypic.analysis.qc.ICC property) (phenotypic.analysis.qc.MaxModifiedZScore property) (phenotypic.analysis.qc.RelativeMAD property) (phenotypic.analysis.qc.ReplicateAgreement property) (phenotypic.analysis.qc.TukeyOutlierFraction property) (phenotypic.analysis.RelativeMAD property), [1] (phenotypic.analysis.ReplicateAgreement property), [1] (phenotypic.analysis.TukeyOutlierFraction property), [1] (phenotypic.analysis.TukeyOutlierRemover property), [1] (phenotypic.correction.BayesShrinkCorrector property), [1] (phenotypic.correction.CaptureMetadata property), [1] (phenotypic.correction.ColorCheckerProfile property), [1] (phenotypic.correction.ColorCorrector property), [1] (phenotypic.correction.ColorDenoise property), [1] (phenotypic.correction.DenoiseBlockMatch property), [1] (phenotypic.correction.GridAligner property), [1] (phenotypic.correction.ImageCropper property), [1] (phenotypic.correction.ImagePadder property), [1] (phenotypic.correction.VisuShrinkCorrector property), [1] (phenotypic.detect.CannyDetector property), [1] (phenotypic.detect.ChanVeseDetector property), [1] (phenotypic.detect.CompositeDetector property), [1] (phenotypic.detect.FilamentousFungiDetector property), [1] (phenotypic.detect.HysteresisDetector property), [1] (phenotypic.detect.InoculumDetector property), [1] (phenotypic.detect.IsodataDetector property), [1] (phenotypic.detect.LiDetector property), [1] (phenotypic.detect.MadHysteresisDetector property), [1] (phenotypic.detect.ManualGridPointDetector property), [1] (phenotypic.detect.ManualPointDetector property), [1] (phenotypic.detect.MeanDetector property), [1] (phenotypic.detect.MinimumDetector property), [1] (phenotypic.detect.OtsuDetector property), [1] (phenotypic.detect.RankOtsuDetector property), [1] (phenotypic.detect.RoundPeaksDetector property), [1] (phenotypic.detect.SecondaryOtsuDetector property), [1] (phenotypic.detect.SinePeakDetector property), [1] (phenotypic.detect.TriangleDetector property), [1] (phenotypic.detect.UserThreshold property), [1] (phenotypic.detect.WatershedDetector property), [1] (phenotypic.detect.YenDetector property), [1] (phenotypic.enhance.BayesShrinkEnhancer property), [1] (phenotypic.enhance.ContrastStretching property), [1] (phenotypic.enhance.EnhanceBlockMatch property), [1] (phenotypic.enhance.EnhanceLocalContrast property), [1] (phenotypic.enhance.FlattenIllumination property), [1] (phenotypic.enhance.FocusBlobLoG property), [1] (phenotypic.enhance.FocusEdgeFrangi property), [1] (phenotypic.enhance.FocusEdgeHessian property), [1] (phenotypic.enhance.FocusEdgeLaplace property), [1] (phenotypic.enhance.FocusEdgeMeijering property), [1] (phenotypic.enhance.FocusEdgePhase property), [1] (phenotypic.enhance.FocusEdgeSato property), [1] (phenotypic.enhance.FocusEdgeSobel property), [1] (phenotypic.enhance.GaussianBlur property), [1] (phenotypic.enhance.GrayOpening property), [1] (phenotypic.enhance.ImageInverter property), [1] (phenotypic.enhance.LocalEdgeDenoise property), [1] (phenotypic.enhance.MedianFilter property), [1] (phenotypic.enhance.NonLocalMeansDenoiser property), [1] (phenotypic.enhance.RankMedianEnhancer property), [1] (phenotypic.enhance.SetDetectMode property), [1] (phenotypic.enhance.SharpenEdgeGauss property), [1] (phenotypic.enhance.StructureSmoothing property), [1] (phenotypic.enhance.SubtractGaussian property), [1] (phenotypic.enhance.SubtractOpening property), [1] (phenotypic.enhance.SubtractRollingBall property), [1] (phenotypic.enhance.SubtractWhiteTophat property), [1] (phenotypic.enhance.VisuShrinkEnhancer property), [1] (phenotypic.enhance.WhiteTophatEnhance property), [1] (phenotypic.grid.AutoGridFinder property), [1] (phenotypic.grid.CenteredAutoGridFinder property), [1] (phenotypic.grid.GridApply property), [1] (phenotypic.grid.ManualGridFinder property), [1] (phenotypic.measure.MeasureBounds property), [1] (phenotypic.measure.MeasureColor property), [1] (phenotypic.measure.MeasureGridLinRegStats property), [1] (phenotypic.measure.MeasureGridSpatial property), [1] (phenotypic.measure.MeasureGridSpread property), [1] (phenotypic.measure.MeasureIntensity property), [1] (phenotypic.measure.MeasureShape property), [1] (phenotypic.measure.MeasureSize property), [1] (phenotypic.measure.MeasureSymmetricZones property), [1] (phenotypic.measure.MeasureTexture property), [1] (phenotypic.post.AppendString property) (phenotypic.post.ExpandMetadata property) (phenotypic.post.MergeMetadata property) (phenotypic.post.PrependString property) (phenotypic.prefab.FilamentousFungiPipeline property), [1] (phenotypic.prefab.GridSectionPipeline property), [1] (phenotypic.prefab.HeavyOtsuPipeline property), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline property), [1] (phenotypic.prefab.HeavyWatershedPipeline property), [1] (phenotypic.prefab.RoundPeaksPipeline property), [1] (phenotypic.prefab.SpImagerPipeline property), [1] (phenotypic.refine.ExtractColonyCore property), [1] (phenotypic.refine.GridAlignmentRefiner property), [1] (phenotypic.refine.GridOversizedObjectRemover property), [1] (phenotypic.refine.KeepNearestCenter property), [1] (phenotypic.refine.KeepSectionLargest property), [1] (phenotypic.refine.ManualRefine property), [1] (phenotypic.refine.MaskClosing property), [1] (phenotypic.refine.MaskDilation property), [1] (phenotypic.refine.MaskErosion property), [1] (phenotypic.refine.MaskFill property), [1] (phenotypic.refine.MaskGradient property), [1] (phenotypic.refine.MaskOpening property), [1] (phenotypic.refine.MaskWhiteTophat property), [1] (phenotypic.refine.MergeFragmentChains property), [1] (phenotypic.refine.NearestNeighborMerger property), [1] (phenotypic.refine.ReduceSectionsByLine property), [1] (phenotypic.refine.RefineBySineFit property), [1] (phenotypic.refine.RemoveBorderObjects property), [1] (phenotypic.refine.RemoveByFeature property), [1] (phenotypic.refine.RemoveGridOutliers property), [1] (phenotypic.refine.RemoveLowCircularity property), [1] (phenotypic.refine.SeparateObjects property), [1] (phenotypic.refine.Skeletonize property), [1] (phenotypic.refine.SmallObjectRemover property), [1] (phenotypic.refine.SmallToLargeMerger property), [1] (phenotypic.refine.Thinning property), [1] (phenotypic.refine.TrimAsymmetry property), [1] (phenotypic.tune.Budget property), [1] (phenotypic.tune.Categorical property), [1] (phenotypic.tune.CompositeScorer property), [1] (phenotypic.tune.EvaluationResult property), [1] (phenotypic.tune.Evaluator property), [1] (phenotypic.tune.Excluded property), [1] (phenotypic.tune.Fixed property), [1] (phenotypic.tune.FloatRange property), [1] (phenotypic.tune.GridConfig property), [1] (phenotypic.tune.GroundTruthMasks property), [1] (phenotypic.tune.HeldOutConfig property), [1] (phenotypic.tune.ImportanceReport property), [1] (phenotypic.tune.InferredSearchSpace property), [1] (phenotypic.tune.IntRange property), [1] (phenotypic.tune.Knob property), [1] (phenotypic.tune.OptunaConfig property), [1] (phenotypic.tune.QCScorer property), [1] (phenotypic.tune.RandomConfig property), [1] (phenotypic.tune.ReferenceFreeScorer property), [1] (phenotypic.tune.Scorer property), [1] (phenotypic.tune.SearchSpace property), [1] (phenotypic.tune.StrategyConfig property), [1] (phenotypic.tune.SupervisedScorer property), [1] (phenotypic.tune.targets.Nested property) (phenotypic.tune.targets.Param property) (phenotypic.tune.targets.Presence property) (phenotypic.tune.targets.TunableParam property) (phenotypic.tune.Trial property), [1] (phenotypic.tune.TuningSpec property), [1] model_func() (phenotypic.analysis.abc_.ModelFitter static method) (phenotypic.analysis.DoubleSoftplus static method), [1] (phenotypic.analysis.LinearSoftplus static method), [1] (phenotypic.analysis.LogGrowthModel static method), [1] model_json_schema() (phenotypic.abc_.BackgroundSubtraction class method), [1] (phenotypic.abc_.BaseOperation class method), [1] (phenotypic.abc_.ContrastAdjustment class method), [1] (phenotypic.abc_.FocusBlob class method), [1] (phenotypic.abc_.FocusEdge class method), [1] (phenotypic.abc_.GpuDetector class method), [1] (phenotypic.abc_.GridCorrector class method), [1] (phenotypic.abc_.GridFinder class method), [1] (phenotypic.abc_.GridMeasureFeatures class method), [1] (phenotypic.abc_.GridObjectDetector class method), [1] (phenotypic.abc_.GridObjectRefiner class method), [1] (phenotypic.abc_.GridOperation class method), [1] (phenotypic.abc_.ImageCorrector class method), [1] (phenotypic.abc_.ImageDenoiser class method), [1] (phenotypic.abc_.ImageEnhancer class method), [1] (phenotypic.abc_.ImageOperation class method), [1] (phenotypic.abc_.MeasureFeatures class method), [1] (phenotypic.abc_.MorphologicalFiltering class method), [1] (phenotypic.abc_.ObjectDetector class method), [1] (phenotypic.abc_.ObjectRefiner class method), [1] (phenotypic.abc_.PostMeasurement class method), [1] (phenotypic.abc_.PrefabPipeline class method), [1] (phenotypic.abc_.Smoothing class method), [1] (phenotypic.abc_.ThresholdDetector class method), [1] (phenotypic.analysis.abc_.ModelFitter class method) (phenotypic.analysis.abc_.QualityCheck class method) (phenotypic.analysis.abc_.SetAnalyzer class method) (phenotypic.analysis.DoubleSoftplus class method), [1] (phenotypic.analysis.EdgeCorrector class method), [1] (phenotypic.analysis.ErrorCutoffFinder class method), [1] (phenotypic.analysis.ExpectedVsDetectedCount class method), [1] (phenotypic.analysis.ICC class method), [1] (phenotypic.analysis.LinearSoftplus class method), [1] (phenotypic.analysis.LogGrowthModel class method), [1] (phenotypic.analysis.MADOutlierRemover class method), [1] (phenotypic.analysis.MaxModifiedZScore class method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount class method) (phenotypic.analysis.qc.ICC class method) (phenotypic.analysis.qc.MaxModifiedZScore class method) (phenotypic.analysis.qc.RelativeMAD class method) (phenotypic.analysis.qc.ReplicateAgreement class method) (phenotypic.analysis.qc.TukeyOutlierFraction class method) (phenotypic.analysis.RelativeMAD class method), [1] (phenotypic.analysis.ReplicateAgreement class method), [1] (phenotypic.analysis.TukeyOutlierFraction class method), [1] (phenotypic.analysis.TukeyOutlierRemover class method), [1] (phenotypic.correction.BayesShrinkCorrector class method), [1] (phenotypic.correction.CaptureMetadata class method), [1] (phenotypic.correction.ColorCheckerProfile class method), [1] (phenotypic.correction.ColorCorrector class method), [1] (phenotypic.correction.ColorDenoise class method), [1] (phenotypic.correction.DenoiseBlockMatch class method), [1] (phenotypic.correction.GridAligner class method), [1] (phenotypic.correction.ImageCropper class method), [1] (phenotypic.correction.ImagePadder class method), [1] (phenotypic.correction.VisuShrinkCorrector class method), [1] (phenotypic.detect.CannyDetector class method), [1] (phenotypic.detect.ChanVeseDetector class method), [1] (phenotypic.detect.CompositeDetector class method), [1] (phenotypic.detect.FilamentousFungiDetector class method), [1] (phenotypic.detect.HysteresisDetector class method), [1] (phenotypic.detect.InoculumDetector class method), [1] (phenotypic.detect.IsodataDetector class method), [1] (phenotypic.detect.LiDetector class method), [1] (phenotypic.detect.MadHysteresisDetector class method), [1] (phenotypic.detect.ManualGridPointDetector class method), [1] (phenotypic.detect.ManualPointDetector class method), [1] (phenotypic.detect.MeanDetector class method), [1] (phenotypic.detect.MinimumDetector class method), [1] (phenotypic.detect.OtsuDetector class method), [1] (phenotypic.detect.RankOtsuDetector class method), [1] (phenotypic.detect.RoundPeaksDetector class method), [1] (phenotypic.detect.SecondaryOtsuDetector class method), [1] (phenotypic.detect.SinePeakDetector class method), [1] (phenotypic.detect.TriangleDetector class method), [1] (phenotypic.detect.UserThreshold class method), [1] (phenotypic.detect.WatershedDetector class method), [1] (phenotypic.detect.YenDetector class method), [1] (phenotypic.enhance.BayesShrinkEnhancer class method), [1] (phenotypic.enhance.ContrastStretching class method), [1] (phenotypic.enhance.EnhanceBlockMatch class method), [1] (phenotypic.enhance.EnhanceLocalContrast class method), [1] (phenotypic.enhance.FlattenIllumination class method), [1] (phenotypic.enhance.FocusBlobLoG class method), [1] (phenotypic.enhance.FocusEdgeFrangi class method), [1] (phenotypic.enhance.FocusEdgeHessian class method), [1] (phenotypic.enhance.FocusEdgeLaplace class method), [1] (phenotypic.enhance.FocusEdgeMeijering class method), [1] (phenotypic.enhance.FocusEdgePhase class method), [1] (phenotypic.enhance.FocusEdgeSato class method), [1] (phenotypic.enhance.FocusEdgeSobel class method), [1] (phenotypic.enhance.GaussianBlur class method), [1] (phenotypic.enhance.GrayOpening class method), [1] (phenotypic.enhance.ImageInverter class method), [1] (phenotypic.enhance.LocalEdgeDenoise class method), [1] (phenotypic.enhance.MedianFilter class method), [1] (phenotypic.enhance.NonLocalMeansDenoiser class method), [1] (phenotypic.enhance.RankMedianEnhancer class method), [1] (phenotypic.enhance.SetDetectMode class method), [1] (phenotypic.enhance.SharpenEdgeGauss class method), [1] (phenotypic.enhance.StructureSmoothing class method), [1] (phenotypic.enhance.SubtractGaussian class method), [1] (phenotypic.enhance.SubtractOpening class method), [1] (phenotypic.enhance.SubtractRollingBall class method), [1] (phenotypic.enhance.SubtractWhiteTophat class method), [1] (phenotypic.enhance.VisuShrinkEnhancer class method), [1] (phenotypic.enhance.WhiteTophatEnhance class method), [1] (phenotypic.grid.AutoGridFinder class method), [1] (phenotypic.grid.CenteredAutoGridFinder class method), [1] (phenotypic.grid.GridApply class method), [1] (phenotypic.grid.ManualGridFinder class method), [1] (phenotypic.measure.MeasureBounds class method), [1] (phenotypic.measure.MeasureColor class method), [1] (phenotypic.measure.MeasureGridLinRegStats class method), [1] (phenotypic.measure.MeasureGridSpatial class method), [1] (phenotypic.measure.MeasureGridSpread class method), [1] (phenotypic.measure.MeasureIntensity class method), [1] (phenotypic.measure.MeasureShape class method), [1] (phenotypic.measure.MeasureSize class method), [1] (phenotypic.measure.MeasureSymmetricZones class method), [1] (phenotypic.measure.MeasureTexture class method), [1] (phenotypic.post.AppendString class method) (phenotypic.post.ExpandMetadata class method) (phenotypic.post.MergeMetadata class method) (phenotypic.post.PrependString class method) (phenotypic.prefab.FilamentousFungiPipeline class method), [1] (phenotypic.prefab.GridSectionPipeline class method), [1] (phenotypic.prefab.HeavyOtsuPipeline class method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline class method), [1] (phenotypic.prefab.HeavyWatershedPipeline class method), [1] (phenotypic.prefab.RoundPeaksPipeline class method), [1] (phenotypic.prefab.SpImagerPipeline class method), [1] (phenotypic.refine.ExtractColonyCore class method), [1] (phenotypic.refine.GridAlignmentRefiner class method), [1] (phenotypic.refine.GridOversizedObjectRemover class method), [1] (phenotypic.refine.KeepNearestCenter class method), [1] (phenotypic.refine.KeepSectionLargest class method), [1] (phenotypic.refine.ManualRefine class method), [1] (phenotypic.refine.MaskClosing class method), [1] (phenotypic.refine.MaskDilation class method), [1] (phenotypic.refine.MaskErosion class method), [1] (phenotypic.refine.MaskFill class method), [1] (phenotypic.refine.MaskGradient class method), [1] (phenotypic.refine.MaskOpening class method), [1] (phenotypic.refine.MaskWhiteTophat class method), [1] (phenotypic.refine.MergeFragmentChains class method), [1] (phenotypic.refine.NearestNeighborMerger class method), [1] (phenotypic.refine.ReduceSectionsByLine class method), [1] (phenotypic.refine.RefineBySineFit class method), [1] (phenotypic.refine.RemoveBorderObjects class method), [1] (phenotypic.refine.RemoveByFeature class method), [1] (phenotypic.refine.RemoveGridOutliers class method), [1] (phenotypic.refine.RemoveLowCircularity class method), [1] (phenotypic.refine.SeparateObjects class method), [1] (phenotypic.refine.Skeletonize class method), [1] (phenotypic.refine.SmallObjectRemover class method), [1] (phenotypic.refine.SmallToLargeMerger class method), [1] (phenotypic.refine.Thinning class method), [1] (phenotypic.refine.TrimAsymmetry class method), [1] (phenotypic.tune.Budget class method), [1] (phenotypic.tune.Categorical class method), [1] (phenotypic.tune.CompositeScorer class method), [1] (phenotypic.tune.EvaluationResult class method), [1] (phenotypic.tune.Evaluator class method), [1] (phenotypic.tune.Excluded class method), [1] (phenotypic.tune.Fixed class method), [1] (phenotypic.tune.FloatRange class method), [1] (phenotypic.tune.GridConfig class method), [1] (phenotypic.tune.GroundTruthMasks class method), [1] (phenotypic.tune.HeldOutConfig class method), [1] (phenotypic.tune.ImportanceReport class method), [1] (phenotypic.tune.InferredSearchSpace class method), [1] (phenotypic.tune.IntRange class method), [1] (phenotypic.tune.Knob class method), [1] (phenotypic.tune.OptunaConfig class method), [1] (phenotypic.tune.QCScorer class method), [1] (phenotypic.tune.RandomConfig class method), [1] (phenotypic.tune.ReferenceFreeScorer class method), [1] (phenotypic.tune.Scorer class method), [1] (phenotypic.tune.SearchSpace class method), [1] (phenotypic.tune.StrategyConfig class method), [1] (phenotypic.tune.SupervisedScorer class method), [1] (phenotypic.tune.targets.Nested class method) (phenotypic.tune.targets.Param class method) (phenotypic.tune.targets.Presence class method) (phenotypic.tune.targets.TunableParam class method) (phenotypic.tune.Trial class method), [1] (phenotypic.tune.TuningSpec class method), [1] MODEL_METRICS (class in phenotypic.schema) model_parametrized_name() (phenotypic.abc_.BackgroundSubtraction class method), [1] (phenotypic.abc_.BaseOperation class method), [1] (phenotypic.abc_.ContrastAdjustment class method), [1] (phenotypic.abc_.FocusBlob class method), [1] (phenotypic.abc_.FocusEdge class method), [1] (phenotypic.abc_.GpuDetector class method), [1] (phenotypic.abc_.GridCorrector class method), [1] (phenotypic.abc_.GridFinder class method), [1] (phenotypic.abc_.GridMeasureFeatures class method), [1] (phenotypic.abc_.GridObjectDetector class method), [1] (phenotypic.abc_.GridObjectRefiner class method), [1] (phenotypic.abc_.GridOperation class method), [1] (phenotypic.abc_.ImageCorrector class method), [1] (phenotypic.abc_.ImageDenoiser class method), [1] (phenotypic.abc_.ImageEnhancer class method), [1] (phenotypic.abc_.ImageOperation class method), [1] (phenotypic.abc_.MeasureFeatures class method), [1] (phenotypic.abc_.MorphologicalFiltering class method), [1] (phenotypic.abc_.ObjectDetector class method), [1] (phenotypic.abc_.ObjectRefiner class method), [1] (phenotypic.abc_.PostMeasurement class method), [1] (phenotypic.abc_.PrefabPipeline class method), [1] (phenotypic.abc_.Smoothing class method), [1] (phenotypic.abc_.ThresholdDetector class method), [1] (phenotypic.analysis.abc_.ModelFitter class method) (phenotypic.analysis.abc_.QualityCheck class method) (phenotypic.analysis.abc_.SetAnalyzer class method) (phenotypic.analysis.DoubleSoftplus class method), [1] (phenotypic.analysis.EdgeCorrector class method), [1] (phenotypic.analysis.ErrorCutoffFinder class method), [1] (phenotypic.analysis.ExpectedVsDetectedCount class method), [1] (phenotypic.analysis.ICC class method), [1] (phenotypic.analysis.LinearSoftplus class method), [1] (phenotypic.analysis.LogGrowthModel class method), [1] (phenotypic.analysis.MADOutlierRemover class method), [1] (phenotypic.analysis.MaxModifiedZScore class method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount class method) (phenotypic.analysis.qc.ICC class method) (phenotypic.analysis.qc.MaxModifiedZScore class method) (phenotypic.analysis.qc.RelativeMAD class method) (phenotypic.analysis.qc.ReplicateAgreement class method) (phenotypic.analysis.qc.TukeyOutlierFraction class method) (phenotypic.analysis.RelativeMAD class method), [1] (phenotypic.analysis.ReplicateAgreement class method), [1] (phenotypic.analysis.TukeyOutlierFraction class method), [1] (phenotypic.analysis.TukeyOutlierRemover class method), [1] (phenotypic.correction.BayesShrinkCorrector class method), [1] (phenotypic.correction.CaptureMetadata class method), [1] (phenotypic.correction.ColorCheckerProfile class method), [1] (phenotypic.correction.ColorCorrector class method), [1] (phenotypic.correction.ColorDenoise class method), [1] (phenotypic.correction.DenoiseBlockMatch class method), [1] (phenotypic.correction.GridAligner class method), [1] (phenotypic.correction.ImageCropper class method), [1] (phenotypic.correction.ImagePadder class method), [1] (phenotypic.correction.VisuShrinkCorrector class method), [1] (phenotypic.detect.CannyDetector class method), [1] (phenotypic.detect.ChanVeseDetector class method), [1] (phenotypic.detect.CompositeDetector class method), [1] (phenotypic.detect.FilamentousFungiDetector class method), [1] (phenotypic.detect.HysteresisDetector class method), [1] (phenotypic.detect.InoculumDetector class method), [1] (phenotypic.detect.IsodataDetector class method), [1] (phenotypic.detect.LiDetector class method), [1] (phenotypic.detect.MadHysteresisDetector class method), [1] (phenotypic.detect.ManualGridPointDetector class method), [1] (phenotypic.detect.ManualPointDetector class method), [1] (phenotypic.detect.MeanDetector class method), [1] (phenotypic.detect.MinimumDetector class method), [1] (phenotypic.detect.OtsuDetector class method), [1] (phenotypic.detect.RankOtsuDetector class method), [1] (phenotypic.detect.RoundPeaksDetector class method), [1] (phenotypic.detect.SecondaryOtsuDetector class method), [1] (phenotypic.detect.SinePeakDetector class method), [1] (phenotypic.detect.TriangleDetector class method), [1] (phenotypic.detect.UserThreshold class method), [1] (phenotypic.detect.WatershedDetector class method), [1] (phenotypic.detect.YenDetector class method), [1] (phenotypic.enhance.BayesShrinkEnhancer class method), [1] (phenotypic.enhance.ContrastStretching class method), [1] (phenotypic.enhance.EnhanceBlockMatch class method), [1] (phenotypic.enhance.EnhanceLocalContrast class method), [1] (phenotypic.enhance.FlattenIllumination class method), [1] (phenotypic.enhance.FocusBlobLoG class method), [1] (phenotypic.enhance.FocusEdgeFrangi class method), [1] (phenotypic.enhance.FocusEdgeHessian class method), [1] (phenotypic.enhance.FocusEdgeLaplace class method), [1] (phenotypic.enhance.FocusEdgeMeijering class method), [1] (phenotypic.enhance.FocusEdgePhase class method), [1] (phenotypic.enhance.FocusEdgeSato class method), [1] (phenotypic.enhance.FocusEdgeSobel class method), [1] (phenotypic.enhance.GaussianBlur class method), [1] (phenotypic.enhance.GrayOpening class method), [1] (phenotypic.enhance.ImageInverter class method), [1] (phenotypic.enhance.LocalEdgeDenoise class method), [1] (phenotypic.enhance.MedianFilter class method), [1] (phenotypic.enhance.NonLocalMeansDenoiser class method), [1] (phenotypic.enhance.RankMedianEnhancer class method), [1] (phenotypic.enhance.SetDetectMode class method), [1] (phenotypic.enhance.SharpenEdgeGauss class method), [1] (phenotypic.enhance.StructureSmoothing class method), [1] (phenotypic.enhance.SubtractGaussian class method), [1] (phenotypic.enhance.SubtractOpening class method), [1] (phenotypic.enhance.SubtractRollingBall class method), [1] (phenotypic.enhance.SubtractWhiteTophat class method), [1] (phenotypic.enhance.VisuShrinkEnhancer class method), [1] (phenotypic.enhance.WhiteTophatEnhance class method), [1] (phenotypic.grid.AutoGridFinder class method), [1] (phenotypic.grid.CenteredAutoGridFinder class method), [1] (phenotypic.grid.GridApply class method), [1] (phenotypic.grid.ManualGridFinder class method), [1] (phenotypic.measure.MeasureBounds class method), [1] (phenotypic.measure.MeasureColor class method), [1] (phenotypic.measure.MeasureGridLinRegStats class method), [1] (phenotypic.measure.MeasureGridSpatial class method), [1] (phenotypic.measure.MeasureGridSpread class method), [1] (phenotypic.measure.MeasureIntensity class method), [1] (phenotypic.measure.MeasureShape class method), [1] (phenotypic.measure.MeasureSize class method), [1] (phenotypic.measure.MeasureSymmetricZones class method), [1] (phenotypic.measure.MeasureTexture class method), [1] (phenotypic.post.AppendString class method) (phenotypic.post.ExpandMetadata class method) (phenotypic.post.MergeMetadata class method) (phenotypic.post.PrependString class method) (phenotypic.prefab.FilamentousFungiPipeline class method), [1] (phenotypic.prefab.GridSectionPipeline class method), [1] (phenotypic.prefab.HeavyOtsuPipeline class method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline class method), [1] (phenotypic.prefab.HeavyWatershedPipeline class method), [1] (phenotypic.prefab.RoundPeaksPipeline class method), [1] (phenotypic.prefab.SpImagerPipeline class method), [1] (phenotypic.refine.ExtractColonyCore class method), [1] (phenotypic.refine.GridAlignmentRefiner class method), [1] (phenotypic.refine.GridOversizedObjectRemover class method), [1] (phenotypic.refine.KeepNearestCenter class method), [1] (phenotypic.refine.KeepSectionLargest class method), [1] (phenotypic.refine.ManualRefine class method), [1] (phenotypic.refine.MaskClosing class method), [1] (phenotypic.refine.MaskDilation class method), [1] (phenotypic.refine.MaskErosion class method), [1] (phenotypic.refine.MaskFill class method), [1] (phenotypic.refine.MaskGradient class method), [1] (phenotypic.refine.MaskOpening class method), [1] (phenotypic.refine.MaskWhiteTophat class method), [1] (phenotypic.refine.MergeFragmentChains class method), [1] (phenotypic.refine.NearestNeighborMerger class method), [1] (phenotypic.refine.ReduceSectionsByLine class method), [1] (phenotypic.refine.RefineBySineFit class method), [1] (phenotypic.refine.RemoveBorderObjects class method), [1] (phenotypic.refine.RemoveByFeature class method), [1] (phenotypic.refine.RemoveGridOutliers class method), [1] (phenotypic.refine.RemoveLowCircularity class method), [1] (phenotypic.refine.SeparateObjects class method), [1] (phenotypic.refine.Skeletonize class method), [1] (phenotypic.refine.SmallObjectRemover class method), [1] (phenotypic.refine.SmallToLargeMerger class method), [1] (phenotypic.refine.Thinning class method), [1] (phenotypic.refine.TrimAsymmetry class method), [1] (phenotypic.tune.Budget class method), [1] (phenotypic.tune.Categorical class method), [1] (phenotypic.tune.CompositeScorer class method), [1] (phenotypic.tune.EvaluationResult class method), [1] (phenotypic.tune.Evaluator class method), [1] (phenotypic.tune.Excluded class method), [1] (phenotypic.tune.Fixed class method), [1] (phenotypic.tune.FloatRange class method), [1] (phenotypic.tune.GridConfig class method), [1] (phenotypic.tune.GroundTruthMasks class method), [1] (phenotypic.tune.HeldOutConfig class method), [1] (phenotypic.tune.ImportanceReport class method), [1] (phenotypic.tune.InferredSearchSpace class method), [1] (phenotypic.tune.IntRange class method), [1] (phenotypic.tune.Knob class method), [1] (phenotypic.tune.OptunaConfig class method), [1] (phenotypic.tune.QCScorer class method), [1] (phenotypic.tune.RandomConfig class method), [1] (phenotypic.tune.ReferenceFreeScorer class method), [1] (phenotypic.tune.Scorer class method), [1] (phenotypic.tune.SearchSpace class method), [1] (phenotypic.tune.StrategyConfig class method), [1] (phenotypic.tune.SupervisedScorer class method), [1] (phenotypic.tune.targets.Nested class method) (phenotypic.tune.targets.Param class method) (phenotypic.tune.targets.Presence class method) (phenotypic.tune.targets.TunableParam class method) (phenotypic.tune.Trial class method), [1] (phenotypic.tune.TuningSpec class method), [1] model_post_init() (phenotypic.abc_.BackgroundSubtraction method), [1] (phenotypic.abc_.BaseOperation method), [1] (phenotypic.abc_.ContrastAdjustment method), [1] (phenotypic.abc_.FocusBlob method), [1] (phenotypic.abc_.FocusEdge method), [1] (phenotypic.abc_.GpuDetector method), [1] (phenotypic.abc_.GridCorrector method), [1] (phenotypic.abc_.GridFinder method), [1] (phenotypic.abc_.GridMeasureFeatures method), [1] (phenotypic.abc_.GridObjectDetector method), [1] (phenotypic.abc_.GridObjectRefiner method), [1] (phenotypic.abc_.GridOperation method), [1] (phenotypic.abc_.ImageCorrector method), [1] (phenotypic.abc_.ImageDenoiser method), [1] (phenotypic.abc_.ImageEnhancer method), [1] (phenotypic.abc_.ImageOperation method), [1] (phenotypic.abc_.MeasureFeatures method), [1] (phenotypic.abc_.MorphologicalFiltering method), [1] (phenotypic.abc_.ObjectDetector method), [1] (phenotypic.abc_.ObjectRefiner method), [1] (phenotypic.abc_.PostMeasurement method), [1] (phenotypic.abc_.PrefabPipeline method), [1] (phenotypic.abc_.Smoothing method), [1] (phenotypic.abc_.ThresholdDetector method), [1] (phenotypic.analysis.abc_.ModelFitter method) (phenotypic.analysis.abc_.QualityCheck method) (phenotypic.analysis.abc_.SetAnalyzer method) (phenotypic.analysis.DoubleSoftplus method), [1] (phenotypic.analysis.EdgeCorrector method), [1] (phenotypic.analysis.ErrorCutoffFinder method), [1] (phenotypic.analysis.ExpectedVsDetectedCount method), [1] (phenotypic.analysis.ICC method), [1] (phenotypic.analysis.LinearSoftplus method), [1] (phenotypic.analysis.LogGrowthModel method), [1] (phenotypic.analysis.MADOutlierRemover method), [1] (phenotypic.analysis.MaxModifiedZScore method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount method) (phenotypic.analysis.qc.ICC method) (phenotypic.analysis.qc.MaxModifiedZScore method) (phenotypic.analysis.qc.RelativeMAD method) (phenotypic.analysis.qc.ReplicateAgreement method) (phenotypic.analysis.qc.TukeyOutlierFraction method) (phenotypic.analysis.RelativeMAD method), [1] (phenotypic.analysis.ReplicateAgreement method), [1] (phenotypic.analysis.TukeyOutlierFraction method), [1] (phenotypic.analysis.TukeyOutlierRemover method), [1] (phenotypic.correction.BayesShrinkCorrector method), [1] (phenotypic.correction.CaptureMetadata method), [1] (phenotypic.correction.ColorCheckerProfile method), [1] (phenotypic.correction.ColorCorrector method), [1] (phenotypic.correction.ColorDenoise method), [1] (phenotypic.correction.DenoiseBlockMatch method), [1] (phenotypic.correction.GridAligner method), [1] (phenotypic.correction.ImageCropper method), [1] (phenotypic.correction.ImagePadder method), [1] (phenotypic.correction.VisuShrinkCorrector method), [1] (phenotypic.detect.CannyDetector method), [1] (phenotypic.detect.ChanVeseDetector method), [1] (phenotypic.detect.CompositeDetector method), [1] (phenotypic.detect.FilamentousFungiDetector method), [1] (phenotypic.detect.HysteresisDetector method), [1] (phenotypic.detect.InoculumDetector method), [1] (phenotypic.detect.IsodataDetector method), [1] (phenotypic.detect.LiDetector method), [1] (phenotypic.detect.MadHysteresisDetector method), [1] (phenotypic.detect.ManualGridPointDetector method), [1] (phenotypic.detect.ManualPointDetector method), [1] (phenotypic.detect.MeanDetector method), [1] (phenotypic.detect.MinimumDetector method), [1] (phenotypic.detect.OtsuDetector method), [1] (phenotypic.detect.RankOtsuDetector method), [1] (phenotypic.detect.RoundPeaksDetector method), [1] (phenotypic.detect.SecondaryOtsuDetector method), [1] (phenotypic.detect.SinePeakDetector method), [1] (phenotypic.detect.TriangleDetector method), [1] (phenotypic.detect.UserThreshold method), [1] (phenotypic.detect.WatershedDetector method), [1] (phenotypic.detect.YenDetector method), [1] (phenotypic.enhance.BayesShrinkEnhancer method), [1] (phenotypic.enhance.ContrastStretching method), [1] (phenotypic.enhance.EnhanceBlockMatch method), [1] (phenotypic.enhance.EnhanceLocalContrast method), [1] (phenotypic.enhance.FlattenIllumination method), [1] (phenotypic.enhance.FocusBlobLoG method), [1] (phenotypic.enhance.FocusEdgeFrangi method), [1] (phenotypic.enhance.FocusEdgeHessian method), [1] (phenotypic.enhance.FocusEdgeLaplace method), [1] (phenotypic.enhance.FocusEdgeMeijering method), [1] (phenotypic.enhance.FocusEdgePhase method), [1] (phenotypic.enhance.FocusEdgeSato method), [1] (phenotypic.enhance.FocusEdgeSobel method), [1] (phenotypic.enhance.GaussianBlur method), [1] (phenotypic.enhance.GrayOpening method), [1] (phenotypic.enhance.ImageInverter method), [1] (phenotypic.enhance.LocalEdgeDenoise method), [1] (phenotypic.enhance.MedianFilter method), [1] (phenotypic.enhance.NonLocalMeansDenoiser method), [1] (phenotypic.enhance.RankMedianEnhancer method), [1] (phenotypic.enhance.SetDetectMode method), [1] (phenotypic.enhance.SharpenEdgeGauss method), [1] (phenotypic.enhance.StructureSmoothing method), [1] (phenotypic.enhance.SubtractGaussian method), [1] (phenotypic.enhance.SubtractOpening method), [1] (phenotypic.enhance.SubtractRollingBall method), [1] (phenotypic.enhance.SubtractWhiteTophat method), [1] (phenotypic.enhance.VisuShrinkEnhancer method), [1] (phenotypic.enhance.WhiteTophatEnhance method), [1] (phenotypic.grid.AutoGridFinder method), [1] (phenotypic.grid.CenteredAutoGridFinder method), [1] (phenotypic.grid.GridApply method), [1] (phenotypic.grid.ManualGridFinder method), [1] (phenotypic.measure.MeasureBounds method), [1] (phenotypic.measure.MeasureColor method), [1] (phenotypic.measure.MeasureGridLinRegStats method), [1] (phenotypic.measure.MeasureGridSpatial method), [1] (phenotypic.measure.MeasureGridSpread method), [1] (phenotypic.measure.MeasureIntensity method), [1] (phenotypic.measure.MeasureShape method), [1] (phenotypic.measure.MeasureSize method), [1] (phenotypic.measure.MeasureSymmetricZones method), [1] (phenotypic.measure.MeasureTexture method), [1] (phenotypic.post.AppendString method) (phenotypic.post.ExpandMetadata method) (phenotypic.post.MergeMetadata method) (phenotypic.post.PrependString method) (phenotypic.prefab.FilamentousFungiPipeline method), [1] (phenotypic.prefab.GridSectionPipeline method), [1] (phenotypic.prefab.HeavyOtsuPipeline method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1] (phenotypic.prefab.HeavyWatershedPipeline method), [1] (phenotypic.prefab.RoundPeaksPipeline method), [1] (phenotypic.prefab.SpImagerPipeline method), [1] (phenotypic.refine.ExtractColonyCore method), [1] (phenotypic.refine.GridAlignmentRefiner method), [1] (phenotypic.refine.GridOversizedObjectRemover method), [1] (phenotypic.refine.KeepNearestCenter method), [1] (phenotypic.refine.KeepSectionLargest method), [1] (phenotypic.refine.ManualRefine method), [1] (phenotypic.refine.MaskClosing method), [1] (phenotypic.refine.MaskDilation method), [1] (phenotypic.refine.MaskErosion method), [1] (phenotypic.refine.MaskFill method), [1] (phenotypic.refine.MaskGradient method), [1] (phenotypic.refine.MaskOpening method), [1] (phenotypic.refine.MaskWhiteTophat method), [1] (phenotypic.refine.MergeFragmentChains method), [1] (phenotypic.refine.NearestNeighborMerger method), [1] (phenotypic.refine.ReduceSectionsByLine method), [1] (phenotypic.refine.RefineBySineFit method), [1] (phenotypic.refine.RemoveBorderObjects method), [1] (phenotypic.refine.RemoveByFeature method), [1] (phenotypic.refine.RemoveGridOutliers method), [1] (phenotypic.refine.RemoveLowCircularity method), [1] (phenotypic.refine.SeparateObjects method), [1] (phenotypic.refine.Skeletonize method), [1] (phenotypic.refine.SmallObjectRemover method), [1] (phenotypic.refine.SmallToLargeMerger method), [1] (phenotypic.refine.Thinning method), [1] (phenotypic.refine.TrimAsymmetry method), [1] (phenotypic.tune.Budget method), [1] (phenotypic.tune.Categorical method), [1] (phenotypic.tune.CompositeScorer method), [1] (phenotypic.tune.EvaluationResult method), [1] (phenotypic.tune.Evaluator method), [1] (phenotypic.tune.Excluded method), [1] (phenotypic.tune.Fixed method), [1] (phenotypic.tune.FloatRange method), [1] (phenotypic.tune.GridConfig method), [1] (phenotypic.tune.GroundTruthMasks method), [1] (phenotypic.tune.HeldOutConfig method), [1] (phenotypic.tune.ImportanceReport method), [1] (phenotypic.tune.InferredSearchSpace method), [1] (phenotypic.tune.IntRange method), [1] (phenotypic.tune.Knob method), [1] (phenotypic.tune.OptunaConfig method), [1] (phenotypic.tune.QCScorer method), [1] (phenotypic.tune.RandomConfig method), [1] (phenotypic.tune.ReferenceFreeScorer method), [1] (phenotypic.tune.Scorer method), [1] (phenotypic.tune.SearchSpace method), [1] (phenotypic.tune.StrategyConfig method), [1] (phenotypic.tune.SupervisedScorer method), [1] (phenotypic.tune.targets.Nested method) (phenotypic.tune.targets.Param method) (phenotypic.tune.targets.Presence method) (phenotypic.tune.targets.TunableParam method) (phenotypic.tune.Trial method), [1] (phenotypic.tune.TuningSpec method), [1] model_rebuild() (phenotypic.abc_.BackgroundSubtraction class method), [1] (phenotypic.abc_.BaseOperation class method), [1] (phenotypic.abc_.ContrastAdjustment class method), [1] (phenotypic.abc_.FocusBlob class method), [1] (phenotypic.abc_.FocusEdge class method), [1] (phenotypic.abc_.GpuDetector class method), [1] (phenotypic.abc_.GridCorrector class method), [1] (phenotypic.abc_.GridFinder class method), [1] (phenotypic.abc_.GridMeasureFeatures class method), [1] (phenotypic.abc_.GridObjectDetector class method), [1] (phenotypic.abc_.GridObjectRefiner class method), [1] (phenotypic.abc_.GridOperation class method), [1] (phenotypic.abc_.ImageCorrector class method), [1] (phenotypic.abc_.ImageDenoiser class method), [1] (phenotypic.abc_.ImageEnhancer class method), [1] (phenotypic.abc_.ImageOperation class method), [1] (phenotypic.abc_.MeasureFeatures class method), [1] (phenotypic.abc_.MorphologicalFiltering class method), [1] (phenotypic.abc_.ObjectDetector class method), [1] (phenotypic.abc_.ObjectRefiner class method), [1] (phenotypic.abc_.PostMeasurement class method), [1] (phenotypic.abc_.PrefabPipeline class method), [1] (phenotypic.abc_.Smoothing class method), [1] (phenotypic.abc_.ThresholdDetector class method), [1] (phenotypic.analysis.abc_.ModelFitter class method) (phenotypic.analysis.abc_.QualityCheck class method) (phenotypic.analysis.abc_.SetAnalyzer class method) (phenotypic.analysis.DoubleSoftplus class method), [1] (phenotypic.analysis.EdgeCorrector class method), [1] (phenotypic.analysis.ErrorCutoffFinder class method), [1] (phenotypic.analysis.ExpectedVsDetectedCount class method), [1] (phenotypic.analysis.ICC class method), [1] (phenotypic.analysis.LinearSoftplus class method), [1] (phenotypic.analysis.LogGrowthModel class method), [1] (phenotypic.analysis.MADOutlierRemover class method), [1] (phenotypic.analysis.MaxModifiedZScore class method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount class method) (phenotypic.analysis.qc.ICC class method) (phenotypic.analysis.qc.MaxModifiedZScore class method) (phenotypic.analysis.qc.RelativeMAD class method) (phenotypic.analysis.qc.ReplicateAgreement class method) (phenotypic.analysis.qc.TukeyOutlierFraction class method) (phenotypic.analysis.RelativeMAD class method), [1] (phenotypic.analysis.ReplicateAgreement class method), [1] (phenotypic.analysis.TukeyOutlierFraction class method), [1] (phenotypic.analysis.TukeyOutlierRemover class method), [1] (phenotypic.correction.BayesShrinkCorrector class method), [1] (phenotypic.correction.CaptureMetadata class method), [1] (phenotypic.correction.ColorCheckerProfile class method), [1] (phenotypic.correction.ColorCorrector class method), [1] (phenotypic.correction.ColorDenoise class method), [1] (phenotypic.correction.DenoiseBlockMatch class method), [1] (phenotypic.correction.GridAligner class method), [1] (phenotypic.correction.ImageCropper class method), [1] (phenotypic.correction.ImagePadder class method), [1] (phenotypic.correction.VisuShrinkCorrector class method), [1] (phenotypic.detect.CannyDetector class method), [1] (phenotypic.detect.ChanVeseDetector class method), [1] (phenotypic.detect.CompositeDetector class method), [1] (phenotypic.detect.FilamentousFungiDetector class method), [1] (phenotypic.detect.HysteresisDetector class method), [1] (phenotypic.detect.InoculumDetector class method), [1] (phenotypic.detect.IsodataDetector class method), [1] (phenotypic.detect.LiDetector class method), [1] (phenotypic.detect.MadHysteresisDetector class method), [1] (phenotypic.detect.ManualGridPointDetector class method), [1] (phenotypic.detect.ManualPointDetector class method), [1] (phenotypic.detect.MeanDetector class method), [1] (phenotypic.detect.MinimumDetector class method), [1] (phenotypic.detect.OtsuDetector class method), [1] (phenotypic.detect.RankOtsuDetector class method), [1] (phenotypic.detect.RoundPeaksDetector class method), [1] (phenotypic.detect.SecondaryOtsuDetector class method), [1] (phenotypic.detect.SinePeakDetector class method), [1] (phenotypic.detect.TriangleDetector class method), [1] (phenotypic.detect.UserThreshold class method), [1] (phenotypic.detect.WatershedDetector class method), [1] (phenotypic.detect.YenDetector class method), [1] (phenotypic.enhance.BayesShrinkEnhancer class method), [1] (phenotypic.enhance.ContrastStretching class method), [1] (phenotypic.enhance.EnhanceBlockMatch class method), [1] (phenotypic.enhance.EnhanceLocalContrast class method), [1] (phenotypic.enhance.FlattenIllumination class method), [1] (phenotypic.enhance.FocusBlobLoG class method), [1] (phenotypic.enhance.FocusEdgeFrangi class method), [1] (phenotypic.enhance.FocusEdgeHessian class method), [1] (phenotypic.enhance.FocusEdgeLaplace class method), [1] (phenotypic.enhance.FocusEdgeMeijering class method), [1] (phenotypic.enhance.FocusEdgePhase class method), [1] (phenotypic.enhance.FocusEdgeSato class method), [1] (phenotypic.enhance.FocusEdgeSobel class method), [1] (phenotypic.enhance.GaussianBlur class method), [1] (phenotypic.enhance.GrayOpening class method), [1] (phenotypic.enhance.ImageInverter class method), [1] (phenotypic.enhance.LocalEdgeDenoise class method), [1] (phenotypic.enhance.MedianFilter class method), [1] (phenotypic.enhance.NonLocalMeansDenoiser class method), [1] (phenotypic.enhance.RankMedianEnhancer class method), [1] (phenotypic.enhance.SetDetectMode class method), [1] (phenotypic.enhance.SharpenEdgeGauss class method), [1] (phenotypic.enhance.StructureSmoothing class method), [1] (phenotypic.enhance.SubtractGaussian class method), [1] (phenotypic.enhance.SubtractOpening class method), [1] (phenotypic.enhance.SubtractRollingBall class method), [1] (phenotypic.enhance.SubtractWhiteTophat class method), [1] (phenotypic.enhance.VisuShrinkEnhancer class method), [1] (phenotypic.enhance.WhiteTophatEnhance class method), [1] (phenotypic.grid.AutoGridFinder class method), [1] (phenotypic.grid.CenteredAutoGridFinder class method), [1] (phenotypic.grid.GridApply class method), [1] (phenotypic.grid.ManualGridFinder class method), [1] (phenotypic.measure.MeasureBounds class method), [1] (phenotypic.measure.MeasureColor class method), [1] (phenotypic.measure.MeasureGridLinRegStats class method), [1] (phenotypic.measure.MeasureGridSpatial class method), [1] (phenotypic.measure.MeasureGridSpread class method), [1] (phenotypic.measure.MeasureIntensity class method), [1] (phenotypic.measure.MeasureShape class method), [1] (phenotypic.measure.MeasureSize class method), [1] (phenotypic.measure.MeasureSymmetricZones class method), [1] (phenotypic.measure.MeasureTexture class method), [1] (phenotypic.post.AppendString class method) (phenotypic.post.ExpandMetadata class method) (phenotypic.post.MergeMetadata class method) (phenotypic.post.PrependString class method) (phenotypic.prefab.FilamentousFungiPipeline class method), [1] (phenotypic.prefab.GridSectionPipeline class method), [1] (phenotypic.prefab.HeavyOtsuPipeline class method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline class method), [1] (phenotypic.prefab.HeavyWatershedPipeline class method), [1] (phenotypic.prefab.RoundPeaksPipeline class method), [1] (phenotypic.prefab.SpImagerPipeline class method), [1] (phenotypic.refine.ExtractColonyCore class method), [1] (phenotypic.refine.GridAlignmentRefiner class method), [1] (phenotypic.refine.GridOversizedObjectRemover class method), [1] (phenotypic.refine.KeepNearestCenter class method), [1] (phenotypic.refine.KeepSectionLargest class method), [1] (phenotypic.refine.ManualRefine class method), [1] (phenotypic.refine.MaskClosing class method), [1] (phenotypic.refine.MaskDilation class method), [1] (phenotypic.refine.MaskErosion class method), [1] (phenotypic.refine.MaskFill class method), [1] (phenotypic.refine.MaskGradient class method), [1] (phenotypic.refine.MaskOpening class method), [1] (phenotypic.refine.MaskWhiteTophat class method), [1] (phenotypic.refine.MergeFragmentChains class method), [1] (phenotypic.refine.NearestNeighborMerger class method), [1] (phenotypic.refine.ReduceSectionsByLine class method), [1] (phenotypic.refine.RefineBySineFit class method), [1] (phenotypic.refine.RemoveBorderObjects class method), [1] (phenotypic.refine.RemoveByFeature class method), [1] (phenotypic.refine.RemoveGridOutliers class method), [1] (phenotypic.refine.RemoveLowCircularity class method), [1] (phenotypic.refine.SeparateObjects class method), [1] (phenotypic.refine.Skeletonize class method), [1] (phenotypic.refine.SmallObjectRemover class method), [1] (phenotypic.refine.SmallToLargeMerger class method), [1] (phenotypic.refine.Thinning class method), [1] (phenotypic.refine.TrimAsymmetry class method), [1] (phenotypic.tune.Budget class method), [1] (phenotypic.tune.Categorical class method), [1] (phenotypic.tune.CompositeScorer class method), [1] (phenotypic.tune.EvaluationResult class method), [1] (phenotypic.tune.Evaluator class method), [1] (phenotypic.tune.Excluded class method), [1] (phenotypic.tune.Fixed class method), [1] (phenotypic.tune.FloatRange class method), [1] (phenotypic.tune.GridConfig class method), [1] (phenotypic.tune.GroundTruthMasks class method), [1] (phenotypic.tune.HeldOutConfig class method), [1] (phenotypic.tune.ImportanceReport class method), [1] (phenotypic.tune.InferredSearchSpace class method), [1] (phenotypic.tune.IntRange class method), [1] (phenotypic.tune.Knob class method), [1] (phenotypic.tune.OptunaConfig class method), [1] (phenotypic.tune.QCScorer class method), [1] (phenotypic.tune.RandomConfig class method), [1] (phenotypic.tune.ReferenceFreeScorer class method), [1] (phenotypic.tune.Scorer class method), [1] (phenotypic.tune.SearchSpace class method), [1] (phenotypic.tune.StrategyConfig class method), [1] (phenotypic.tune.SupervisedScorer class method), [1] (phenotypic.tune.targets.Nested class method) (phenotypic.tune.targets.Param class method) (phenotypic.tune.targets.Presence class method) (phenotypic.tune.targets.TunableParam class method) (phenotypic.tune.Trial class method), [1] (phenotypic.tune.TuningSpec class method), [1] model_validate() (phenotypic.abc_.BackgroundSubtraction class method), [1] (phenotypic.abc_.BaseOperation class method), [1] (phenotypic.abc_.ContrastAdjustment class method), [1] (phenotypic.abc_.FocusBlob class method), [1] (phenotypic.abc_.FocusEdge class method), [1] (phenotypic.abc_.GpuDetector class method), [1] (phenotypic.abc_.GridCorrector class method), [1] (phenotypic.abc_.GridFinder class method), [1] (phenotypic.abc_.GridMeasureFeatures class method), [1] (phenotypic.abc_.GridObjectDetector class method), [1] (phenotypic.abc_.GridObjectRefiner class method), [1] (phenotypic.abc_.GridOperation class method), [1] (phenotypic.abc_.ImageCorrector class method), [1] (phenotypic.abc_.ImageDenoiser class method), [1] (phenotypic.abc_.ImageEnhancer class method), [1] (phenotypic.abc_.ImageOperation class method), [1] (phenotypic.abc_.MeasureFeatures class method), [1] (phenotypic.abc_.MorphologicalFiltering class method), [1] (phenotypic.abc_.ObjectDetector class method), [1] (phenotypic.abc_.ObjectRefiner class method), [1] (phenotypic.abc_.PostMeasurement class method), [1] (phenotypic.abc_.PrefabPipeline class method), [1] (phenotypic.abc_.Smoothing class method), [1] (phenotypic.abc_.ThresholdDetector class method), [1] (phenotypic.analysis.abc_.ModelFitter class method) (phenotypic.analysis.abc_.QualityCheck class method) (phenotypic.analysis.abc_.SetAnalyzer class method) (phenotypic.analysis.DoubleSoftplus class method), [1] (phenotypic.analysis.EdgeCorrector class method), [1] (phenotypic.analysis.ErrorCutoffFinder class method), [1] (phenotypic.analysis.ExpectedVsDetectedCount class method), [1] (phenotypic.analysis.ICC class method), [1] (phenotypic.analysis.LinearSoftplus class method), [1] (phenotypic.analysis.LogGrowthModel class method), [1] (phenotypic.analysis.MADOutlierRemover class method), [1] (phenotypic.analysis.MaxModifiedZScore class method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount class method) (phenotypic.analysis.qc.ICC class method) (phenotypic.analysis.qc.MaxModifiedZScore class method) (phenotypic.analysis.qc.RelativeMAD class method) (phenotypic.analysis.qc.ReplicateAgreement class method) (phenotypic.analysis.qc.TukeyOutlierFraction class method) (phenotypic.analysis.RelativeMAD class method), [1] (phenotypic.analysis.ReplicateAgreement class method), [1] (phenotypic.analysis.TukeyOutlierFraction class method), [1] (phenotypic.analysis.TukeyOutlierRemover class method), [1] (phenotypic.correction.BayesShrinkCorrector class method), [1] (phenotypic.correction.CaptureMetadata class method), [1] (phenotypic.correction.ColorCheckerProfile class method), [1] (phenotypic.correction.ColorCorrector class method), [1] (phenotypic.correction.ColorDenoise class method), [1] (phenotypic.correction.DenoiseBlockMatch class method), [1] (phenotypic.correction.GridAligner class method), [1] (phenotypic.correction.ImageCropper class method), [1] (phenotypic.correction.ImagePadder class method), [1] (phenotypic.correction.VisuShrinkCorrector class method), [1] (phenotypic.detect.CannyDetector class method), [1] (phenotypic.detect.ChanVeseDetector class method), [1] (phenotypic.detect.CompositeDetector class method), [1] (phenotypic.detect.FilamentousFungiDetector class method), [1] (phenotypic.detect.HysteresisDetector class method), [1] (phenotypic.detect.InoculumDetector class method), [1] (phenotypic.detect.IsodataDetector class method), [1] (phenotypic.detect.LiDetector class method), [1] (phenotypic.detect.MadHysteresisDetector class method), [1] (phenotypic.detect.ManualGridPointDetector class method), [1] (phenotypic.detect.ManualPointDetector class method), [1] (phenotypic.detect.MeanDetector class method), [1] (phenotypic.detect.MinimumDetector class method), [1] (phenotypic.detect.OtsuDetector class method), [1] (phenotypic.detect.RankOtsuDetector class method), [1] (phenotypic.detect.RoundPeaksDetector class method), [1] (phenotypic.detect.SecondaryOtsuDetector class method), [1] (phenotypic.detect.SinePeakDetector class method), [1] (phenotypic.detect.TriangleDetector class method), [1] (phenotypic.detect.UserThreshold class method), [1] (phenotypic.detect.WatershedDetector class method), [1] (phenotypic.detect.YenDetector class method), [1] (phenotypic.enhance.BayesShrinkEnhancer class method), [1] (phenotypic.enhance.ContrastStretching class method), [1] (phenotypic.enhance.EnhanceBlockMatch class method), [1] (phenotypic.enhance.EnhanceLocalContrast class method), [1] (phenotypic.enhance.FlattenIllumination class method), [1] (phenotypic.enhance.FocusBlobLoG class method), [1] (phenotypic.enhance.FocusEdgeFrangi class method), [1] (phenotypic.enhance.FocusEdgeHessian class method), [1] (phenotypic.enhance.FocusEdgeLaplace class method), [1] (phenotypic.enhance.FocusEdgeMeijering class method), [1] (phenotypic.enhance.FocusEdgePhase class method), [1] (phenotypic.enhance.FocusEdgeSato class method), [1] (phenotypic.enhance.FocusEdgeSobel class method), [1] (phenotypic.enhance.GaussianBlur class method), [1] (phenotypic.enhance.GrayOpening class method), [1] (phenotypic.enhance.ImageInverter class method), [1] (phenotypic.enhance.LocalEdgeDenoise class method), [1] (phenotypic.enhance.MedianFilter class method), [1] (phenotypic.enhance.NonLocalMeansDenoiser class method), [1] (phenotypic.enhance.RankMedianEnhancer class method), [1] (phenotypic.enhance.SetDetectMode class method), [1] (phenotypic.enhance.SharpenEdgeGauss class method), [1] (phenotypic.enhance.StructureSmoothing class method), [1] (phenotypic.enhance.SubtractGaussian class method), [1] (phenotypic.enhance.SubtractOpening class method), [1] (phenotypic.enhance.SubtractRollingBall class method), [1] (phenotypic.enhance.SubtractWhiteTophat class method), [1] (phenotypic.enhance.VisuShrinkEnhancer class method), [1] (phenotypic.enhance.WhiteTophatEnhance class method), [1] (phenotypic.grid.AutoGridFinder class method), [1] (phenotypic.grid.CenteredAutoGridFinder class method), [1] (phenotypic.grid.GridApply class method), [1] (phenotypic.grid.ManualGridFinder class method), [1] (phenotypic.measure.MeasureBounds class method), [1] (phenotypic.measure.MeasureColor class method), [1] (phenotypic.measure.MeasureGridLinRegStats class method), [1] (phenotypic.measure.MeasureGridSpatial class method), [1] (phenotypic.measure.MeasureGridSpread class method), [1] (phenotypic.measure.MeasureIntensity class method), [1] (phenotypic.measure.MeasureShape class method), [1] (phenotypic.measure.MeasureSize class method), [1] (phenotypic.measure.MeasureSymmetricZones class method), [1] (phenotypic.measure.MeasureTexture class method), [1] (phenotypic.post.AppendString class method) (phenotypic.post.ExpandMetadata class method) (phenotypic.post.MergeMetadata class method) (phenotypic.post.PrependString class method) (phenotypic.prefab.FilamentousFungiPipeline class method), [1] (phenotypic.prefab.GridSectionPipeline class method), [1] (phenotypic.prefab.HeavyOtsuPipeline class method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline class method), [1] (phenotypic.prefab.HeavyWatershedPipeline class method), [1] (phenotypic.prefab.RoundPeaksPipeline class method), [1] (phenotypic.prefab.SpImagerPipeline class method), [1] (phenotypic.refine.ExtractColonyCore class method), [1] (phenotypic.refine.GridAlignmentRefiner class method), [1] (phenotypic.refine.GridOversizedObjectRemover class method), [1] (phenotypic.refine.KeepNearestCenter class method), [1] (phenotypic.refine.KeepSectionLargest class method), [1] (phenotypic.refine.ManualRefine class method), [1] (phenotypic.refine.MaskClosing class method), [1] (phenotypic.refine.MaskDilation class method), [1] (phenotypic.refine.MaskErosion class method), [1] (phenotypic.refine.MaskFill class method), [1] (phenotypic.refine.MaskGradient class method), [1] (phenotypic.refine.MaskOpening class method), [1] (phenotypic.refine.MaskWhiteTophat class method), [1] (phenotypic.refine.MergeFragmentChains class method), [1] (phenotypic.refine.NearestNeighborMerger class method), [1] (phenotypic.refine.ReduceSectionsByLine class method), [1] (phenotypic.refine.RefineBySineFit class method), [1] (phenotypic.refine.RemoveBorderObjects class method), [1] (phenotypic.refine.RemoveByFeature class method), [1] (phenotypic.refine.RemoveGridOutliers class method), [1] (phenotypic.refine.RemoveLowCircularity class method), [1] (phenotypic.refine.SeparateObjects class method), [1] (phenotypic.refine.Skeletonize class method), [1] (phenotypic.refine.SmallObjectRemover class method), [1] (phenotypic.refine.SmallToLargeMerger class method), [1] (phenotypic.refine.Thinning class method), [1] (phenotypic.refine.TrimAsymmetry class method), [1] (phenotypic.tune.Budget class method), [1] (phenotypic.tune.Categorical class method), [1] (phenotypic.tune.CompositeScorer class method), [1] (phenotypic.tune.EvaluationResult class method), [1] (phenotypic.tune.Evaluator class method), [1] (phenotypic.tune.Excluded class method), [1] (phenotypic.tune.Fixed class method), [1] (phenotypic.tune.FloatRange class method), [1] (phenotypic.tune.GridConfig class method), [1] (phenotypic.tune.GroundTruthMasks class method), [1] (phenotypic.tune.HeldOutConfig class method), [1] (phenotypic.tune.ImportanceReport class method), [1] (phenotypic.tune.InferredSearchSpace class method), [1] (phenotypic.tune.IntRange class method), [1] (phenotypic.tune.Knob class method), [1] (phenotypic.tune.OptunaConfig class method), [1] (phenotypic.tune.QCScorer class method), [1] (phenotypic.tune.RandomConfig class method), [1] (phenotypic.tune.ReferenceFreeScorer class method), [1] (phenotypic.tune.Scorer class method), [1] (phenotypic.tune.SearchSpace class method), [1] (phenotypic.tune.StrategyConfig class method), [1] (phenotypic.tune.SupervisedScorer class method), [1] (phenotypic.tune.targets.Nested class method) (phenotypic.tune.targets.Param class method) (phenotypic.tune.targets.Presence class method) (phenotypic.tune.targets.TunableParam class method) (phenotypic.tune.Trial class method), [1] (phenotypic.tune.TuningSpec class method), [1] model_validate_json() (phenotypic.abc_.BackgroundSubtraction class method), [1] (phenotypic.abc_.BaseOperation class method), [1] (phenotypic.abc_.ContrastAdjustment class method), [1] (phenotypic.abc_.FocusBlob class method), [1] (phenotypic.abc_.FocusEdge class method), [1] (phenotypic.abc_.GpuDetector class method), [1] (phenotypic.abc_.GridCorrector class method), [1] (phenotypic.abc_.GridFinder class method), [1] (phenotypic.abc_.GridMeasureFeatures class method), [1] (phenotypic.abc_.GridObjectDetector class method), [1] (phenotypic.abc_.GridObjectRefiner class method), [1] (phenotypic.abc_.GridOperation class method), [1] (phenotypic.abc_.ImageCorrector class method), [1] (phenotypic.abc_.ImageDenoiser class method), [1] (phenotypic.abc_.ImageEnhancer class method), [1] (phenotypic.abc_.ImageOperation class method), [1] (phenotypic.abc_.MeasureFeatures class method), [1] (phenotypic.abc_.MorphologicalFiltering class method), [1] (phenotypic.abc_.ObjectDetector class method), [1] (phenotypic.abc_.ObjectRefiner class method), [1] (phenotypic.abc_.PostMeasurement class method), [1] (phenotypic.abc_.PrefabPipeline class method), [1] (phenotypic.abc_.Smoothing class method), [1] (phenotypic.abc_.ThresholdDetector class method), [1] (phenotypic.analysis.abc_.ModelFitter class method) (phenotypic.analysis.abc_.QualityCheck class method) (phenotypic.analysis.abc_.SetAnalyzer class method) (phenotypic.analysis.DoubleSoftplus class method), [1] (phenotypic.analysis.EdgeCorrector class method), [1] (phenotypic.analysis.ErrorCutoffFinder class method), [1] (phenotypic.analysis.ExpectedVsDetectedCount class method), [1] (phenotypic.analysis.ICC class method), [1] (phenotypic.analysis.LinearSoftplus class method), [1] (phenotypic.analysis.LogGrowthModel class method), [1] (phenotypic.analysis.MADOutlierRemover class method), [1] (phenotypic.analysis.MaxModifiedZScore class method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount class method) (phenotypic.analysis.qc.ICC class method) (phenotypic.analysis.qc.MaxModifiedZScore class method) (phenotypic.analysis.qc.RelativeMAD class method) (phenotypic.analysis.qc.ReplicateAgreement class method) (phenotypic.analysis.qc.TukeyOutlierFraction class method) (phenotypic.analysis.RelativeMAD class method), [1] (phenotypic.analysis.ReplicateAgreement class method), [1] (phenotypic.analysis.TukeyOutlierFraction class method), [1] (phenotypic.analysis.TukeyOutlierRemover class method), [1] (phenotypic.correction.BayesShrinkCorrector class method), [1] (phenotypic.correction.CaptureMetadata class method), [1] (phenotypic.correction.ColorCheckerProfile class method), [1] (phenotypic.correction.ColorCorrector class method), [1] (phenotypic.correction.ColorDenoise class method), [1] (phenotypic.correction.DenoiseBlockMatch class method), [1] (phenotypic.correction.GridAligner class method), [1] (phenotypic.correction.ImageCropper class method), [1] (phenotypic.correction.ImagePadder class method), [1] (phenotypic.correction.VisuShrinkCorrector class method), [1] (phenotypic.detect.CannyDetector class method), [1] (phenotypic.detect.ChanVeseDetector class method), [1] (phenotypic.detect.CompositeDetector class method), [1] (phenotypic.detect.FilamentousFungiDetector class method), [1] (phenotypic.detect.HysteresisDetector class method), [1] (phenotypic.detect.InoculumDetector class method), [1] (phenotypic.detect.IsodataDetector class method), [1] (phenotypic.detect.LiDetector class method), [1] (phenotypic.detect.MadHysteresisDetector class method), [1] (phenotypic.detect.ManualGridPointDetector class method), [1] (phenotypic.detect.ManualPointDetector class method), [1] (phenotypic.detect.MeanDetector class method), [1] (phenotypic.detect.MinimumDetector class method), [1] (phenotypic.detect.OtsuDetector class method), [1] (phenotypic.detect.RankOtsuDetector class method), [1] (phenotypic.detect.RoundPeaksDetector class method), [1] (phenotypic.detect.SecondaryOtsuDetector class method), [1] (phenotypic.detect.SinePeakDetector class method), [1] (phenotypic.detect.TriangleDetector class method), [1] (phenotypic.detect.UserThreshold class method), [1] (phenotypic.detect.WatershedDetector class method), [1] (phenotypic.detect.YenDetector class method), [1] (phenotypic.enhance.BayesShrinkEnhancer class method), [1] (phenotypic.enhance.ContrastStretching class method), [1] (phenotypic.enhance.EnhanceBlockMatch class method), [1] (phenotypic.enhance.EnhanceLocalContrast class method), [1] (phenotypic.enhance.FlattenIllumination class method), [1] (phenotypic.enhance.FocusBlobLoG class method), [1] (phenotypic.enhance.FocusEdgeFrangi class method), [1] (phenotypic.enhance.FocusEdgeHessian class method), [1] (phenotypic.enhance.FocusEdgeLaplace class method), [1] (phenotypic.enhance.FocusEdgeMeijering class method), [1] (phenotypic.enhance.FocusEdgePhase class method), [1] (phenotypic.enhance.FocusEdgeSato class method), [1] (phenotypic.enhance.FocusEdgeSobel class method), [1] (phenotypic.enhance.GaussianBlur class method), [1] (phenotypic.enhance.GrayOpening class method), [1] (phenotypic.enhance.ImageInverter class method), [1] (phenotypic.enhance.LocalEdgeDenoise class method), [1] (phenotypic.enhance.MedianFilter class method), [1] (phenotypic.enhance.NonLocalMeansDenoiser class method), [1] (phenotypic.enhance.RankMedianEnhancer class method), [1] (phenotypic.enhance.SetDetectMode class method), [1] (phenotypic.enhance.SharpenEdgeGauss class method), [1] (phenotypic.enhance.StructureSmoothing class method), [1] (phenotypic.enhance.SubtractGaussian class method), [1] (phenotypic.enhance.SubtractOpening class method), [1] (phenotypic.enhance.SubtractRollingBall class method), [1] (phenotypic.enhance.SubtractWhiteTophat class method), [1] (phenotypic.enhance.VisuShrinkEnhancer class method), [1] (phenotypic.enhance.WhiteTophatEnhance class method), [1] (phenotypic.grid.AutoGridFinder class method), [1] (phenotypic.grid.CenteredAutoGridFinder class method), [1] (phenotypic.grid.GridApply class method), [1] (phenotypic.grid.ManualGridFinder class method), [1] (phenotypic.measure.MeasureBounds class method), [1] (phenotypic.measure.MeasureColor class method), [1] (phenotypic.measure.MeasureGridLinRegStats class method), [1] (phenotypic.measure.MeasureGridSpatial class method), [1] (phenotypic.measure.MeasureGridSpread class method), [1] (phenotypic.measure.MeasureIntensity class method), [1] (phenotypic.measure.MeasureShape class method), [1] (phenotypic.measure.MeasureSize class method), [1] (phenotypic.measure.MeasureSymmetricZones class method), [1] (phenotypic.measure.MeasureTexture class method), [1] (phenotypic.post.AppendString class method) (phenotypic.post.ExpandMetadata class method) (phenotypic.post.MergeMetadata class method) (phenotypic.post.PrependString class method) (phenotypic.prefab.FilamentousFungiPipeline class method), [1] (phenotypic.prefab.GridSectionPipeline class method), [1] (phenotypic.prefab.HeavyOtsuPipeline class method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline class method), [1] (phenotypic.prefab.HeavyWatershedPipeline class method), [1] (phenotypic.prefab.RoundPeaksPipeline class method), [1] (phenotypic.prefab.SpImagerPipeline class method), [1] (phenotypic.refine.ExtractColonyCore class method), [1] (phenotypic.refine.GridAlignmentRefiner class method), [1] (phenotypic.refine.GridOversizedObjectRemover class method), [1] (phenotypic.refine.KeepNearestCenter class method), [1] (phenotypic.refine.KeepSectionLargest class method), [1] (phenotypic.refine.ManualRefine class method), [1] (phenotypic.refine.MaskClosing class method), [1] (phenotypic.refine.MaskDilation class method), [1] (phenotypic.refine.MaskErosion class method), [1] (phenotypic.refine.MaskFill class method), [1] (phenotypic.refine.MaskGradient class method), [1] (phenotypic.refine.MaskOpening class method), [1] (phenotypic.refine.MaskWhiteTophat class method), [1] (phenotypic.refine.MergeFragmentChains class method), [1] (phenotypic.refine.NearestNeighborMerger class method), [1] (phenotypic.refine.ReduceSectionsByLine class method), [1] (phenotypic.refine.RefineBySineFit class method), [1] (phenotypic.refine.RemoveBorderObjects class method), [1] (phenotypic.refine.RemoveByFeature class method), [1] (phenotypic.refine.RemoveGridOutliers class method), [1] (phenotypic.refine.RemoveLowCircularity class method), [1] (phenotypic.refine.SeparateObjects class method), [1] (phenotypic.refine.Skeletonize class method), [1] (phenotypic.refine.SmallObjectRemover class method), [1] (phenotypic.refine.SmallToLargeMerger class method), [1] (phenotypic.refine.Thinning class method), [1] (phenotypic.refine.TrimAsymmetry class method), [1] (phenotypic.tune.Budget class method), [1] (phenotypic.tune.Categorical class method), [1] (phenotypic.tune.CompositeScorer class method), [1] (phenotypic.tune.EvaluationResult class method), [1] (phenotypic.tune.Evaluator class method), [1] (phenotypic.tune.Excluded class method), [1] (phenotypic.tune.Fixed class method), [1] (phenotypic.tune.FloatRange class method), [1] (phenotypic.tune.GridConfig class method), [1] (phenotypic.tune.GroundTruthMasks class method), [1] (phenotypic.tune.HeldOutConfig class method), [1] (phenotypic.tune.ImportanceReport class method), [1] (phenotypic.tune.InferredSearchSpace class method), [1] (phenotypic.tune.IntRange class method), [1] (phenotypic.tune.Knob class method), [1] (phenotypic.tune.OptunaConfig class method), [1] (phenotypic.tune.QCScorer class method), [1] (phenotypic.tune.RandomConfig class method), [1] (phenotypic.tune.ReferenceFreeScorer class method), [1] (phenotypic.tune.Scorer class method), [1] (phenotypic.tune.SearchSpace class method), [1] (phenotypic.tune.StrategyConfig class method), [1] (phenotypic.tune.SupervisedScorer class method), [1] (phenotypic.tune.targets.Nested class method) (phenotypic.tune.targets.Param class method) (phenotypic.tune.targets.Presence class method) (phenotypic.tune.targets.TunableParam class method) (phenotypic.tune.Trial class method), [1] (phenotypic.tune.TuningSpec class method), [1] model_validate_strings() (phenotypic.abc_.BackgroundSubtraction class method), [1] (phenotypic.abc_.BaseOperation class method), [1] (phenotypic.abc_.ContrastAdjustment class method), [1] (phenotypic.abc_.FocusBlob class method), [1] (phenotypic.abc_.FocusEdge class method), [1] (phenotypic.abc_.GpuDetector class method), [1] (phenotypic.abc_.GridCorrector class method), [1] (phenotypic.abc_.GridFinder class method), [1] (phenotypic.abc_.GridMeasureFeatures class method), [1] (phenotypic.abc_.GridObjectDetector class method), [1] (phenotypic.abc_.GridObjectRefiner class method), [1] (phenotypic.abc_.GridOperation class method), [1] (phenotypic.abc_.ImageCorrector class method), [1] (phenotypic.abc_.ImageDenoiser class method), [1] (phenotypic.abc_.ImageEnhancer class method), [1] (phenotypic.abc_.ImageOperation class method), [1] (phenotypic.abc_.MeasureFeatures class method), [1] (phenotypic.abc_.MorphologicalFiltering class method), [1] (phenotypic.abc_.ObjectDetector class method), [1] (phenotypic.abc_.ObjectRefiner class method), [1] (phenotypic.abc_.PostMeasurement class method), [1] (phenotypic.abc_.PrefabPipeline class method), [1] (phenotypic.abc_.Smoothing class method), [1] (phenotypic.abc_.ThresholdDetector class method), [1] (phenotypic.analysis.abc_.ModelFitter class method) (phenotypic.analysis.abc_.QualityCheck class method) (phenotypic.analysis.abc_.SetAnalyzer class method) (phenotypic.analysis.DoubleSoftplus class method), [1] (phenotypic.analysis.EdgeCorrector class method), [1] (phenotypic.analysis.ErrorCutoffFinder class method), [1] (phenotypic.analysis.ExpectedVsDetectedCount class method), [1] (phenotypic.analysis.ICC class method), [1] (phenotypic.analysis.LinearSoftplus class method), [1] (phenotypic.analysis.LogGrowthModel class method), [1] (phenotypic.analysis.MADOutlierRemover class method), [1] (phenotypic.analysis.MaxModifiedZScore class method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount class method) (phenotypic.analysis.qc.ICC class method) (phenotypic.analysis.qc.MaxModifiedZScore class method) (phenotypic.analysis.qc.RelativeMAD class method) (phenotypic.analysis.qc.ReplicateAgreement class method) (phenotypic.analysis.qc.TukeyOutlierFraction class method) (phenotypic.analysis.RelativeMAD class method), [1] (phenotypic.analysis.ReplicateAgreement class method), [1] (phenotypic.analysis.TukeyOutlierFraction class method), [1] (phenotypic.analysis.TukeyOutlierRemover class method), [1] (phenotypic.correction.BayesShrinkCorrector class method), [1] (phenotypic.correction.CaptureMetadata class method), [1] (phenotypic.correction.ColorCheckerProfile class method), [1] (phenotypic.correction.ColorCorrector class method), [1] (phenotypic.correction.ColorDenoise class method), [1] (phenotypic.correction.DenoiseBlockMatch class method), [1] (phenotypic.correction.GridAligner class method), [1] (phenotypic.correction.ImageCropper class method), [1] (phenotypic.correction.ImagePadder class method), [1] (phenotypic.correction.VisuShrinkCorrector class method), [1] (phenotypic.detect.CannyDetector class method), [1] (phenotypic.detect.ChanVeseDetector class method), [1] (phenotypic.detect.CompositeDetector class method), [1] (phenotypic.detect.FilamentousFungiDetector class method), [1] (phenotypic.detect.HysteresisDetector class method), [1] (phenotypic.detect.InoculumDetector class method), [1] (phenotypic.detect.IsodataDetector class method), [1] (phenotypic.detect.LiDetector class method), [1] (phenotypic.detect.MadHysteresisDetector class method), [1] (phenotypic.detect.ManualGridPointDetector class method), [1] (phenotypic.detect.ManualPointDetector class method), [1] (phenotypic.detect.MeanDetector class method), [1] (phenotypic.detect.MinimumDetector class method), [1] (phenotypic.detect.OtsuDetector class method), [1] (phenotypic.detect.RankOtsuDetector class method), [1] (phenotypic.detect.RoundPeaksDetector class method), [1] (phenotypic.detect.SecondaryOtsuDetector class method), [1] (phenotypic.detect.SinePeakDetector class method), [1] (phenotypic.detect.TriangleDetector class method), [1] (phenotypic.detect.UserThreshold class method), [1] (phenotypic.detect.WatershedDetector class method), [1] (phenotypic.detect.YenDetector class method), [1] (phenotypic.enhance.BayesShrinkEnhancer class method), [1] (phenotypic.enhance.ContrastStretching class method), [1] (phenotypic.enhance.EnhanceBlockMatch class method), [1] (phenotypic.enhance.EnhanceLocalContrast class method), [1] (phenotypic.enhance.FlattenIllumination class method), [1] (phenotypic.enhance.FocusBlobLoG class method), [1] (phenotypic.enhance.FocusEdgeFrangi class method), [1] (phenotypic.enhance.FocusEdgeHessian class method), [1] (phenotypic.enhance.FocusEdgeLaplace class method), [1] (phenotypic.enhance.FocusEdgeMeijering class method), [1] (phenotypic.enhance.FocusEdgePhase class method), [1] (phenotypic.enhance.FocusEdgeSato class method), [1] (phenotypic.enhance.FocusEdgeSobel class method), [1] (phenotypic.enhance.GaussianBlur class method), [1] (phenotypic.enhance.GrayOpening class method), [1] (phenotypic.enhance.ImageInverter class method), [1] (phenotypic.enhance.LocalEdgeDenoise class method), [1] (phenotypic.enhance.MedianFilter class method), [1] (phenotypic.enhance.NonLocalMeansDenoiser class method), [1] (phenotypic.enhance.RankMedianEnhancer class method), [1] (phenotypic.enhance.SetDetectMode class method), [1] (phenotypic.enhance.SharpenEdgeGauss class method), [1] (phenotypic.enhance.StructureSmoothing class method), [1] (phenotypic.enhance.SubtractGaussian class method), [1] (phenotypic.enhance.SubtractOpening class method), [1] (phenotypic.enhance.SubtractRollingBall class method), [1] (phenotypic.enhance.SubtractWhiteTophat class method), [1] (phenotypic.enhance.VisuShrinkEnhancer class method), [1] (phenotypic.enhance.WhiteTophatEnhance class method), [1] (phenotypic.grid.AutoGridFinder class method), [1] (phenotypic.grid.CenteredAutoGridFinder class method), [1] (phenotypic.grid.GridApply class method), [1] (phenotypic.grid.ManualGridFinder class method), [1] (phenotypic.measure.MeasureBounds class method), [1] (phenotypic.measure.MeasureColor class method), [1] (phenotypic.measure.MeasureGridLinRegStats class method), [1] (phenotypic.measure.MeasureGridSpatial class method), [1] (phenotypic.measure.MeasureGridSpread class method), [1] (phenotypic.measure.MeasureIntensity class method), [1] (phenotypic.measure.MeasureShape class method), [1] (phenotypic.measure.MeasureSize class method), [1] (phenotypic.measure.MeasureSymmetricZones class method), [1] (phenotypic.measure.MeasureTexture class method), [1] (phenotypic.post.AppendString class method) (phenotypic.post.ExpandMetadata class method) (phenotypic.post.MergeMetadata class method) (phenotypic.post.PrependString class method) (phenotypic.prefab.FilamentousFungiPipeline class method), [1] (phenotypic.prefab.GridSectionPipeline class method), [1] (phenotypic.prefab.HeavyOtsuPipeline class method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline class method), [1] (phenotypic.prefab.HeavyWatershedPipeline class method), [1] (phenotypic.prefab.RoundPeaksPipeline class method), [1] (phenotypic.prefab.SpImagerPipeline class method), [1] (phenotypic.refine.ExtractColonyCore class method), [1] (phenotypic.refine.GridAlignmentRefiner class method), [1] (phenotypic.refine.GridOversizedObjectRemover class method), [1] (phenotypic.refine.KeepNearestCenter class method), [1] (phenotypic.refine.KeepSectionLargest class method), [1] (phenotypic.refine.ManualRefine class method), [1] (phenotypic.refine.MaskClosing class method), [1] (phenotypic.refine.MaskDilation class method), [1] (phenotypic.refine.MaskErosion class method), [1] (phenotypic.refine.MaskFill class method), [1] (phenotypic.refine.MaskGradient class method), [1] (phenotypic.refine.MaskOpening class method), [1] (phenotypic.refine.MaskWhiteTophat class method), [1] (phenotypic.refine.MergeFragmentChains class method), [1] (phenotypic.refine.NearestNeighborMerger class method), [1] (phenotypic.refine.ReduceSectionsByLine class method), [1] (phenotypic.refine.RefineBySineFit class method), [1] (phenotypic.refine.RemoveBorderObjects class method), [1] (phenotypic.refine.RemoveByFeature class method), [1] (phenotypic.refine.RemoveGridOutliers class method), [1] (phenotypic.refine.RemoveLowCircularity class method), [1] (phenotypic.refine.SeparateObjects class method), [1] (phenotypic.refine.Skeletonize class method), [1] (phenotypic.refine.SmallObjectRemover class method), [1] (phenotypic.refine.SmallToLargeMerger class method), [1] (phenotypic.refine.Thinning class method), [1] (phenotypic.refine.TrimAsymmetry class method), [1] (phenotypic.tune.Budget class method), [1] (phenotypic.tune.Categorical class method), [1] (phenotypic.tune.CompositeScorer class method), [1] (phenotypic.tune.EvaluationResult class method), [1] (phenotypic.tune.Evaluator class method), [1] (phenotypic.tune.Excluded class method), [1] (phenotypic.tune.Fixed class method), [1] (phenotypic.tune.FloatRange class method), [1] (phenotypic.tune.GridConfig class method), [1] (phenotypic.tune.GroundTruthMasks class method), [1] (phenotypic.tune.HeldOutConfig class method), [1] (phenotypic.tune.ImportanceReport class method), [1] (phenotypic.tune.InferredSearchSpace class method), [1] (phenotypic.tune.IntRange class method), [1] (phenotypic.tune.Knob class method), [1] (phenotypic.tune.OptunaConfig class method), [1] (phenotypic.tune.QCScorer class method), [1] (phenotypic.tune.RandomConfig class method), [1] (phenotypic.tune.ReferenceFreeScorer class method), [1] (phenotypic.tune.Scorer class method), [1] (phenotypic.tune.SearchSpace class method), [1] (phenotypic.tune.StrategyConfig class method), [1] (phenotypic.tune.SupervisedScorer class method), [1] (phenotypic.tune.targets.Nested class method) (phenotypic.tune.targets.Param class method) (phenotypic.tune.targets.Presence class method) (phenotypic.tune.targets.TunableParam class method) (phenotypic.tune.Trial class method), [1] (phenotypic.tune.TuningSpec class method), [1] ModelFitter (class in phenotypic.analysis.abc_) module phenotypic phenotypic.abc_ phenotypic.analysis phenotypic.analysis.abc_ phenotypic.analysis.qc phenotypic.correction phenotypic.data phenotypic.detect phenotypic.detect.nn phenotypic.enhance phenotypic.grid phenotypic.gui phenotypic.gui.analysis phenotypic.gui.browse phenotypic.gui.builder phenotypic.gui.results_viewer phenotypic.gui.results_viewer.colony_view phenotypic.gui.run_console phenotypic.gui.shell phenotypic.gui.tune phenotypic.measure phenotypic.phenotypicCLI phenotypic.post phenotypic.prefab phenotypic.refine phenotypic.schema phenotypic.sdk_ phenotypic.sdk_.branch_pathfinding phenotypic.sdk_.colourspace phenotypic.sdk_.constants_ phenotypic.sdk_.exceptions_ phenotypic.sdk_.funcs_ phenotypic.sdk_.generate_report phenotypic.sdk_.hdf_ phenotypic.sdk_.mixin phenotypic.sdk_.monitor_slurm_jobs phenotypic.sdk_.napari_ phenotypic.sdk_.register phenotypic.sdk_.slurm phenotypic.sdk_.slurm_ phenotypic.sdk_.submitit_ phenotypic.sdk_.typing_ phenotypic.sdk_.viz phenotypic.sdk_.viz.figures phenotypic.sdk_.viz.notebook phenotypic.settings_ phenotypic.tune phenotypic.tune.targets phenotypic.util phenotypic.util.image_metrics ModulePath (class in phenotypic.sdk_), [1] morph_close_radius (phenotypic.refine.ExtractColonyCore attribute), [1] morph_open_radius (phenotypic.refine.ExtractColonyCore attribute), [1] morph_progression() (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) MorphologicalFiltering (class in phenotypic.abc_), [1] MPL (class in phenotypic.settings_) MSE (phenotypic.schema.MODEL_METRICS attribute) mu (phenotypic.correction.DenoiseBlockMatch attribute), [1] (phenotypic.detect.ChanVeseDetector attribute), [1] mult (phenotypic.enhance.FocusEdgePhase attribute), [1] multi_objective (phenotypic.tune.CompositeScorer attribute), [1] murmur3_array_signature() (in module phenotypic.sdk_.funcs_) mycelium

N

N0_FIT (phenotypic.schema.LOG_GROWTH_MODEL attribute) n_angular_bins (phenotypic.measure.MeasureSymmetricZones attribute), [1] (phenotypic.refine.TrimAsymmetry attribute), [1] n_annuli (phenotypic.measure.MeasureSymmetricZones attribute), [1] (phenotypic.refine.TrimAsymmetry attribute), [1] n_components (phenotypic.refine.ExtractColonyCore attribute), [1] n_excluded (phenotypic.tune.InferredSearchSpace property), [1] n_images (phenotypic.tune.EvaluationResult attribute), [1] (phenotypic.tune.Trial attribute), [1] n_iter (phenotypic.enhance.GrayOpening attribute), [1] (phenotypic.enhance.SharpenEdgeGauss attribute), [1] (phenotypic.enhance.SubtractGaussian attribute), [1] (phenotypic.enhance.SubtractOpening attribute), [1] (phenotypic.refine.MaskClosing attribute), [1] (phenotypic.refine.MaskDilation attribute), [1] (phenotypic.refine.MaskErosion attribute), [1] (phenotypic.refine.MaskOpening attribute), [1] n_jobs (phenotypic.analysis.abc_.ModelFitter attribute) (phenotypic.analysis.abc_.QualityCheck attribute) (phenotypic.analysis.abc_.SetAnalyzer attribute) (phenotypic.analysis.DoubleSoftplus attribute), [1] (phenotypic.analysis.EdgeCorrector attribute), [1] (phenotypic.analysis.ExpectedVsDetectedCount attribute), [1] (phenotypic.analysis.ICC attribute), [1] (phenotypic.analysis.LinearSoftplus attribute), [1] (phenotypic.analysis.LogGrowthModel attribute), [1] (phenotypic.analysis.MADOutlierRemover attribute), [1], [2], [3] (phenotypic.analysis.MaxModifiedZScore attribute), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount attribute) (phenotypic.analysis.qc.ICC attribute) (phenotypic.analysis.qc.MaxModifiedZScore attribute) (phenotypic.analysis.qc.RelativeMAD attribute) (phenotypic.analysis.qc.ReplicateAgreement attribute) (phenotypic.analysis.qc.TukeyOutlierFraction attribute) (phenotypic.analysis.RelativeMAD attribute), [1] (phenotypic.analysis.ReplicateAgreement attribute), [1] (phenotypic.analysis.TukeyOutlierFraction attribute), [1] (phenotypic.analysis.TukeyOutlierRemover attribute), [1], [2], [3] n_knobs (phenotypic.tune.InferredSearchSpace property), [1] n_needs_review (phenotypic.tune.InferredSearchSpace property), [1] n_orient (phenotypic.enhance.FocusEdgePhase attribute), [1] n_pitch_samples (phenotypic.grid.CenteredAutoGridFinder attribute), [1] n_scale (phenotypic.enhance.FocusEdgePhase attribute), [1] n_trials (phenotypic.tune.Budget attribute), [1] (phenotypic.tune.OptunaConfig attribute), [1] (phenotypic.tune.RandomConfig attribute), [1] name (phenotypic.abc_.DetectionMode property), [1] (phenotypic.abc_.FigureSpec attribute), [1], [2], [3] (phenotypic.abc_.PrefabPipeline attribute), [1] (phenotypic.analysis.abc_.QualityCheck attribute), [1] (phenotypic.analysis.ExpectedVsDetectedCount attribute), [1] (phenotypic.analysis.ICC attribute), [1] (phenotypic.analysis.MaxModifiedZScore attribute), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount attribute) (phenotypic.analysis.qc.ICC attribute) (phenotypic.analysis.qc.MaxModifiedZScore attribute) (phenotypic.analysis.qc.RelativeMAD attribute) (phenotypic.analysis.qc.ReplicateAgreement attribute) (phenotypic.analysis.qc.TukeyOutlierFraction attribute) (phenotypic.analysis.RelativeMAD attribute), [1] (phenotypic.analysis.ReplicateAgreement attribute), [1] (phenotypic.analysis.TukeyOutlierFraction attribute), [1] (phenotypic.gui.builder._state._DagBuilderScope attribute), [1] (phenotypic.prefab.FilamentousFungiPipeline attribute), [1] (phenotypic.prefab.GridSectionPipeline attribute), [1] (phenotypic.prefab.HeavyOtsuPipeline attribute), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] (phenotypic.prefab.HeavyWatershedPipeline attribute), [1] (phenotypic.prefab.RoundPeaksPipeline attribute), [1] (phenotypic.prefab.SpImagerPipeline attribute), [1] NAME (phenotypic.sdk_.ChunkManifestKey attribute), [1] name (phenotypic.sdk_.exceptions_.DataIntegrityError attribute), [1] (phenotypic.sdk_.exceptions_.EmptyImageError attribute), [1] (phenotypic.sdk_.exceptions_.IllegalElementAssignmentError attribute), [1] (phenotypic.sdk_.exceptions_.ImmutableComponentError attribute), [1] (phenotypic.sdk_.exceptions_.InvalidHsvSchemaError attribute), [1] (phenotypic.sdk_.exceptions_.NoArrayError attribute), [1] (phenotypic.sdk_.exceptions_.NoComponentError attribute), [1] (phenotypic.sdk_.exceptions_.NoImageDataError attribute), [1] (phenotypic.sdk_.exceptions_.NoObjectsError attribute), [1] (phenotypic.sdk_.exceptions_.ObjectNotFoundError attribute), [1] (phenotypic.sdk_.exceptions_.OperationIntegrityError attribute), [1] (phenotypic.sdk_.exceptions_.UuidAssignmentError attribute), [1] (phenotypic.sdk_.exceptions_.UUIDReassignmentError attribute), [1] (phenotypic.sdk_.HDF attribute), [1], [2], [3] (phenotypic.sdk_.hdf_.HDF attribute), [1] nansafe (phenotypic.enhance.SubtractRollingBall attribute), [1] napari() (phenotypic._core._image_parts.accessors._detect_mat_accessor.DetectMatAccessor method) (phenotypic._core._image_parts.accessors._grayscale_accessor.Grayscale method) (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap method) (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask method) (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) (phenotypic._core._image_parts.accessors._rgb_accessor.ImageRGB method) (phenotypic.detect.ManualGridPointDetector method), [1] (phenotypic.detect.ManualPointDetector method), [1] (phenotypic.refine.ManualRefine method), [1] (phenotypic.sdk_.mixin.PointPickerMixin method)

nbytes (phenotypic._core._image_parts.accessors._detect_mat_accessor.DetectMatAccessor property) (phenotypic._core._image_parts.accessors._grayscale_accessor.Grayscale property) (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap property) (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask property) (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor property) (phenotypic._core._image_parts.accessors._rgb_accessor.ImageRGB property) ncols (phenotypic.abc_.GridFinder attribute), [1] (phenotypic.abc_.PrefabPipeline attribute), [1] (phenotypic.analysis.EdgeCorrector attribute), [1] (phenotypic.grid.AutoGridFinder attribute), [1] (phenotypic.grid.CenteredAutoGridFinder attribute), [1] (phenotypic.grid.ManualGridFinder attribute), [1], [2], [3] (phenotypic.gui.builder._state._DagBuilderScope attribute), [1] (phenotypic.prefab.FilamentousFungiPipeline attribute), [1] (phenotypic.prefab.GridSectionPipeline attribute), [1] (phenotypic.prefab.HeavyOtsuPipeline attribute), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] (phenotypic.prefab.HeavyWatershedPipeline attribute), [1] (phenotypic.prefab.RoundPeaksPipeline attribute), [1] (phenotypic.prefab.SpImagerPipeline attribute), [1] NdArrayField (in module phenotypic.sdk_.typing_) ndim (phenotypic._core._image_parts.accessors._detect_mat_accessor.DetectMatAccessor property) (phenotypic._core._image_parts.accessors._grayscale_accessor.Grayscale property) (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap property) (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask property) (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor property) (phenotypic._core._image_parts.accessors._rgb_accessor.ImageRGB property) NearestNeighborMerger (class in phenotypic.refine), [1] needs_review (phenotypic.tune.InferredSearchSpace property), [1] (phenotypic.tune.Knob attribute), [1] (phenotypic.tune.targets.TunableParam attribute) Nested (class in phenotypic.tune.targets) nested (phenotypic.gui.builder._state.BlockNode attribute), [1] NEW_VAL (phenotypic.schema.EDGE_CORRECTION attribute) NEXT_CHUNK_ID (phenotypic.sdk_.ChunkStateKey attribute), [1] NITROGEN_SOURCE (phenotypic.schema.CONDITION_METADATA attribute) NO_QC (phenotypic.sdk_.JobMetadataKey attribute), [1] NoArrayError, [1] NoComponentError, [1] NoImageDataError, [1] noise_method (phenotypic.enhance.FocusEdgePhase attribute), [1] noise_radius (phenotypic.detect.RoundPeaksDetector attribute), [1] (phenotypic.detect.SinePeakDetector attribute), [1] NoiseMetrics (class in phenotypic.util), [1] (class in phenotypic.util.image_metrics) None (phenotypic.abc_.FootprintMixin attribute), [1] (phenotypic.abc_.ImageOperation attribute), [1] (phenotypic.abc_.ObjectDetector attribute), [1] NONE (phenotypic.sdk_.constants_.IMAGE_MODE attribute), [1] None (phenotypic.sdk_.FootprintMixin attribute), [1] (phenotypic.sdk_.mixin.FootprintMixin attribute) NonLocalMeansDenoiser (class in phenotypic.enhance), [1] nonuniformity_ratio (phenotypic.util.BackgroundMetrics attribute), [1] (phenotypic.util.image_metrics.BackgroundMetrics attribute) NoObjectsError, [1] NoOutputError, [1] normalize_rgb_bitdepth() (in module phenotypic.sdk_.funcs_) normed() (phenotypic._core._image_parts.accessors._rgb_accessor.ImageRGB method) NOTES (phenotypic.schema.EXPERIMENT_METADATA attribute) nrows (phenotypic.abc_.GridFinder attribute), [1] (phenotypic.abc_.PrefabPipeline attribute), [1] (phenotypic.analysis.EdgeCorrector attribute), [1] (phenotypic.grid.AutoGridFinder attribute), [1] (phenotypic.grid.CenteredAutoGridFinder attribute), [1] (phenotypic.grid.ManualGridFinder attribute), [1], [2], [3] (phenotypic.gui.builder._state._DagBuilderScope attribute), [1] (phenotypic.prefab.FilamentousFungiPipeline attribute), [1] (phenotypic.prefab.GridSectionPipeline attribute), [1] (phenotypic.prefab.HeavyOtsuPipeline attribute), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] (phenotypic.prefab.HeavyWatershedPipeline attribute), [1] (phenotypic.prefab.RoundPeaksPipeline attribute), [1] (phenotypic.prefab.SpImagerPipeline attribute), [1] NUM_BRANCHES (phenotypic.schema.RADIAL_EXPANSION attribute) num_iter (phenotypic.enhance.StructureSmoothing attribute), [1] NUM_MEMBERS (phenotypic.schema.QUALITY_ICC attribute) (phenotypic.schema.QUALITY_MAD attribute) (phenotypic.schema.QUALITY_TUKEY attribute) (phenotypic.schema.QUALITY_ZMAX attribute) num_objects (phenotypic._core._image_parts.accessors._objects_accessor.ObjectsAccessor property) NUM_OUTLIERS (phenotypic.schema.QUALITY_TUKEY attribute) NUM_RATERS (phenotypic.schema.QUALITY_ICC attribute) NUM_REPLICATES (phenotypic.schema.QUALITY_SE attribute) NUM_SAMPLES (phenotypic.schema.MODEL_METRICS attribute) num_scales (phenotypic.enhance.FocusBlobLoG attribute), [1] NUM_SUBJECTS (phenotypic.schema.QUALITY_ICC attribute) number (phenotypic.tune.Trial attribute), [1]

O

obj (phenotypic.sdk_.exceptions_.DataIntegrityError attribute), [1] (phenotypic.sdk_.exceptions_.EmptyImageError attribute), [1] (phenotypic.sdk_.exceptions_.IllegalElementAssignmentError attribute), [1] (phenotypic.sdk_.exceptions_.ImmutableComponentError attribute), [1] (phenotypic.sdk_.exceptions_.InvalidHsvSchemaError attribute), [1] (phenotypic.sdk_.exceptions_.NoArrayError attribute), [1] (phenotypic.sdk_.exceptions_.NoComponentError attribute), [1] (phenotypic.sdk_.exceptions_.NoImageDataError attribute), [1] (phenotypic.sdk_.exceptions_.NoObjectsError attribute), [1] (phenotypic.sdk_.exceptions_.ObjectNotFoundError attribute), [1] (phenotypic.sdk_.exceptions_.OperationIntegrityError attribute), [1] (phenotypic.sdk_.exceptions_.UuidAssignmentError attribute), [1] (phenotypic.sdk_.exceptions_.UUIDReassignmentError attribute), [1] OBJECT (class in phenotypic.schema) (phenotypic.sdk_.constants_.IMAGE_TYPES attribute), [1] OBJECT_SPREAD (phenotypic.schema.GRID_SPREAD attribute) ObjectDetector (class in phenotypic.abc_), [1] objective_names() (phenotypic.tune.CompositeScorer method), [1] objectives (phenotypic.tune.EvaluationResult attribute), [1] (phenotypic.tune.Trial attribute), [1] ObjectMap (class in phenotypic._core._image_parts.accessors._objmap_accessor) ObjectMask (class in phenotypic._core._image_parts.accessors._objmask_accessor) ObjectNotFoundError, [1] ObjectRefiner (class in phenotypic.abc_), [1] objects (phenotypic.Image property) ObjectsAccessor (class in phenotypic._core._image_parts.accessors._objects_accessor) objmap (phenotypic.Image property) objmask (phenotypic.Image property) on (phenotypic.analysis.abc_.ModelFitter attribute) (phenotypic.analysis.abc_.QualityCheck attribute) (phenotypic.analysis.abc_.SetAnalyzer attribute) (phenotypic.analysis.DoubleSoftplus attribute), [1] (phenotypic.analysis.EdgeCorrector attribute), [1] (phenotypic.analysis.ExpectedVsDetectedCount attribute), [1] (phenotypic.analysis.ICC attribute), [1] (phenotypic.analysis.LinearSoftplus attribute), [1] (phenotypic.analysis.LogGrowthModel attribute), [1] (phenotypic.analysis.MADOutlierRemover attribute), [1], [2], [3] (phenotypic.analysis.MaxModifiedZScore attribute), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount attribute) (phenotypic.analysis.qc.ICC attribute) (phenotypic.analysis.qc.MaxModifiedZScore attribute) (phenotypic.analysis.qc.RelativeMAD attribute) (phenotypic.analysis.qc.ReplicateAgreement attribute) (phenotypic.analysis.qc.TukeyOutlierFraction attribute) (phenotypic.analysis.RelativeMAD attribute), [1] (phenotypic.analysis.ReplicateAgreement attribute), [1] (phenotypic.analysis.TukeyOutlierFraction attribute), [1] (phenotypic.analysis.TukeyOutlierRemover attribute), [1], [2], [3]

op (phenotypic.tune.targets.Nested attribute) (phenotypic.tune.targets.Param attribute) (phenotypic.tune.targets.Presence attribute) op_class (phenotypic.tune.targets.Nested attribute) (phenotypic.tune.targets.Param attribute) (phenotypic.tune.targets.Presence attribute) (phenotypic.tune.targets.TunableParam attribute) open_port_menu (phenotypic.gui.builder._state._DagBuilderState attribute) OperationFailedError, [1] OperationField (in module phenotypic.sdk_.typing_) OperationIntegrityError, [1] ops (phenotypic.abc_.PrefabPipeline attribute), [1] (phenotypic.prefab.FilamentousFungiPipeline attribute), [1] (phenotypic.prefab.GridSectionPipeline attribute), [1] (phenotypic.prefab.HeavyOtsuPipeline attribute), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] (phenotypic.prefab.HeavyWatershedPipeline attribute), [1] (phenotypic.prefab.RoundPeaksPipeline attribute), [1] (phenotypic.prefab.SpImagerPipeline attribute), [1] optimal_scale (phenotypic.util.image_metrics.StructureMetrics attribute) (phenotypic.util.StructureMetrics attribute), [1] optimize() (phenotypic.tune.TuningEngine method), [1] options (phenotypic.abc_.Control attribute), [1] OptunaConfig (class in phenotypic.tune), [1] ORANGE_PCT (phenotypic.schema.ColorComposition attribute) order (phenotypic.abc_.FigureSpec attribute), [1], [2], [3] ORGANISM (phenotypic.schema.GENETIC_METADATA attribute) ORIENTATION (phenotypic.schema.SHAPE attribute) origin (phenotypic.refine.MaskFill attribute), [1] OTHER (phenotypic.schema.ErrorCategory attribute) OtsuDetector (class in phenotypic.detect), [1] outlier_sigma (phenotypic.correction.ColorCheckerProfile attribute), [1] output (phenotypic.enhance.FocusEdgePhase attribute), [1] OUTPUT_DIR (phenotypic.sdk_.ProcessingStateKey attribute), [1] output_illuminant (phenotypic.correction.ColorCorrector attribute), [1] output_kind (phenotypic.abc_.GpuDetector attribute), [1] OutputValueError, [1] overlay_manifest_path() (in module phenotypic.sdk_), [1] OVERSEGMENTED (phenotypic.schema.ErrorCategory attribute)

P

p1 (phenotypic.util.ContrastMetrics attribute), [1] (phenotypic.util.image_metrics.ContrastMetrics attribute) p99 (phenotypic.util.ContrastMetrics attribute), [1] (phenotypic.util.image_metrics.ContrastMetrics attribute) pad_checker (phenotypic.correction.ColorCheckerProfile attribute), [1] pair (phenotypic.abc_.MeasurementInfo attribute), [1], [2], [3] (phenotypic.schema.ACQUISITION_METADATA attribute) (phenotypic.schema.BBOX attribute) (phenotypic.schema.ColorComposition attribute) (phenotypic.schema.ColorHSV attribute) (phenotypic.schema.ColorLab attribute) (phenotypic.schema.Colorxy attribute) (phenotypic.schema.ColorXYZ attribute) (phenotypic.schema.CONDITION_METADATA attribute) (phenotypic.schema.CURATION attribute) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL attribute) (phenotypic.schema.EDGE_CORRECTION attribute) (phenotypic.schema.ErrorCategory attribute) (phenotypic.schema.EXPERIMENT_METADATA attribute) (phenotypic.schema.GENETIC_METADATA attribute) (phenotypic.schema.GRID attribute) (phenotypic.schema.GRID_LINREG_STATS attribute) (phenotypic.schema.GRID_SPATIAL attribute) (phenotypic.schema.GRID_SPREAD attribute) (phenotypic.schema.INCUBATION_METADATA attribute) (phenotypic.schema.INTENSITY attribute) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL attribute) (phenotypic.schema.LOG_GROWTH_MODEL attribute) (phenotypic.schema.MeasurementInfo attribute), [1] (phenotypic.schema.METADATA attribute) (phenotypic.schema.MODEL_METRICS attribute) (phenotypic.schema.OBJECT attribute) (phenotypic.schema.PLATE_METADATA attribute) (phenotypic.schema.QUALITY_CHECK attribute) (phenotypic.schema.QUALITY_COUNT attribute) (phenotypic.schema.QUALITY_ICC attribute) (phenotypic.schema.QUALITY_MAD attribute) (phenotypic.schema.QUALITY_SE attribute) (phenotypic.schema.QUALITY_TUKEY attribute) (phenotypic.schema.QUALITY_ZMAX attribute) (phenotypic.schema.RADIAL_EXPANSION attribute) (phenotypic.schema.SAMPLE_METADATA attribute) (phenotypic.schema.SHAPE attribute) (phenotypic.schema.SIZE attribute) (phenotypic.schema.SYMMETRIC_ZONES attribute) (phenotypic.schema.TEXTURE attribute) (phenotypic.sdk_.constants_.ConstantLabels attribute), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS attribute), [1] (phenotypic.sdk_.constants_.PIPE_STATUS attribute), [1] Param (class in phenotypic.tune.targets) param_importance_path() (in module phenotypic.sdk_), [1] param_importances() (phenotypic.tune.JournalStudyStore method), [1] params (phenotypic.gui.builder._state.BlockNode attribute), [1] (phenotypic.tune.Trial attribute), [1] PARENT_IMAGE_NAME (phenotypic.schema.METADATA attribute) PARENT_UUID (phenotypic.schema.METADATA attribute) pareto_best_pipeline_path() (in module phenotypic.sdk_), [1] pareto_dir() (in module phenotypic.sdk_), [1] pareto_front() (phenotypic.tune.JournalStudyStore method), [1] pareto_front_parquet_path() (in module phenotypic.sdk_), [1] pareto_importance_path() (in module phenotypic.sdk_), [1] parse_file() (phenotypic.abc_.BackgroundSubtraction class method), [1] (phenotypic.abc_.BaseOperation class method), [1] (phenotypic.abc_.ContrastAdjustment class method), [1] (phenotypic.abc_.FocusBlob class method), [1] (phenotypic.abc_.FocusEdge class method), [1] (phenotypic.abc_.GpuDetector class method), [1] (phenotypic.abc_.GridCorrector class method), [1] (phenotypic.abc_.GridFinder class method), [1] (phenotypic.abc_.GridMeasureFeatures class method), [1] (phenotypic.abc_.GridObjectDetector class method), [1] (phenotypic.abc_.GridObjectRefiner class method), [1] (phenotypic.abc_.GridOperation class method), [1] (phenotypic.abc_.ImageCorrector class method), [1] (phenotypic.abc_.ImageDenoiser class method), [1] (phenotypic.abc_.ImageEnhancer class method), [1] (phenotypic.abc_.ImageOperation class method), [1] (phenotypic.abc_.MeasureFeatures class method), [1] (phenotypic.abc_.MorphologicalFiltering class method), [1] (phenotypic.abc_.ObjectDetector class method), [1] (phenotypic.abc_.ObjectRefiner class method), [1] (phenotypic.abc_.PostMeasurement class method), [1] (phenotypic.abc_.PrefabPipeline class method), [1] (phenotypic.abc_.Smoothing class method), [1] (phenotypic.abc_.ThresholdDetector class method), [1] (phenotypic.analysis.abc_.ModelFitter class method) (phenotypic.analysis.abc_.QualityCheck class method) (phenotypic.analysis.abc_.SetAnalyzer class method) (phenotypic.analysis.DoubleSoftplus class method), [1] (phenotypic.analysis.EdgeCorrector class method), [1] (phenotypic.analysis.ErrorCutoffFinder class method), [1] (phenotypic.analysis.ExpectedVsDetectedCount class method), [1] (phenotypic.analysis.ICC class method), [1] (phenotypic.analysis.LinearSoftplus class method), [1] (phenotypic.analysis.LogGrowthModel class method), [1] (phenotypic.analysis.MADOutlierRemover class method), [1] (phenotypic.analysis.MaxModifiedZScore class method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount class method) (phenotypic.analysis.qc.ICC class method) (phenotypic.analysis.qc.MaxModifiedZScore class method) (phenotypic.analysis.qc.RelativeMAD class method) (phenotypic.analysis.qc.ReplicateAgreement class method) (phenotypic.analysis.qc.TukeyOutlierFraction class method) (phenotypic.analysis.RelativeMAD class method), [1] (phenotypic.analysis.ReplicateAgreement class method), [1] (phenotypic.analysis.TukeyOutlierFraction class method), [1] (phenotypic.analysis.TukeyOutlierRemover class method), [1] (phenotypic.correction.BayesShrinkCorrector class method), [1] (phenotypic.correction.CaptureMetadata class method), [1] (phenotypic.correction.ColorCheckerProfile class method), [1] (phenotypic.correction.ColorCorrector class method), [1] (phenotypic.correction.ColorDenoise class method), [1] (phenotypic.correction.DenoiseBlockMatch class method), [1] (phenotypic.correction.GridAligner class method), [1] (phenotypic.correction.ImageCropper class method), [1] (phenotypic.correction.ImagePadder class method), [1] (phenotypic.correction.VisuShrinkCorrector class method), [1] (phenotypic.detect.CannyDetector class method), [1] (phenotypic.detect.ChanVeseDetector class method), [1] (phenotypic.detect.CompositeDetector class method), [1] (phenotypic.detect.FilamentousFungiDetector class method), [1] (phenotypic.detect.HysteresisDetector class method), [1] (phenotypic.detect.InoculumDetector class method), [1] (phenotypic.detect.IsodataDetector class method), [1] (phenotypic.detect.LiDetector class method), [1] (phenotypic.detect.MadHysteresisDetector class method), [1] (phenotypic.detect.ManualGridPointDetector class method), [1] (phenotypic.detect.ManualPointDetector class method), [1] (phenotypic.detect.MeanDetector class method), [1] (phenotypic.detect.MinimumDetector class method), [1] (phenotypic.detect.OtsuDetector class method), [1] (phenotypic.detect.RankOtsuDetector class method), [1] (phenotypic.detect.RoundPeaksDetector class method), [1] (phenotypic.detect.SecondaryOtsuDetector class method), [1] (phenotypic.detect.SinePeakDetector class method), [1] (phenotypic.detect.TriangleDetector class method), [1] (phenotypic.detect.UserThreshold class method), [1] (phenotypic.detect.WatershedDetector class method), [1] (phenotypic.detect.YenDetector class method), [1] (phenotypic.enhance.BayesShrinkEnhancer class method), [1] (phenotypic.enhance.ContrastStretching class method), [1] (phenotypic.enhance.EnhanceBlockMatch class method), [1] (phenotypic.enhance.EnhanceLocalContrast class method), [1] (phenotypic.enhance.FlattenIllumination class method), [1] (phenotypic.enhance.FocusBlobLoG class method), [1] (phenotypic.enhance.FocusEdgeFrangi class method), [1] (phenotypic.enhance.FocusEdgeHessian class method), [1] (phenotypic.enhance.FocusEdgeLaplace class method), [1] (phenotypic.enhance.FocusEdgeMeijering class method), [1] (phenotypic.enhance.FocusEdgePhase class method), [1] (phenotypic.enhance.FocusEdgeSato class method), [1] (phenotypic.enhance.FocusEdgeSobel class method), [1] (phenotypic.enhance.GaussianBlur class method), [1] (phenotypic.enhance.GrayOpening class method), [1] (phenotypic.enhance.ImageInverter class method), [1] (phenotypic.enhance.LocalEdgeDenoise class method), [1] (phenotypic.enhance.MedianFilter class method), [1] (phenotypic.enhance.NonLocalMeansDenoiser class method), [1] (phenotypic.enhance.RankMedianEnhancer class method), [1] (phenotypic.enhance.SetDetectMode class method), [1] (phenotypic.enhance.SharpenEdgeGauss class method), [1] (phenotypic.enhance.StructureSmoothing class method), [1] (phenotypic.enhance.SubtractGaussian class method), [1] (phenotypic.enhance.SubtractOpening class method), [1] (phenotypic.enhance.SubtractRollingBall class method), [1] (phenotypic.enhance.SubtractWhiteTophat class method), [1] (phenotypic.enhance.VisuShrinkEnhancer class method), [1] (phenotypic.enhance.WhiteTophatEnhance class method), [1] (phenotypic.grid.AutoGridFinder class method), [1] (phenotypic.grid.CenteredAutoGridFinder class method), [1] (phenotypic.grid.GridApply class method), [1] (phenotypic.grid.ManualGridFinder class method), [1] (phenotypic.measure.MeasureBounds class method), [1] (phenotypic.measure.MeasureColor class method), [1] (phenotypic.measure.MeasureGridLinRegStats class method), [1] (phenotypic.measure.MeasureGridSpatial class method), [1] (phenotypic.measure.MeasureGridSpread class method), [1] (phenotypic.measure.MeasureIntensity class method), [1] (phenotypic.measure.MeasureShape class method), [1] (phenotypic.measure.MeasureSize class method), [1] (phenotypic.measure.MeasureSymmetricZones class method), [1] (phenotypic.measure.MeasureTexture class method), [1] (phenotypic.post.AppendString class method) (phenotypic.post.ExpandMetadata class method) (phenotypic.post.MergeMetadata class method) (phenotypic.post.PrependString class method) (phenotypic.prefab.FilamentousFungiPipeline class method), [1] (phenotypic.prefab.GridSectionPipeline class method), [1] (phenotypic.prefab.HeavyOtsuPipeline class method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline class method), [1] (phenotypic.prefab.HeavyWatershedPipeline class method), [1] (phenotypic.prefab.RoundPeaksPipeline class method), [1] (phenotypic.prefab.SpImagerPipeline class method), [1] (phenotypic.refine.ExtractColonyCore class method), [1] (phenotypic.refine.GridAlignmentRefiner class method), [1] (phenotypic.refine.GridOversizedObjectRemover class method), [1] (phenotypic.refine.KeepNearestCenter class method), [1] (phenotypic.refine.KeepSectionLargest class method), [1] (phenotypic.refine.ManualRefine class method), [1] (phenotypic.refine.MaskClosing class method), [1] (phenotypic.refine.MaskDilation class method), [1] (phenotypic.refine.MaskErosion class method), [1] (phenotypic.refine.MaskFill class method), [1] (phenotypic.refine.MaskGradient class method), [1] (phenotypic.refine.MaskOpening class method), [1] (phenotypic.refine.MaskWhiteTophat class method), [1] (phenotypic.refine.MergeFragmentChains class method), [1] (phenotypic.refine.NearestNeighborMerger class method), [1] (phenotypic.refine.ReduceSectionsByLine class method), [1] (phenotypic.refine.RefineBySineFit class method), [1] (phenotypic.refine.RemoveBorderObjects class method), [1] (phenotypic.refine.RemoveByFeature class method), [1] (phenotypic.refine.RemoveGridOutliers class method), [1] (phenotypic.refine.RemoveLowCircularity class method), [1] (phenotypic.refine.SeparateObjects class method), [1] (phenotypic.refine.Skeletonize class method), [1] (phenotypic.refine.SmallObjectRemover class method), [1] (phenotypic.refine.SmallToLargeMerger class method), [1] (phenotypic.refine.Thinning class method), [1] (phenotypic.refine.TrimAsymmetry class method), [1] (phenotypic.tune.Budget class method), [1] (phenotypic.tune.Categorical class method), [1] (phenotypic.tune.CompositeScorer class method), [1] (phenotypic.tune.EvaluationResult class method), [1] (phenotypic.tune.Evaluator class method), [1] (phenotypic.tune.Excluded class method), [1] (phenotypic.tune.Fixed class method), [1] (phenotypic.tune.FloatRange class method), [1] (phenotypic.tune.GridConfig class method), [1] (phenotypic.tune.GroundTruthMasks class method), [1] (phenotypic.tune.HeldOutConfig class method), [1] (phenotypic.tune.ImportanceReport class method), [1] (phenotypic.tune.InferredSearchSpace class method), [1] (phenotypic.tune.IntRange class method), [1] (phenotypic.tune.Knob class method), [1] (phenotypic.tune.OptunaConfig class method), [1] (phenotypic.tune.QCScorer class method), [1] (phenotypic.tune.RandomConfig class method), [1] (phenotypic.tune.ReferenceFreeScorer class method), [1] (phenotypic.tune.Scorer class method), [1] (phenotypic.tune.SearchSpace class method), [1] (phenotypic.tune.StrategyConfig class method), [1] (phenotypic.tune.SupervisedScorer class method), [1] (phenotypic.tune.targets.Nested class method) (phenotypic.tune.targets.Param class method) (phenotypic.tune.targets.Presence class method) (phenotypic.tune.targets.TunableParam class method) (phenotypic.tune.Trial class method), [1] (phenotypic.tune.TuningSpec class method), [1] parse_job_id() (in module phenotypic.sdk_.slurm), [1] parse_key() (in module phenotypic.tune.targets) parse_obj() (phenotypic.abc_.BackgroundSubtraction class method), [1] (phenotypic.abc_.BaseOperation class method), [1] (phenotypic.abc_.ContrastAdjustment class method), [1] (phenotypic.abc_.FocusBlob class method), [1] (phenotypic.abc_.FocusEdge class method), [1] (phenotypic.abc_.GpuDetector class method), [1] (phenotypic.abc_.GridCorrector class method), [1] (phenotypic.abc_.GridFinder class method), [1] (phenotypic.abc_.GridMeasureFeatures class method), [1] (phenotypic.abc_.GridObjectDetector class method), [1] (phenotypic.abc_.GridObjectRefiner class method), [1] (phenotypic.abc_.GridOperation class method), [1] (phenotypic.abc_.ImageCorrector class method), [1] (phenotypic.abc_.ImageDenoiser class method), [1] (phenotypic.abc_.ImageEnhancer class method), [1] (phenotypic.abc_.ImageOperation class method), [1] (phenotypic.abc_.MeasureFeatures class method), [1] (phenotypic.abc_.MorphologicalFiltering class method), [1] (phenotypic.abc_.ObjectDetector class method), [1] (phenotypic.abc_.ObjectRefiner class method), [1] (phenotypic.abc_.PostMeasurement class method), [1] (phenotypic.abc_.PrefabPipeline class method), [1] (phenotypic.abc_.Smoothing class method), [1] (phenotypic.abc_.ThresholdDetector class method), [1] (phenotypic.analysis.abc_.ModelFitter class method) (phenotypic.analysis.abc_.QualityCheck class method) (phenotypic.analysis.abc_.SetAnalyzer class method) (phenotypic.analysis.DoubleSoftplus class method), [1] (phenotypic.analysis.EdgeCorrector class method), [1] (phenotypic.analysis.ErrorCutoffFinder class method), [1] (phenotypic.analysis.ExpectedVsDetectedCount class method), [1] (phenotypic.analysis.ICC class method), [1] (phenotypic.analysis.LinearSoftplus class method), [1] (phenotypic.analysis.LogGrowthModel class method), [1] (phenotypic.analysis.MADOutlierRemover class method), [1] (phenotypic.analysis.MaxModifiedZScore class method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount class method) (phenotypic.analysis.qc.ICC class method) (phenotypic.analysis.qc.MaxModifiedZScore class method) (phenotypic.analysis.qc.RelativeMAD class method) (phenotypic.analysis.qc.ReplicateAgreement class method) (phenotypic.analysis.qc.TukeyOutlierFraction class method) (phenotypic.analysis.RelativeMAD class method), [1] (phenotypic.analysis.ReplicateAgreement class method), [1] (phenotypic.analysis.TukeyOutlierFraction class method), [1] (phenotypic.analysis.TukeyOutlierRemover class method), [1] (phenotypic.correction.BayesShrinkCorrector class method), [1] (phenotypic.correction.CaptureMetadata class method), [1] (phenotypic.correction.ColorCheckerProfile class method), [1] (phenotypic.correction.ColorCorrector class method), [1] (phenotypic.correction.ColorDenoise class method), [1] (phenotypic.correction.DenoiseBlockMatch class method), [1] (phenotypic.correction.GridAligner class method), [1] (phenotypic.correction.ImageCropper class method), [1] (phenotypic.correction.ImagePadder class method), [1] (phenotypic.correction.VisuShrinkCorrector class method), [1] (phenotypic.detect.CannyDetector class method), [1] (phenotypic.detect.ChanVeseDetector class method), [1] (phenotypic.detect.CompositeDetector class method), [1] (phenotypic.detect.FilamentousFungiDetector class method), [1] (phenotypic.detect.HysteresisDetector class method), [1] (phenotypic.detect.InoculumDetector class method), [1] (phenotypic.detect.IsodataDetector class method), [1] (phenotypic.detect.LiDetector class method), [1] (phenotypic.detect.MadHysteresisDetector class method), [1] (phenotypic.detect.ManualGridPointDetector class method), [1] (phenotypic.detect.ManualPointDetector class method), [1] (phenotypic.detect.MeanDetector class method), [1] (phenotypic.detect.MinimumDetector class method), [1] (phenotypic.detect.OtsuDetector class method), [1] (phenotypic.detect.RankOtsuDetector class method), [1] (phenotypic.detect.RoundPeaksDetector class method), [1] (phenotypic.detect.SecondaryOtsuDetector class method), [1] (phenotypic.detect.SinePeakDetector class method), [1] (phenotypic.detect.TriangleDetector class method), [1] (phenotypic.detect.UserThreshold class method), [1] (phenotypic.detect.WatershedDetector class method), [1] (phenotypic.detect.YenDetector class method), [1] (phenotypic.enhance.BayesShrinkEnhancer class method), [1] (phenotypic.enhance.ContrastStretching class method), [1] (phenotypic.enhance.EnhanceBlockMatch class method), [1] (phenotypic.enhance.EnhanceLocalContrast class method), [1] (phenotypic.enhance.FlattenIllumination class method), [1] (phenotypic.enhance.FocusBlobLoG class method), [1] (phenotypic.enhance.FocusEdgeFrangi class method), [1] (phenotypic.enhance.FocusEdgeHessian class method), [1] (phenotypic.enhance.FocusEdgeLaplace class method), [1] (phenotypic.enhance.FocusEdgeMeijering class method), [1] (phenotypic.enhance.FocusEdgePhase class method), [1] (phenotypic.enhance.FocusEdgeSato class method), [1] (phenotypic.enhance.FocusEdgeSobel class method), [1] (phenotypic.enhance.GaussianBlur class method), [1] (phenotypic.enhance.GrayOpening class method), [1] (phenotypic.enhance.ImageInverter class method), [1] (phenotypic.enhance.LocalEdgeDenoise class method), [1] (phenotypic.enhance.MedianFilter class method), [1] (phenotypic.enhance.NonLocalMeansDenoiser class method), [1] (phenotypic.enhance.RankMedianEnhancer class method), [1] (phenotypic.enhance.SetDetectMode class method), [1] (phenotypic.enhance.SharpenEdgeGauss class method), [1] (phenotypic.enhance.StructureSmoothing class method), [1] (phenotypic.enhance.SubtractGaussian class method), [1] (phenotypic.enhance.SubtractOpening class method), [1] (phenotypic.enhance.SubtractRollingBall class method), [1] (phenotypic.enhance.SubtractWhiteTophat class method), [1] (phenotypic.enhance.VisuShrinkEnhancer class method), [1] (phenotypic.enhance.WhiteTophatEnhance class method), [1] (phenotypic.grid.AutoGridFinder class method), [1] (phenotypic.grid.CenteredAutoGridFinder class method), [1] (phenotypic.grid.GridApply class method), [1] (phenotypic.grid.ManualGridFinder class method), [1] (phenotypic.measure.MeasureBounds class method), [1] (phenotypic.measure.MeasureColor class method), [1] (phenotypic.measure.MeasureGridLinRegStats class method), [1] (phenotypic.measure.MeasureGridSpatial class method), [1] (phenotypic.measure.MeasureGridSpread class method), [1] (phenotypic.measure.MeasureIntensity class method), [1] (phenotypic.measure.MeasureShape class method), [1] (phenotypic.measure.MeasureSize class method), [1] (phenotypic.measure.MeasureSymmetricZones class method), [1] (phenotypic.measure.MeasureTexture class method), [1] (phenotypic.post.AppendString class method) (phenotypic.post.ExpandMetadata class method) (phenotypic.post.MergeMetadata class method) (phenotypic.post.PrependString class method) (phenotypic.prefab.FilamentousFungiPipeline class method), [1] (phenotypic.prefab.GridSectionPipeline class method), [1] (phenotypic.prefab.HeavyOtsuPipeline class method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline class method), [1] (phenotypic.prefab.HeavyWatershedPipeline class method), [1] (phenotypic.prefab.RoundPeaksPipeline class method), [1] (phenotypic.prefab.SpImagerPipeline class method), [1] (phenotypic.refine.ExtractColonyCore class method), [1] (phenotypic.refine.GridAlignmentRefiner class method), [1] (phenotypic.refine.GridOversizedObjectRemover class method), [1] (phenotypic.refine.KeepNearestCenter class method), [1] (phenotypic.refine.KeepSectionLargest class method), [1] (phenotypic.refine.ManualRefine class method), [1] (phenotypic.refine.MaskClosing class method), [1] (phenotypic.refine.MaskDilation class method), [1] (phenotypic.refine.MaskErosion class method), [1] (phenotypic.refine.MaskFill class method), [1] (phenotypic.refine.MaskGradient class method), [1] (phenotypic.refine.MaskOpening class method), [1] (phenotypic.refine.MaskWhiteTophat class method), [1] (phenotypic.refine.MergeFragmentChains class method), [1] (phenotypic.refine.NearestNeighborMerger class method), [1] (phenotypic.refine.ReduceSectionsByLine class method), [1] (phenotypic.refine.RefineBySineFit class method), [1] (phenotypic.refine.RemoveBorderObjects class method), [1] (phenotypic.refine.RemoveByFeature class method), [1] (phenotypic.refine.RemoveGridOutliers class method), [1] (phenotypic.refine.RemoveLowCircularity class method), [1] (phenotypic.refine.SeparateObjects class method), [1] (phenotypic.refine.Skeletonize class method), [1] (phenotypic.refine.SmallObjectRemover class method), [1] (phenotypic.refine.SmallToLargeMerger class method), [1] (phenotypic.refine.Thinning class method), [1] (phenotypic.refine.TrimAsymmetry class method), [1] (phenotypic.tune.Budget class method), [1] (phenotypic.tune.Categorical class method), [1] (phenotypic.tune.CompositeScorer class method), [1] (phenotypic.tune.EvaluationResult class method), [1] (phenotypic.tune.Evaluator class method), [1] (phenotypic.tune.Excluded class method), [1] (phenotypic.tune.Fixed class method), [1] (phenotypic.tune.FloatRange class method), [1] (phenotypic.tune.GridConfig class method), [1] (phenotypic.tune.GroundTruthMasks class method), [1] (phenotypic.tune.HeldOutConfig class method), [1] (phenotypic.tune.ImportanceReport class method), [1] (phenotypic.tune.InferredSearchSpace class method), [1] (phenotypic.tune.IntRange class method), [1] (phenotypic.tune.Knob class method), [1] (phenotypic.tune.OptunaConfig class method), [1] (phenotypic.tune.QCScorer class method), [1] (phenotypic.tune.RandomConfig class method), [1] (phenotypic.tune.ReferenceFreeScorer class method), [1] (phenotypic.tune.Scorer class method), [1] (phenotypic.tune.SearchSpace class method), [1] (phenotypic.tune.StrategyConfig class method), [1] (phenotypic.tune.SupervisedScorer class method), [1] (phenotypic.tune.targets.Nested class method) (phenotypic.tune.targets.Param class method) (phenotypic.tune.targets.Presence class method) (phenotypic.tune.targets.TunableParam class method) (phenotypic.tune.Trial class method), [1] (phenotypic.tune.TuningSpec class method), [1] parse_raw() (phenotypic.abc_.BackgroundSubtraction class method), [1] (phenotypic.abc_.BaseOperation class method), [1] (phenotypic.abc_.ContrastAdjustment class method), [1] (phenotypic.abc_.FocusBlob class method), [1] (phenotypic.abc_.FocusEdge class method), [1] (phenotypic.abc_.GpuDetector class method), [1] (phenotypic.abc_.GridCorrector class method), [1] (phenotypic.abc_.GridFinder class method), [1] (phenotypic.abc_.GridMeasureFeatures class method), [1] (phenotypic.abc_.GridObjectDetector class method), [1] (phenotypic.abc_.GridObjectRefiner class method), [1] (phenotypic.abc_.GridOperation class method), [1] (phenotypic.abc_.ImageCorrector class method), [1] (phenotypic.abc_.ImageDenoiser class method), [1] (phenotypic.abc_.ImageEnhancer class method), [1] (phenotypic.abc_.ImageOperation class method), [1] (phenotypic.abc_.MeasureFeatures class method), [1] (phenotypic.abc_.MorphologicalFiltering class method), [1] (phenotypic.abc_.ObjectDetector class method), [1] (phenotypic.abc_.ObjectRefiner class method), [1] (phenotypic.abc_.PostMeasurement class method), [1] (phenotypic.abc_.PrefabPipeline class method), [1] (phenotypic.abc_.Smoothing class method), [1] (phenotypic.abc_.ThresholdDetector class method), [1] (phenotypic.analysis.abc_.ModelFitter class method) (phenotypic.analysis.abc_.QualityCheck class method) (phenotypic.analysis.abc_.SetAnalyzer class method) (phenotypic.analysis.DoubleSoftplus class method), [1] (phenotypic.analysis.EdgeCorrector class method), [1] (phenotypic.analysis.ErrorCutoffFinder class method), [1] (phenotypic.analysis.ExpectedVsDetectedCount class method), [1] (phenotypic.analysis.ICC class method), [1] (phenotypic.analysis.LinearSoftplus class method), [1] (phenotypic.analysis.LogGrowthModel class method), [1] (phenotypic.analysis.MADOutlierRemover class method), [1] (phenotypic.analysis.MaxModifiedZScore class method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount class method) (phenotypic.analysis.qc.ICC class method) (phenotypic.analysis.qc.MaxModifiedZScore class method) (phenotypic.analysis.qc.RelativeMAD class method) (phenotypic.analysis.qc.ReplicateAgreement class method) (phenotypic.analysis.qc.TukeyOutlierFraction class method) (phenotypic.analysis.RelativeMAD class method), [1] (phenotypic.analysis.ReplicateAgreement class method), [1] (phenotypic.analysis.TukeyOutlierFraction class method), [1] (phenotypic.analysis.TukeyOutlierRemover class method), [1] (phenotypic.correction.BayesShrinkCorrector class method), [1] (phenotypic.correction.CaptureMetadata class method), [1] (phenotypic.correction.ColorCheckerProfile class method), [1] (phenotypic.correction.ColorCorrector class method), [1] (phenotypic.correction.ColorDenoise class method), [1] (phenotypic.correction.DenoiseBlockMatch class method), [1] (phenotypic.correction.GridAligner class method), [1] (phenotypic.correction.ImageCropper class method), [1] (phenotypic.correction.ImagePadder class method), [1] (phenotypic.correction.VisuShrinkCorrector class method), [1] (phenotypic.detect.CannyDetector class method), [1] (phenotypic.detect.ChanVeseDetector class method), [1] (phenotypic.detect.CompositeDetector class method), [1] (phenotypic.detect.FilamentousFungiDetector class method), [1] (phenotypic.detect.HysteresisDetector class method), [1] (phenotypic.detect.InoculumDetector class method), [1] (phenotypic.detect.IsodataDetector class method), [1] (phenotypic.detect.LiDetector class method), [1] (phenotypic.detect.MadHysteresisDetector class method), [1] (phenotypic.detect.ManualGridPointDetector class method), [1] (phenotypic.detect.ManualPointDetector class method), [1] (phenotypic.detect.MeanDetector class method), [1] (phenotypic.detect.MinimumDetector class method), [1] (phenotypic.detect.OtsuDetector class method), [1] (phenotypic.detect.RankOtsuDetector class method), [1] (phenotypic.detect.RoundPeaksDetector class method), [1] (phenotypic.detect.SecondaryOtsuDetector class method), [1] (phenotypic.detect.SinePeakDetector class method), [1] (phenotypic.detect.TriangleDetector class method), [1] (phenotypic.detect.UserThreshold class method), [1] (phenotypic.detect.WatershedDetector class method), [1] (phenotypic.detect.YenDetector class method), [1] (phenotypic.enhance.BayesShrinkEnhancer class method), [1] (phenotypic.enhance.ContrastStretching class method), [1] (phenotypic.enhance.EnhanceBlockMatch class method), [1] (phenotypic.enhance.EnhanceLocalContrast class method), [1] (phenotypic.enhance.FlattenIllumination class method), [1] (phenotypic.enhance.FocusBlobLoG class method), [1] (phenotypic.enhance.FocusEdgeFrangi class method), [1] (phenotypic.enhance.FocusEdgeHessian class method), [1] (phenotypic.enhance.FocusEdgeLaplace class method), [1] (phenotypic.enhance.FocusEdgeMeijering class method), [1] (phenotypic.enhance.FocusEdgePhase class method), [1] (phenotypic.enhance.FocusEdgeSato class method), [1] (phenotypic.enhance.FocusEdgeSobel class method), [1] (phenotypic.enhance.GaussianBlur class method), [1] (phenotypic.enhance.GrayOpening class method), [1] (phenotypic.enhance.ImageInverter class method), [1] (phenotypic.enhance.LocalEdgeDenoise class method), [1] (phenotypic.enhance.MedianFilter class method), [1] (phenotypic.enhance.NonLocalMeansDenoiser class method), [1] (phenotypic.enhance.RankMedianEnhancer class method), [1] (phenotypic.enhance.SetDetectMode class method), [1] (phenotypic.enhance.SharpenEdgeGauss class method), [1] (phenotypic.enhance.StructureSmoothing class method), [1] (phenotypic.enhance.SubtractGaussian class method), [1] (phenotypic.enhance.SubtractOpening class method), [1] (phenotypic.enhance.SubtractRollingBall class method), [1] (phenotypic.enhance.SubtractWhiteTophat class method), [1] (phenotypic.enhance.VisuShrinkEnhancer class method), [1] (phenotypic.enhance.WhiteTophatEnhance class method), [1] (phenotypic.grid.AutoGridFinder class method), [1] (phenotypic.grid.CenteredAutoGridFinder class method), [1] (phenotypic.grid.GridApply class method), [1] (phenotypic.grid.ManualGridFinder class method), [1] (phenotypic.measure.MeasureBounds class method), [1] (phenotypic.measure.MeasureColor class method), [1] (phenotypic.measure.MeasureGridLinRegStats class method), [1] (phenotypic.measure.MeasureGridSpatial class method), [1] (phenotypic.measure.MeasureGridSpread class method), [1] (phenotypic.measure.MeasureIntensity class method), [1] (phenotypic.measure.MeasureShape class method), [1] (phenotypic.measure.MeasureSize class method), [1] (phenotypic.measure.MeasureSymmetricZones class method), [1] (phenotypic.measure.MeasureTexture class method), [1] (phenotypic.post.AppendString class method) (phenotypic.post.ExpandMetadata class method) (phenotypic.post.MergeMetadata class method) (phenotypic.post.PrependString class method) (phenotypic.prefab.FilamentousFungiPipeline class method), [1] (phenotypic.prefab.GridSectionPipeline class method), [1] (phenotypic.prefab.HeavyOtsuPipeline class method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline class method), [1] (phenotypic.prefab.HeavyWatershedPipeline class method), [1] (phenotypic.prefab.RoundPeaksPipeline class method), [1] (phenotypic.prefab.SpImagerPipeline class method), [1] (phenotypic.refine.ExtractColonyCore class method), [1] (phenotypic.refine.GridAlignmentRefiner class method), [1] (phenotypic.refine.GridOversizedObjectRemover class method), [1] (phenotypic.refine.KeepNearestCenter class method), [1] (phenotypic.refine.KeepSectionLargest class method), [1] (phenotypic.refine.ManualRefine class method), [1] (phenotypic.refine.MaskClosing class method), [1] (phenotypic.refine.MaskDilation class method), [1] (phenotypic.refine.MaskErosion class method), [1] (phenotypic.refine.MaskFill class method), [1] (phenotypic.refine.MaskGradient class method), [1] (phenotypic.refine.MaskOpening class method), [1] (phenotypic.refine.MaskWhiteTophat class method), [1] (phenotypic.refine.MergeFragmentChains class method), [1] (phenotypic.refine.NearestNeighborMerger class method), [1] (phenotypic.refine.ReduceSectionsByLine class method), [1] (phenotypic.refine.RefineBySineFit class method), [1] (phenotypic.refine.RemoveBorderObjects class method), [1] (phenotypic.refine.RemoveByFeature class method), [1] (phenotypic.refine.RemoveGridOutliers class method), [1] (phenotypic.refine.RemoveLowCircularity class method), [1] (phenotypic.refine.SeparateObjects class method), [1] (phenotypic.refine.Skeletonize class method), [1] (phenotypic.refine.SmallObjectRemover class method), [1] (phenotypic.refine.SmallToLargeMerger class method), [1] (phenotypic.refine.Thinning class method), [1] (phenotypic.refine.TrimAsymmetry class method), [1] (phenotypic.tune.Budget class method), [1] (phenotypic.tune.Categorical class method), [1] (phenotypic.tune.CompositeScorer class method), [1] (phenotypic.tune.EvaluationResult class method), [1] (phenotypic.tune.Evaluator class method), [1] (phenotypic.tune.Excluded class method), [1] (phenotypic.tune.Fixed class method), [1] (phenotypic.tune.FloatRange class method), [1] (phenotypic.tune.GridConfig class method), [1] (phenotypic.tune.GroundTruthMasks class method), [1] (phenotypic.tune.HeldOutConfig class method), [1] (phenotypic.tune.ImportanceReport class method), [1] (phenotypic.tune.InferredSearchSpace class method), [1] (phenotypic.tune.IntRange class method), [1] (phenotypic.tune.Knob class method), [1] (phenotypic.tune.OptunaConfig class method), [1] (phenotypic.tune.QCScorer class method), [1] (phenotypic.tune.RandomConfig class method), [1] (phenotypic.tune.ReferenceFreeScorer class method), [1] (phenotypic.tune.Scorer class method), [1] (phenotypic.tune.SearchSpace class method), [1] (phenotypic.tune.StrategyConfig class method), [1] (phenotypic.tune.SupervisedScorer class method), [1] (phenotypic.tune.targets.Nested class method) (phenotypic.tune.targets.Param class method) (phenotypic.tune.targets.Presence class method) (phenotypic.tune.targets.TunableParam class method) (phenotypic.tune.Trial class method), [1] (phenotypic.tune.TuningSpec class method), [1]

partition() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] passed_ids (phenotypic.sdk_.branch_pathfinding.FilterResult attribute), [1] (phenotypic.sdk_.branch_pathfinding.PrescreenResult attribute), [1] patch_size (phenotypic.enhance.NonLocalMeansDenoiser attribute), [1] path (phenotypic.gui.tune.TuneRunRoot attribute) path_dilation_radius (phenotypic.detect.FilamentousFungiDetector attribute), [1] path_length (phenotypic.sdk_.branch_pathfinding.FragmentPath attribute), [1] PathMetrics (class in phenotypic.sdk_.branch_pathfinding) paths_metrics_dataframe() (in module phenotypic.sdk_.branch_pathfinding) pct_energy_band_median (phenotypic.sdk_.branch_pathfinding.PathMetrics attribute), [1] pct_energy_median_values (phenotypic.sdk_.branch_pathfinding.CalibrationData attribute), [1] pct_min_wavelength (phenotypic.detect.FilamentousFungiDetector attribute), [1] pct_n_orient (phenotypic.detect.FilamentousFungiDetector attribute), [1] peak_prominence (phenotypic.detect.RoundPeaksDetector attribute), [1] (phenotypic.detect.SinePeakDetector attribute), [1] (phenotypic.refine.GridAlignmentRefiner attribute), [1] (phenotypic.refine.RefineBySineFit attribute), [1] peak_response (phenotypic.util.image_metrics.StructureMetrics attribute) (phenotypic.util.StructureMetrics attribute), [1] pelt_penalty (phenotypic.measure.MeasureSymmetricZones attribute), [1] (phenotypic.refine.TrimAsymmetry attribute), [1] PENDING (phenotypic.sdk_.DashboardManifestKey attribute), [1] PENDING_CHUNKS (phenotypic.sdk_.DashboardManifestSlurmInfoKey attribute), [1] pending_delete_block_id (phenotypic.gui.builder._state._DagBuilderState attribute), [1] per_filter_rejections (phenotypic.sdk_.branch_pathfinding.FilterResult attribute), [1] PERIMETER (phenotypic.schema.SHAPE attribute) PH (phenotypic.schema.CONDITION_METADATA attribute) phenotypic module phenotypic.abc_ module phenotypic.analysis module phenotypic.analysis.abc_ module phenotypic.analysis.qc module phenotypic.correction module phenotypic.data module phenotypic.detect module phenotypic.detect.nn module phenotypic.enhance module phenotypic.grid module phenotypic.gui module phenotypic.gui.analysis module phenotypic.gui.browse module phenotypic.gui.builder module phenotypic.gui.results_viewer module phenotypic.gui.results_viewer.colony_view module phenotypic.gui.run_console module phenotypic.gui.shell module phenotypic.gui.tune module phenotypic.measure module phenotypic.phenotypicCLI module phenotypic.post module phenotypic.prefab module phenotypic.refine module phenotypic.schema module phenotypic.sdk_ module phenotypic.sdk_.branch_pathfinding module phenotypic.sdk_.colourspace module phenotypic.sdk_.constants_ module phenotypic.sdk_.exceptions_ module phenotypic.sdk_.funcs_ module phenotypic.sdk_.generate_report module phenotypic.sdk_.hdf_ module phenotypic.sdk_.mixin module phenotypic.sdk_.monitor_slurm_jobs module phenotypic.sdk_.napari_ module phenotypic.sdk_.register module phenotypic.sdk_.slurm module phenotypic.sdk_.slurm_ module phenotypic.sdk_.submitit_ module phenotypic.sdk_.typing_ module phenotypic.sdk_.viz module phenotypic.sdk_.viz.figures module phenotypic.sdk_.viz.notebook module phenotypic.settings_ module phenotypic.tune module phenotypic.tune.targets module phenotypic.util module phenotypic.util.image_metrics module phenotypic_cache_dir() (in module phenotypic.sdk_), [1] phenotypic_cache_pipeline_json_path() (in module phenotypic.sdk_), [1] PHENOTYPIC_CLASS (phenotypic.sdk_.HdfAttr attribute), [1] PHENOTYPIC_METADATA_KEY (phenotypic.sdk_.constants_.IO attribute), [1] phenotypic_mpl_context() (in module phenotypic.sdk_.viz.figures) phenotypic_rc() (in module phenotypic.sdk_.viz.figures) phenotypic_version (phenotypic.tune.TuningSpec attribute), [1] PhenoTypicError, [1] PINK_PCT (phenotypic.schema.ColorComposition attribute) PIPE_STATUS (class in phenotypic.sdk_.constants_), [1] pipeline (phenotypic.tune.TuningSpec attribute), [1] PIPELINE_CLASS_NAME (in module phenotypic.gui.builder._state) pipeline_json_path() (in module phenotypic.sdk_), [1] PIPELINE_PATH (phenotypic.sdk_.ProcessingStateKey attribute), [1] pipeline_targets() (in module phenotypic.tune.targets) PLASMID (phenotypic.schema.GENETIC_METADATA attribute) PLATE_ID (phenotypic.schema.PLATE_METADATA attribute) PLATE_METADATA (class in phenotypic.schema) PLOIDY (phenotypic.schema.GENETIC_METADATA attribute) plot_cost_distance_heatmap() (in module phenotypic.sdk_.branch_pathfinding) plot_paths_over_image() (in module phenotypic.sdk_.branch_pathfinding) PlotAccessor (class in phenotypic._core._image_parts.accessors._plot_accessor) PlotterRegistry (class in phenotypic.sdk_.register), [1] PNG_FILE_EXTENSIONS (phenotypic.sdk_.constants_.IO attribute), [1] PointPickerMixin (class in phenotypic.sdk_.mixin) PointPickerWidget (class in phenotypic.sdk_.napari_), [1] polymorphic_field() (in module phenotypic.sdk_.typing_) pop() (phenotypic._core._image_parts.accessors._metadata_accessor.MetadataAccessor method) (phenotypic.util.BackgroundMetrics method), [1] (phenotypic.util.ContrastMetrics method), [1] (phenotypic.util.image_metrics.BackgroundMetrics method) (phenotypic.util.image_metrics.ContrastMetrics method) (phenotypic.util.image_metrics.NoiseMetrics method) (phenotypic.util.image_metrics.QualityScores method) (phenotypic.util.image_metrics.StructureMetrics method) (phenotypic.util.NoiseMetrics method), [1] (phenotypic.util.QualityScores method), [1] (phenotypic.util.StructureMetrics method), [1] popitem() (phenotypic.util.BackgroundMetrics method), [1] (phenotypic.util.ContrastMetrics method), [1] (phenotypic.util.image_metrics.BackgroundMetrics method) (phenotypic.util.image_metrics.ContrastMetrics method) (phenotypic.util.image_metrics.NoiseMetrics method) (phenotypic.util.image_metrics.QualityScores method) (phenotypic.util.image_metrics.StructureMetrics method) (phenotypic.util.NoiseMetrics method), [1] (phenotypic.util.QualityScores method), [1] (phenotypic.util.StructureMetrics method), [1] post (phenotypic.abc_.PrefabPipeline attribute), [1] (phenotypic.prefab.FilamentousFungiPipeline attribute), [1] (phenotypic.prefab.GridSectionPipeline attribute), [1] (phenotypic.prefab.HeavyOtsuPipeline attribute), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] (phenotypic.prefab.HeavyWatershedPipeline attribute), [1] (phenotypic.prefab.RoundPeaksPipeline attribute), [1] (phenotypic.prefab.SpImagerPipeline attribute), [1] POST (phenotypic.sdk_.ModulePath attribute), [1] PostMeasurement (class in phenotypic.abc_), [1] preallocate_frame_layout() (phenotypic.sdk_.HDF static method), [1] (phenotypic.sdk_.hdf_.HDF static method) preallocate_series_layout() (phenotypic.sdk_.HDF static method), [1] (phenotypic.sdk_.hdf_.HDF static method) PRED_CC (phenotypic.schema.GRID_LINREG_STATS attribute) (phenotypic.sdk_.constants_.GRID_LINREG_STATS_EXTRACTOR attribute), [1] PRED_RR (phenotypic.schema.GRID_LINREG_STATS attribute) (phenotypic.sdk_.constants_.GRID_LINREG_STATS_EXTRACTOR attribute), [1] predecessor (phenotypic.sdk_.branch_pathfinding.DijkstraResult attribute), [1] prefab pipeline PrefabPipeline (class in phenotypic.abc_), [1] PrependString (class in phenotypic.post) preprocess() (phenotypic.abc_.GpuDetector method), [1] prescreen_fragments() (in module phenotypic.sdk_.branch_pathfinding) PrescreenResult (class in phenotypic.sdk_.branch_pathfinding) Presence (class in phenotypic.tune.targets) preserve_range (phenotypic.enhance.SharpenEdgeGauss attribute), [1] (phenotypic.enhance.SubtractGaussian attribute), [1] preview_modes() (phenotypic._core._image_parts.accessors._detect_mat_accessor.DetectMatAccessor method) primary (phenotypic.abc_.FigureSpec attribute), [1], [2], [3] PROCESSED (phenotypic.sdk_.constants_.PIPE_STATUS attribute), [1] processing_report_html_path() (in module phenotypic.sdk_), [1] processing_state_path() (in module phenotypic.sdk_), [1] ProcessingStateKey (class in phenotypic.sdk_), [1] ProcessingStatus (in module phenotypic.sdk_.typing_) ProcessOnlyLayer (in module phenotypic.sdk_.typing_) profile (phenotypic.correction.ColorCorrector attribute), [1] progress_dir() (in module phenotypic.sdk_), [1] PROJECT (phenotypic.schema.EXPERIMENT_METADATA attribute) props (phenotypic._core._image_parts.accessors._objects_accessor.ObjectsAccessor property) PROTECTED_METADATA_SUBGROUP_KEY (phenotypic.sdk_.HDF attribute), [1] (phenotypic.sdk_.hdf_.HDF attribute) PROTOCOL (phenotypic.schema.EXPERIMENT_METADATA attribute) prune (phenotypic.tune.OptunaConfig attribute), [1] prune_saturated (phenotypic.analysis.LinearSoftplus attribute), [1] pruned (phenotypic.tune.EvaluationResult attribute), [1] (phenotypic.tune.Trial attribute), [1] PUBLIC_METADATA_SUBGROUP_KEY (phenotypic.sdk_.HDF attribute), [1] (phenotypic.sdk_.hdf_.HDF attribute) PURPLE_PCT (phenotypic.schema.ColorComposition attribute) pvalue (phenotypic.analysis.EdgeCorrector attribute), [1]

Q

Q1_INTENSITY (phenotypic.schema.INTENSITY attribute) Q3_INTENSITY (phenotypic.schema.INTENSITY attribute) qc (phenotypic.abc_.PrefabPipeline attribute), [1] (phenotypic.prefab.FilamentousFungiPipeline attribute), [1] (phenotypic.prefab.GridSectionPipeline attribute), [1] (phenotypic.prefab.HeavyOtsuPipeline attribute), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] (phenotypic.prefab.HeavyWatershedPipeline attribute), [1] (phenotypic.prefab.RoundPeaksPipeline attribute), [1] (phenotypic.prefab.SpImagerPipeline attribute), [1] qc_config_json_path() (in module phenotypic.sdk_), [1] qc_dir() (in module phenotypic.sdk_), [1] qc_members_parquet_path() (in module phenotypic.sdk_), [1]

qc_review_state_path() (in module phenotypic.sdk_), [1] qc_summary_parquet_path() (in module phenotypic.sdk_), [1] QCScorer (class in phenotypic.tune), [1] QUALITY_CHECK (class in phenotypic.schema) QUALITY_COUNT (class in phenotypic.schema) QUALITY_ICC (class in phenotypic.schema) QUALITY_MAD (class in phenotypic.schema) QUALITY_SE (class in phenotypic.schema) QUALITY_TUKEY (class in phenotypic.schema) QUALITY_ZMAX (class in phenotypic.schema) QualityCheck (class in phenotypic.analysis.abc_) QualityScores (class in phenotypic.util), [1] (class in phenotypic.util.image_metrics) quant_lvl (phenotypic.measure.MeasureTexture attribute), [1]

R

R2 (phenotypic.schema.MODEL_METRICS attribute) R_FIT (phenotypic.schema.LOG_GROWTH_MODEL attribute) RADIAL_EXPANSION (class in phenotypic.schema) radius (phenotypic.enhance.SharpenEdgeGauss attribute), [1] (phenotypic.enhance.SubtractRollingBall attribute), [1] random_seed (phenotypic.measure.MeasureColor attribute), [1] RandomConfig (class in phenotypic.tune), [1] RankMedianEnhancer (class in phenotypic.enhance), [1] RankOtsuDetector (class in phenotypic.detect), [1] rater_label (phenotypic.analysis.ICC attribute), [1] (phenotypic.analysis.qc.ICC attribute) RAW_FILE_EXTENSIONS (phenotypic.sdk_.constants_.IO attribute), [1] read_run_manifest() (in module phenotypic.sdk_), [1] reader() (phenotypic.sdk_.HDF method), [1] (phenotypic.sdk_.hdf_.HDF method) readme_md_path() (in module phenotypic.sdk_), [1] reason (phenotypic.tune.Excluded attribute), [1] recommendation (phenotypic.tune.ScreeningResult attribute), [1] recompile_dir() (in module phenotypic.sdk_), [1] recompile_status_dir() (in module phenotypic.sdk_), [1] RecompileTaskType (in module phenotypic.sdk_.typing_) reconnection_tolerance (phenotypic.detect.FilamentousFungiDetector attribute), [1] RED_PCT (phenotypic.schema.ColorComposition attribute) reduced_space (phenotypic.tune.ScreeningResult attribute), [1] ReduceSectionsByLine (class in phenotypic.refine), [1] ReferenceFreeScorer (class in phenotypic.tune), [1] RefineBySineFit (class in phenotypic.refine), [1] regex (phenotypic.post.ExpandMetadata attribute) region_metric (phenotypic.tune.SupervisedScorer attribute), [1] region_term_name (phenotypic.tune.SupervisedScorer attribute), [1] register() (phenotypic.sdk_.register.AnalysisPluginRegistry class method), [1] (phenotypic.sdk_.register.BaseRegistry class method), [1] (phenotypic.sdk_.register.PlotterRegistry class method), [1] register_analysis() (in module phenotypic.sdk_.register), [1] register_detection_mode() (in module phenotypic.abc_), [1] register_phenotypic_template() (in module phenotypic.sdk_.viz.figures) register_plotter() (in module phenotypic.sdk_.register), [1] rejected_ids (phenotypic.sdk_.branch_pathfinding.FilterResult attribute), [1] (phenotypic.sdk_.branch_pathfinding.PrescreenResult attribute), [1] relabel (phenotypic.detect.WatershedDetector attribute), [1] relabel() (phenotypic._core._image_parts.accessors._objects_accessor.ObjectsAccessor method) (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap method) relative_drop (phenotypic.tune.GeneralizationReport attribute), [1] RelativeMAD (class in phenotypic.analysis), [1] (class in phenotypic.analysis.qc) release() (phenotypic.gui.shell.ToolSession method) remove_noise (phenotypic.detect.RoundPeaksDetector attribute), [1] (phenotypic.detect.SinePeakDetector attribute), [1] RemoveBorderObjects (class in phenotypic.refine), [1] RemoveByFeature (class in phenotypic.refine), [1] RemoveGridOutliers (class in phenotypic.refine), [1] RemoveLowCircularity (class in phenotypic.refine), [1] removeprefix() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] removesuffix() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] render() (phenotypic.abc_.BoundFigures method), [1] render_error_analysis_html() (in module phenotypic.analysis), [1] render_error_analysis_report() (in module phenotypic.analysis), [1] replace() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] REPLICATE (phenotypic.schema.SAMPLE_METADATA attribute) replicate_groupby (phenotypic.tune.ReferenceFreeScorer attribute), [1] ReplicateAgreement (class in phenotypic.analysis), [1] (class in phenotypic.analysis.qc) requires_rgb (phenotypic.abc_.DetectionMode property), [1] rescale_sigma (phenotypic.correction.BayesShrinkCorrector attribute), [1] (phenotypic.correction.VisuShrinkCorrector attribute), [1] (phenotypic.enhance.BayesShrinkEnhancer attribute), [1] (phenotypic.enhance.VisuShrinkEnhancer attribute), [1] reset (phenotypic.abc_.PrefabPipeline attribute), [1] (phenotypic.prefab.FilamentousFungiPipeline attribute), [1] (phenotypic.prefab.GridSectionPipeline attribute), [1] (phenotypic.prefab.HeavyOtsuPipeline attribute), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] (phenotypic.prefab.HeavyWatershedPipeline attribute), [1] (phenotypic.prefab.RoundPeaksPipeline attribute), [1] (phenotypic.prefab.SpImagerPipeline attribute), [1] reset() (phenotypic._core._image_parts.accessors._detect_mat_accessor.DetectMatAccessor method) (phenotypic._core._image_parts.accessors._objects_accessor.ObjectsAccessor method) (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap method) (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask method) reset_enh_matrix (phenotypic.grid.GridApply attribute), [1] RESIDUAL_ERR (phenotypic.schema.GRID_LINREG_STATS attribute) (phenotypic.sdk_.constants_.GRID_LINREG_STATS_EXTRACTOR attribute), [1] residual_fraction (phenotypic.grid.AutoGridFinder attribute), [1] (phenotypic.grid.CenteredAutoGridFinder attribute), [1] RESOLUTION (phenotypic.schema.ACQUISITION_METADATA attribute) resolve() (phenotypic.gui.shell.SandboxRoot method) resolve_best_pipeline_path() (in module phenotypic.sdk_), [1] resolve_event_log_path() (in module phenotypic.sdk_), [1] resolve_execution_mode() (in module phenotypic.sdk_), [1] resolve_manifest_json_path() (in module phenotypic.sdk_), [1] resolve_pipeline_config_path() (in module phenotypic.sdk_), [1] resolve_processing_state_path() (in module phenotypic.sdk_), [1] resolve_progress_dir() (in module phenotypic.sdk_), [1] resolve_split_assignment_path() (in module phenotypic.sdk_), [1] resolve_study_db_path() (in module phenotypic.sdk_), [1] resolve_tuning_spec_path() (in module phenotypic.sdk_), [1] response_floor (phenotypic.grid.CenteredAutoGridFinder attribute), [1] results() (phenotypic.analysis.abc_.ModelFitter method) (phenotypic.analysis.abc_.QualityCheck method) (phenotypic.analysis.abc_.SetAnalyzer method) (phenotypic.analysis.DoubleSoftplus method), [1] (phenotypic.analysis.EdgeCorrector method), [1] (phenotypic.analysis.ExpectedVsDetectedCount method), [1] (phenotypic.analysis.ICC method), [1] (phenotypic.analysis.LinearSoftplus method), [1] (phenotypic.analysis.LogGrowthModel method), [1] (phenotypic.analysis.MADOutlierRemover method), [1] (phenotypic.analysis.MaxModifiedZScore method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount method) (phenotypic.analysis.qc.ICC method) (phenotypic.analysis.qc.MaxModifiedZScore method) (phenotypic.analysis.qc.RelativeMAD method) (phenotypic.analysis.qc.ReplicateAgreement method) (phenotypic.analysis.qc.TukeyOutlierFraction method) (phenotypic.analysis.RelativeMAD method), [1] (phenotypic.analysis.ReplicateAgreement method), [1] (phenotypic.analysis.TukeyOutlierFraction method), [1] (phenotypic.analysis.TukeyOutlierRemover method), [1] results_dir() (in module phenotypic.sdk_), [1] rfind() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] rgb (phenotypic.Image property) RGB (phenotypic.sdk_.constants_.IMAGE_MODE attribute), [1] RGB_OR_BGR (phenotypic.sdk_.constants_.IMAGE_MODE attribute), [1] RGBA (phenotypic.sdk_.constants_.IMAGE_MODE attribute), [1] RGBA_OR_BGRA (phenotypic.sdk_.constants_.IMAGE_MODE attribute), [1] rho (phenotypic.enhance.StructureSmoothing attribute), [1] (phenotypic.tune.CompositeScorer attribute), [1] ridge_lambda (phenotypic.correction.ColorCheckerProfile attribute), [1] ridge_method (phenotypic.util.image_metrics.StructureMetrics attribute) (phenotypic.util.StructureMetrics attribute), [1] ridge_responses (phenotypic.util.image_metrics.StructureMetrics attribute) (phenotypic.util.StructureMetrics attribute), [1]

right (phenotypic.correction.ImageCropper attribute), [1] (phenotypic.correction.ImagePadder attribute), [1] RIGHT_DISTANCE (phenotypic.schema.GRID_SPATIAL attribute) RIGHT_NEIGHBOR_OBJ_LABEL (phenotypic.schema.GRID_SPATIAL attribute) rindex() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] rjust() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] rms_contrast (phenotypic.util.ContrastMetrics attribute), [1] (phenotypic.util.image_metrics.ContrastMetrics attribute) RMSE (phenotypic.schema.MODEL_METRICS attribute) robust_color_center() (in module phenotypic.util), [1] robust_headers() (phenotypic.schema.ColorHSV class method) (phenotypic.schema.ColorLab class method) ROBUST_MEAN_RADIUS (phenotypic.schema.RADIAL_EXPANSION attribute) rois (phenotypic.correction.ColorCheckerProfile attribute), [1] root (phenotypic.gui.builder._state._DagBuilderState attribute), [1] (phenotypic.gui.shell.SandboxRoot attribute), [1] root_posix (phenotypic.sdk_.HDF attribute), [1], [2], [3] (phenotypic.sdk_.hdf_.HDF attribute), [1] rotate() (phenotypic.Image method) RoundPeaksDetector (class in phenotypic.detect), [1] RoundPeaksPipeline (class in phenotypic.prefab), [1] row_edges (phenotypic.grid.ManualGridFinder attribute), [1], [2], [3] ROW_INTERVAL_END (phenotypic.schema.GRID attribute) ROW_INTERVAL_START (phenotypic.schema.GRID attribute) ROW_LINREG_B (phenotypic.schema.GRID_LINREG_STATS attribute) (phenotypic.sdk_.constants_.GRID_LINREG_STATS_EXTRACTOR attribute), [1] ROW_LINREG_M (phenotypic.schema.GRID_LINREG_STATS attribute) (phenotypic.sdk_.constants_.GRID_LINREG_STATS_EXTRACTOR attribute), [1] ROW_MAJOR_IDX (phenotypic.schema.GRID attribute) ROW_NUM (phenotypic.schema.GRID attribute) ROWS (phenotypic.sdk_.ChunkManifestKey attribute), [1] rpartition() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] rsplit() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] rst_table() (phenotypic.abc_.MeasurementInfo class method), [1] (phenotypic.schema.ACQUISITION_METADATA class method) (phenotypic.schema.BBOX class method) (phenotypic.schema.ColorComposition class method) (phenotypic.schema.ColorHSV class method) (phenotypic.schema.ColorLab class method) (phenotypic.schema.Colorxy class method) (phenotypic.schema.ColorXYZ class method) (phenotypic.schema.CONDITION_METADATA class method) (phenotypic.schema.CURATION class method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL class method) (phenotypic.schema.EDGE_CORRECTION class method) (phenotypic.schema.ErrorCategory class method) (phenotypic.schema.EXPERIMENT_METADATA class method) (phenotypic.schema.GENETIC_METADATA class method) (phenotypic.schema.GRID class method) (phenotypic.schema.GRID_LINREG_STATS class method) (phenotypic.schema.GRID_SPATIAL class method) (phenotypic.schema.GRID_SPREAD class method) (phenotypic.schema.INCUBATION_METADATA class method) (phenotypic.schema.INTENSITY class method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL class method) (phenotypic.schema.LOG_GROWTH_MODEL class method) (phenotypic.schema.MeasurementInfo class method) (phenotypic.schema.METADATA class method) (phenotypic.schema.MODEL_METRICS class method) (phenotypic.schema.OBJECT class method) (phenotypic.schema.PLATE_METADATA class method) (phenotypic.schema.QUALITY_CHECK class method) (phenotypic.schema.QUALITY_COUNT class method) (phenotypic.schema.QUALITY_ICC class method) (phenotypic.schema.QUALITY_MAD class method) (phenotypic.schema.QUALITY_SE class method) (phenotypic.schema.QUALITY_TUKEY class method) (phenotypic.schema.QUALITY_ZMAX class method) (phenotypic.schema.RADIAL_EXPANSION class method) (phenotypic.schema.SAMPLE_METADATA class method) (phenotypic.schema.SHAPE class method) (phenotypic.schema.SIZE class method) (phenotypic.schema.SYMMETRIC_ZONES class method) (phenotypic.schema.TEXTURE class method) (phenotypic.sdk_.constants_.ConstantLabels class method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS class method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS class method), [1] rstrip() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] run() (phenotypic.sdk_.napari_.LabelEditorWidget method), [1] (phenotypic.sdk_.napari_.PointPickerWidget method), [1] (phenotypic.tune.ScreeningController method), [1] run_auto_space() (in module phenotypic.tune), [1] run_held_out() (in module phenotypic.tune), [1] run_multisource_dijkstra() (in module phenotypic.sdk_.branch_pathfinding) run_tuning() (in module phenotypic.tune), [1] rung_factor (phenotypic.tune.Evaluator attribute), [1] rung_floor (phenotypic.tune.Evaluator attribute), [1] RUNNER_DETECTED (phenotypic.schema.RADIAL_EXPANSION attribute) RUNNER_LENGTH (phenotypic.schema.RADIAL_EXPANSION attribute)

S

s0 (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL attribute) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL attribute) s0_prior (phenotypic.analysis.DoubleSoftplus attribute), [1] (phenotypic.analysis.LinearSoftplus attribute), [1] s0_prior_cv (phenotypic.analysis.DoubleSoftplus attribute), [1] (phenotypic.analysis.LinearSoftplus attribute), [1] s0_prior_groupby (phenotypic.analysis.DoubleSoftplus attribute), [1] (phenotypic.analysis.LinearSoftplus attribute), [1] s0_prior_sigma (phenotypic.analysis.DoubleSoftplus attribute), [1] (phenotypic.analysis.LinearSoftplus attribute), [1] safe_writer() (phenotypic.sdk_.HDF method), [1] (phenotypic.sdk_.hdf_.HDF method) SAMPLE_ID (phenotypic.schema.SAMPLE_METADATA attribute) SAMPLE_METADATA (class in phenotypic.schema) sampler (phenotypic.tune.OptunaConfig attribute), [1] SandboxRoot (class in phenotypic.gui.shell) SATURATION_ROBUST_MEAN (phenotypic.schema.ColorHSV attribute) save2hdf5() (phenotypic.Image method) save2pickle() (phenotypic.Image method) save_array2hdf5() (phenotypic.sdk_.HDF static method), [1] (phenotypic.sdk_.hdf_.HDF static method) save_frame_append() (phenotypic.sdk_.HDF static method), [1] (phenotypic.sdk_.hdf_.HDF static method) save_frame_new() (phenotypic.sdk_.HDF static method), [1] (phenotypic.sdk_.hdf_.HDF static method) save_frame_update() (phenotypic.sdk_.HDF static method), [1] (phenotypic.sdk_.hdf_.HDF static method) save_overlay() (phenotypic._core._image_parts.accessors._detect_mat_accessor.DetectMatAccessor method) (phenotypic._core._image_parts.accessors._grayscale_accessor.Grayscale method) (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap method) (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask method) (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) (phenotypic._core._image_parts.accessors._rgb_accessor.ImageRGB method) save_series_append() (phenotypic.sdk_.HDF static method), [1] (phenotypic.sdk_.hdf_.HDF static method) save_series_new() (phenotypic.sdk_.HDF static method), [1] (phenotypic.sdk_.hdf_.HDF static method) save_series_update() (phenotypic.sdk_.HDF static method), [1] (phenotypic.sdk_.hdf_.HDF static method) scale (phenotypic.measure.MeasureTexture attribute), [1] scale_factor (phenotypic.correction.DenoiseBlockMatch attribute), [1] scales (phenotypic.util.image_metrics.StructureMetrics attribute) (phenotypic.util.StructureMetrics attribute), [1] schema() (phenotypic.abc_.BackgroundSubtraction class method), [1] (phenotypic.abc_.BaseOperation class method), [1] (phenotypic.abc_.ContrastAdjustment class method), [1] (phenotypic.abc_.FocusBlob class method), [1] (phenotypic.abc_.FocusEdge class method), [1] (phenotypic.abc_.GpuDetector class method), [1] (phenotypic.abc_.GridCorrector class method), [1] (phenotypic.abc_.GridFinder class method), [1] (phenotypic.abc_.GridMeasureFeatures class method), [1] (phenotypic.abc_.GridObjectDetector class method), [1] (phenotypic.abc_.GridObjectRefiner class method), [1] (phenotypic.abc_.GridOperation class method), [1] (phenotypic.abc_.ImageCorrector class method), [1] (phenotypic.abc_.ImageDenoiser class method), [1] (phenotypic.abc_.ImageEnhancer class method), [1] (phenotypic.abc_.ImageOperation class method), [1] (phenotypic.abc_.MeasureFeatures class method), [1] (phenotypic.abc_.MorphologicalFiltering class method), [1] (phenotypic.abc_.ObjectDetector class method), [1] (phenotypic.abc_.ObjectRefiner class method), [1] (phenotypic.abc_.PostMeasurement class method), [1] (phenotypic.abc_.PrefabPipeline class method), [1] (phenotypic.abc_.Smoothing class method), [1] (phenotypic.abc_.ThresholdDetector class method), [1] (phenotypic.analysis.abc_.ModelFitter class method) (phenotypic.analysis.abc_.QualityCheck class method) (phenotypic.analysis.abc_.SetAnalyzer class method) (phenotypic.analysis.DoubleSoftplus class method), [1] (phenotypic.analysis.EdgeCorrector class method), [1] (phenotypic.analysis.ErrorCutoffFinder class method), [1] (phenotypic.analysis.ExpectedVsDetectedCount class method), [1] (phenotypic.analysis.ICC class method), [1] (phenotypic.analysis.LinearSoftplus class method), [1] (phenotypic.analysis.LogGrowthModel class method), [1] (phenotypic.analysis.MADOutlierRemover class method), [1] (phenotypic.analysis.MaxModifiedZScore class method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount class method) (phenotypic.analysis.qc.ICC class method) (phenotypic.analysis.qc.MaxModifiedZScore class method) (phenotypic.analysis.qc.RelativeMAD class method) (phenotypic.analysis.qc.ReplicateAgreement class method) (phenotypic.analysis.qc.TukeyOutlierFraction class method) (phenotypic.analysis.RelativeMAD class method), [1] (phenotypic.analysis.ReplicateAgreement class method), [1] (phenotypic.analysis.TukeyOutlierFraction class method), [1] (phenotypic.analysis.TukeyOutlierRemover class method), [1] (phenotypic.correction.BayesShrinkCorrector class method), [1] (phenotypic.correction.CaptureMetadata class method), [1] (phenotypic.correction.ColorCheckerProfile class method), [1] (phenotypic.correction.ColorCorrector class method), [1] (phenotypic.correction.ColorDenoise class method), [1] (phenotypic.correction.DenoiseBlockMatch class method), [1] (phenotypic.correction.GridAligner class method), [1] (phenotypic.correction.ImageCropper class method), [1] (phenotypic.correction.ImagePadder class method), [1] (phenotypic.correction.VisuShrinkCorrector class method), [1] (phenotypic.detect.CannyDetector class method), [1] (phenotypic.detect.ChanVeseDetector class method), [1] (phenotypic.detect.CompositeDetector class method), [1] (phenotypic.detect.FilamentousFungiDetector class method), [1] (phenotypic.detect.HysteresisDetector class method), [1] (phenotypic.detect.InoculumDetector class method), [1] (phenotypic.detect.IsodataDetector class method), [1] (phenotypic.detect.LiDetector class method), [1] (phenotypic.detect.MadHysteresisDetector class method), [1] (phenotypic.detect.ManualGridPointDetector class method), [1] (phenotypic.detect.ManualPointDetector class method), [1] (phenotypic.detect.MeanDetector class method), [1] (phenotypic.detect.MinimumDetector class method), [1] (phenotypic.detect.OtsuDetector class method), [1] (phenotypic.detect.RankOtsuDetector class method), [1] (phenotypic.detect.RoundPeaksDetector class method), [1] (phenotypic.detect.SecondaryOtsuDetector class method), [1] (phenotypic.detect.SinePeakDetector class method), [1] (phenotypic.detect.TriangleDetector class method), [1] (phenotypic.detect.UserThreshold class method), [1] (phenotypic.detect.WatershedDetector class method), [1] (phenotypic.detect.YenDetector class method), [1] (phenotypic.enhance.BayesShrinkEnhancer class method), [1] (phenotypic.enhance.ContrastStretching class method), [1] (phenotypic.enhance.EnhanceBlockMatch class method), [1] (phenotypic.enhance.EnhanceLocalContrast class method), [1] (phenotypic.enhance.FlattenIllumination class method), [1] (phenotypic.enhance.FocusBlobLoG class method), [1] (phenotypic.enhance.FocusEdgeFrangi class method), [1] (phenotypic.enhance.FocusEdgeHessian class method), [1] (phenotypic.enhance.FocusEdgeLaplace class method), [1] (phenotypic.enhance.FocusEdgeMeijering class method), [1] (phenotypic.enhance.FocusEdgePhase class method), [1] (phenotypic.enhance.FocusEdgeSato class method), [1] (phenotypic.enhance.FocusEdgeSobel class method), [1] (phenotypic.enhance.GaussianBlur class method), [1] (phenotypic.enhance.GrayOpening class method), [1] (phenotypic.enhance.ImageInverter class method), [1] (phenotypic.enhance.LocalEdgeDenoise class method), [1] (phenotypic.enhance.MedianFilter class method), [1] (phenotypic.enhance.NonLocalMeansDenoiser class method), [1] (phenotypic.enhance.RankMedianEnhancer class method), [1] (phenotypic.enhance.SetDetectMode class method), [1] (phenotypic.enhance.SharpenEdgeGauss class method), [1] (phenotypic.enhance.StructureSmoothing class method), [1] (phenotypic.enhance.SubtractGaussian class method), [1] (phenotypic.enhance.SubtractOpening class method), [1] (phenotypic.enhance.SubtractRollingBall class method), [1] (phenotypic.enhance.SubtractWhiteTophat class method), [1] (phenotypic.enhance.VisuShrinkEnhancer class method), [1] (phenotypic.enhance.WhiteTophatEnhance class method), [1] (phenotypic.grid.AutoGridFinder class method), [1] (phenotypic.grid.CenteredAutoGridFinder class method), [1] (phenotypic.grid.GridApply class method), [1] (phenotypic.grid.ManualGridFinder class method), [1] (phenotypic.measure.MeasureBounds class method), [1] (phenotypic.measure.MeasureColor class method), [1] (phenotypic.measure.MeasureGridLinRegStats class method), [1] (phenotypic.measure.MeasureGridSpatial class method), [1] (phenotypic.measure.MeasureGridSpread class method), [1] (phenotypic.measure.MeasureIntensity class method), [1] (phenotypic.measure.MeasureShape class method), [1] (phenotypic.measure.MeasureSize class method), [1] (phenotypic.measure.MeasureSymmetricZones class method), [1] (phenotypic.measure.MeasureTexture class method), [1] (phenotypic.post.AppendString class method) (phenotypic.post.ExpandMetadata class method) (phenotypic.post.MergeMetadata class method) (phenotypic.post.PrependString class method) (phenotypic.prefab.FilamentousFungiPipeline class method), [1] (phenotypic.prefab.GridSectionPipeline class method), [1] (phenotypic.prefab.HeavyOtsuPipeline class method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline class method), [1] (phenotypic.prefab.HeavyWatershedPipeline class method), [1] (phenotypic.prefab.RoundPeaksPipeline class method), [1] (phenotypic.prefab.SpImagerPipeline class method), [1] (phenotypic.refine.ExtractColonyCore class method), [1] (phenotypic.refine.GridAlignmentRefiner class method), [1] (phenotypic.refine.GridOversizedObjectRemover class method), [1] (phenotypic.refine.KeepNearestCenter class method), [1] (phenotypic.refine.KeepSectionLargest class method), [1] (phenotypic.refine.ManualRefine class method), [1] (phenotypic.refine.MaskClosing class method), [1] (phenotypic.refine.MaskDilation class method), [1] (phenotypic.refine.MaskErosion class method), [1] (phenotypic.refine.MaskFill class method), [1] (phenotypic.refine.MaskGradient class method), [1] (phenotypic.refine.MaskOpening class method), [1] (phenotypic.refine.MaskWhiteTophat class method), [1] (phenotypic.refine.MergeFragmentChains class method), [1] (phenotypic.refine.NearestNeighborMerger class method), [1] (phenotypic.refine.ReduceSectionsByLine class method), [1] (phenotypic.refine.RefineBySineFit class method), [1] (phenotypic.refine.RemoveBorderObjects class method), [1] (phenotypic.refine.RemoveByFeature class method), [1] (phenotypic.refine.RemoveGridOutliers class method), [1] (phenotypic.refine.RemoveLowCircularity class method), [1] (phenotypic.refine.SeparateObjects class method), [1] (phenotypic.refine.Skeletonize class method), [1] (phenotypic.refine.SmallObjectRemover class method), [1] (phenotypic.refine.SmallToLargeMerger class method), [1] (phenotypic.refine.Thinning class method), [1] (phenotypic.refine.TrimAsymmetry class method), [1] (phenotypic.tune.Budget class method), [1] (phenotypic.tune.Categorical class method), [1] (phenotypic.tune.CompositeScorer class method), [1] (phenotypic.tune.EvaluationResult class method), [1] (phenotypic.tune.Evaluator class method), [1] (phenotypic.tune.Excluded class method), [1] (phenotypic.tune.Fixed class method), [1] (phenotypic.tune.FloatRange class method), [1] (phenotypic.tune.GridConfig class method), [1] (phenotypic.tune.GroundTruthMasks class method), [1] (phenotypic.tune.HeldOutConfig class method), [1] (phenotypic.tune.ImportanceReport class method), [1] (phenotypic.tune.InferredSearchSpace class method), [1] (phenotypic.tune.IntRange class method), [1] (phenotypic.tune.Knob class method), [1] (phenotypic.tune.OptunaConfig class method), [1] (phenotypic.tune.QCScorer class method), [1] (phenotypic.tune.RandomConfig class method), [1] (phenotypic.tune.ReferenceFreeScorer class method), [1] (phenotypic.tune.Scorer class method), [1] (phenotypic.tune.SearchSpace class method), [1] (phenotypic.tune.StrategyConfig class method), [1] (phenotypic.tune.SupervisedScorer class method), [1] (phenotypic.tune.targets.Nested class method) (phenotypic.tune.targets.Param class method) (phenotypic.tune.targets.Presence class method) (phenotypic.tune.targets.TunableParam class method) (phenotypic.tune.Trial class method), [1] (phenotypic.tune.TuningSpec class method), [1] schema_json() (phenotypic.abc_.BackgroundSubtraction class method), [1] (phenotypic.abc_.BaseOperation class method), [1] (phenotypic.abc_.ContrastAdjustment class method), [1] (phenotypic.abc_.FocusBlob class method), [1] (phenotypic.abc_.FocusEdge class method), [1] (phenotypic.abc_.GpuDetector class method), [1] (phenotypic.abc_.GridCorrector class method), [1] (phenotypic.abc_.GridFinder class method), [1] (phenotypic.abc_.GridMeasureFeatures class method), [1] (phenotypic.abc_.GridObjectDetector class method), [1] (phenotypic.abc_.GridObjectRefiner class method), [1] (phenotypic.abc_.GridOperation class method), [1] (phenotypic.abc_.ImageCorrector class method), [1] (phenotypic.abc_.ImageDenoiser class method), [1] (phenotypic.abc_.ImageEnhancer class method), [1] (phenotypic.abc_.ImageOperation class method), [1] (phenotypic.abc_.MeasureFeatures class method), [1] (phenotypic.abc_.MorphologicalFiltering class method), [1] (phenotypic.abc_.ObjectDetector class method), [1] (phenotypic.abc_.ObjectRefiner class method), [1] (phenotypic.abc_.PostMeasurement class method), [1] (phenotypic.abc_.PrefabPipeline class method), [1] (phenotypic.abc_.Smoothing class method), [1] (phenotypic.abc_.ThresholdDetector class method), [1] (phenotypic.analysis.abc_.ModelFitter class method) (phenotypic.analysis.abc_.QualityCheck class method) (phenotypic.analysis.abc_.SetAnalyzer class method) (phenotypic.analysis.DoubleSoftplus class method), [1] (phenotypic.analysis.EdgeCorrector class method), [1] (phenotypic.analysis.ErrorCutoffFinder class method), [1] (phenotypic.analysis.ExpectedVsDetectedCount class method), [1] (phenotypic.analysis.ICC class method), [1] (phenotypic.analysis.LinearSoftplus class method), [1] (phenotypic.analysis.LogGrowthModel class method), [1] (phenotypic.analysis.MADOutlierRemover class method), [1] (phenotypic.analysis.MaxModifiedZScore class method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount class method) (phenotypic.analysis.qc.ICC class method) (phenotypic.analysis.qc.MaxModifiedZScore class method) (phenotypic.analysis.qc.RelativeMAD class method) (phenotypic.analysis.qc.ReplicateAgreement class method) (phenotypic.analysis.qc.TukeyOutlierFraction class method) (phenotypic.analysis.RelativeMAD class method), [1] (phenotypic.analysis.ReplicateAgreement class method), [1] (phenotypic.analysis.TukeyOutlierFraction class method), [1] (phenotypic.analysis.TukeyOutlierRemover class method), [1] (phenotypic.correction.BayesShrinkCorrector class method), [1] (phenotypic.correction.CaptureMetadata class method), [1] (phenotypic.correction.ColorCheckerProfile class method), [1] (phenotypic.correction.ColorCorrector class method), [1] (phenotypic.correction.ColorDenoise class method), [1] (phenotypic.correction.DenoiseBlockMatch class method), [1] (phenotypic.correction.GridAligner class method), [1] (phenotypic.correction.ImageCropper class method), [1] (phenotypic.correction.ImagePadder class method), [1] (phenotypic.correction.VisuShrinkCorrector class method), [1] (phenotypic.detect.CannyDetector class method), [1] (phenotypic.detect.ChanVeseDetector class method), [1] (phenotypic.detect.CompositeDetector class method), [1] (phenotypic.detect.FilamentousFungiDetector class method), [1] (phenotypic.detect.HysteresisDetector class method), [1] (phenotypic.detect.InoculumDetector class method), [1] (phenotypic.detect.IsodataDetector class method), [1] (phenotypic.detect.LiDetector class method), [1] (phenotypic.detect.MadHysteresisDetector class method), [1] (phenotypic.detect.ManualGridPointDetector class method), [1] (phenotypic.detect.ManualPointDetector class method), [1] (phenotypic.detect.MeanDetector class method), [1] (phenotypic.detect.MinimumDetector class method), [1] (phenotypic.detect.OtsuDetector class method), [1] (phenotypic.detect.RankOtsuDetector class method), [1] (phenotypic.detect.RoundPeaksDetector class method), [1] (phenotypic.detect.SecondaryOtsuDetector class method), [1] (phenotypic.detect.SinePeakDetector class method), [1] (phenotypic.detect.TriangleDetector class method), [1] (phenotypic.detect.UserThreshold class method), [1] (phenotypic.detect.WatershedDetector class method), [1] (phenotypic.detect.YenDetector class method), [1] (phenotypic.enhance.BayesShrinkEnhancer class method), [1] (phenotypic.enhance.ContrastStretching class method), [1] (phenotypic.enhance.EnhanceBlockMatch class method), [1] (phenotypic.enhance.EnhanceLocalContrast class method), [1] (phenotypic.enhance.FlattenIllumination class method), [1] (phenotypic.enhance.FocusBlobLoG class method), [1] (phenotypic.enhance.FocusEdgeFrangi class method), [1] (phenotypic.enhance.FocusEdgeHessian class method), [1] (phenotypic.enhance.FocusEdgeLaplace class method), [1] (phenotypic.enhance.FocusEdgeMeijering class method), [1] (phenotypic.enhance.FocusEdgePhase class method), [1] (phenotypic.enhance.FocusEdgeSato class method), [1] (phenotypic.enhance.FocusEdgeSobel class method), [1] (phenotypic.enhance.GaussianBlur class method), [1] (phenotypic.enhance.GrayOpening class method), [1] (phenotypic.enhance.ImageInverter class method), [1] (phenotypic.enhance.LocalEdgeDenoise class method), [1] (phenotypic.enhance.MedianFilter class method), [1] (phenotypic.enhance.NonLocalMeansDenoiser class method), [1] (phenotypic.enhance.RankMedianEnhancer class method), [1] (phenotypic.enhance.SetDetectMode class method), [1] (phenotypic.enhance.SharpenEdgeGauss class method), [1] (phenotypic.enhance.StructureSmoothing class method), [1] (phenotypic.enhance.SubtractGaussian class method), [1] (phenotypic.enhance.SubtractOpening class method), [1] (phenotypic.enhance.SubtractRollingBall class method), [1] (phenotypic.enhance.SubtractWhiteTophat class method), [1] (phenotypic.enhance.VisuShrinkEnhancer class method), [1] (phenotypic.enhance.WhiteTophatEnhance class method), [1] (phenotypic.grid.AutoGridFinder class method), [1] (phenotypic.grid.CenteredAutoGridFinder class method), [1] (phenotypic.grid.GridApply class method), [1] (phenotypic.grid.ManualGridFinder class method), [1] (phenotypic.measure.MeasureBounds class method), [1] (phenotypic.measure.MeasureColor class method), [1] (phenotypic.measure.MeasureGridLinRegStats class method), [1] (phenotypic.measure.MeasureGridSpatial class method), [1] (phenotypic.measure.MeasureGridSpread class method), [1] (phenotypic.measure.MeasureIntensity class method), [1] (phenotypic.measure.MeasureShape class method), [1] (phenotypic.measure.MeasureSize class method), [1] (phenotypic.measure.MeasureSymmetricZones class method), [1] (phenotypic.measure.MeasureTexture class method), [1] (phenotypic.post.AppendString class method) (phenotypic.post.ExpandMetadata class method) (phenotypic.post.MergeMetadata class method) (phenotypic.post.PrependString class method) (phenotypic.prefab.FilamentousFungiPipeline class method), [1] (phenotypic.prefab.GridSectionPipeline class method), [1] (phenotypic.prefab.HeavyOtsuPipeline class method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline class method), [1] (phenotypic.prefab.HeavyWatershedPipeline class method), [1] (phenotypic.prefab.RoundPeaksPipeline class method), [1] (phenotypic.prefab.SpImagerPipeline class method), [1] (phenotypic.refine.ExtractColonyCore class method), [1] (phenotypic.refine.GridAlignmentRefiner class method), [1] (phenotypic.refine.GridOversizedObjectRemover class method), [1] (phenotypic.refine.KeepNearestCenter class method), [1] (phenotypic.refine.KeepSectionLargest class method), [1] (phenotypic.refine.ManualRefine class method), [1] (phenotypic.refine.MaskClosing class method), [1] (phenotypic.refine.MaskDilation class method), [1] (phenotypic.refine.MaskErosion class method), [1] (phenotypic.refine.MaskFill class method), [1] (phenotypic.refine.MaskGradient class method), [1] (phenotypic.refine.MaskOpening class method), [1] (phenotypic.refine.MaskWhiteTophat class method), [1] (phenotypic.refine.MergeFragmentChains class method), [1] (phenotypic.refine.NearestNeighborMerger class method), [1] (phenotypic.refine.ReduceSectionsByLine class method), [1] (phenotypic.refine.RefineBySineFit class method), [1] (phenotypic.refine.RemoveBorderObjects class method), [1] (phenotypic.refine.RemoveByFeature class method), [1] (phenotypic.refine.RemoveGridOutliers class method), [1] (phenotypic.refine.RemoveLowCircularity class method), [1] (phenotypic.refine.SeparateObjects class method), [1] (phenotypic.refine.Skeletonize class method), [1] (phenotypic.refine.SmallObjectRemover class method), [1] (phenotypic.refine.SmallToLargeMerger class method), [1] (phenotypic.refine.Thinning class method), [1] (phenotypic.refine.TrimAsymmetry class method), [1] (phenotypic.tune.Budget class method), [1] (phenotypic.tune.Categorical class method), [1] (phenotypic.tune.CompositeScorer class method), [1] (phenotypic.tune.EvaluationResult class method), [1] (phenotypic.tune.Evaluator class method), [1] (phenotypic.tune.Excluded class method), [1] (phenotypic.tune.Fixed class method), [1] (phenotypic.tune.FloatRange class method), [1] (phenotypic.tune.GridConfig class method), [1] (phenotypic.tune.GroundTruthMasks class method), [1] (phenotypic.tune.HeldOutConfig class method), [1] (phenotypic.tune.ImportanceReport class method), [1] (phenotypic.tune.InferredSearchSpace class method), [1] (phenotypic.tune.IntRange class method), [1] (phenotypic.tune.Knob class method), [1] (phenotypic.tune.OptunaConfig class method), [1] (phenotypic.tune.QCScorer class method), [1] (phenotypic.tune.RandomConfig class method), [1] (phenotypic.tune.ReferenceFreeScorer class method), [1] (phenotypic.tune.Scorer class method), [1] (phenotypic.tune.SearchSpace class method), [1] (phenotypic.tune.StrategyConfig class method), [1] (phenotypic.tune.SupervisedScorer class method), [1] (phenotypic.tune.targets.Nested class method) (phenotypic.tune.targets.Param class method) (phenotypic.tune.targets.Presence class method) (phenotypic.tune.targets.TunableParam class method) (phenotypic.tune.Trial class method), [1] (phenotypic.tune.TuningSpec class method), [1] scope_path (phenotypic.gui.builder._validation.Issue attribute), [1] score (phenotypic.tune.EvaluationResult attribute), [1] (phenotypic.tune.Trial attribute), [1] score_image() (phenotypic.tune.CompositeScorer method), [1] (phenotypic.tune.QCScorer method), [1] (phenotypic.tune.ReferenceFreeScorer method), [1] (phenotypic.tune.Scorer method), [1] (phenotypic.tune.SupervisedScorer method), [1] Scorer (class in phenotypic.tune), [1] scorer (phenotypic.tune.TuningSpec attribute), [1] scorers (phenotypic.tune.CompositeScorer attribute), [1] SCRATCH (phenotypic.sdk_.EnvVar attribute), [1] screened (phenotypic.tune.ScreeningResult attribute), [1] screened_fragment_labels (phenotypic.sdk_.branch_pathfinding.PrescreenResult attribute), [1] screening_warmup_floor() (in module phenotypic.tune), [1] ScreeningConfig (class in phenotypic.tune), [1] ScreeningController (class in phenotypic.tune), [1] ScreeningResult (class in phenotypic.tune), [1] search_dist (phenotypic.enhance.NonLocalMeansDenoiser attribute), [1] search_space (phenotypic.tune.TuningSpec attribute), [1] SearchSpace (class in phenotypic.tune), [1] SecondaryOtsuDetector (class in phenotypic.detect), [1] section (phenotypic.abc_.FigureSpec attribute), [1], [2], [3] section_num (phenotypic.measure.MeasureGridLinRegStats attribute), [1] seed (phenotypic.tune.GridConfig attribute), [1] (phenotypic.tune.OptunaConfig attribute), [1] (phenotypic.tune.RandomConfig attribute), [1] (phenotypic.tune.StrategyConfig attribute), [1] select_params_to_freeze() (in module phenotypic.tune), [1] selected_block_id (phenotypic.gui.builder._state._DagBuilderState attribute), [1] selected_edge_id (phenotypic.gui.builder._state._DagBuilderState attribute), [1] selected_targets_by_scope (phenotypic.gui.builder._state._DagBuilderState attribute) SELECTION_MARKER (phenotypic.schema.GENETIC_METADATA attribute) selection_mode (phenotypic.detect.RoundPeaksDetector attribute), [1] (phenotypic.detect.SinePeakDetector attribute), [1] (phenotypic.refine.GridAlignmentRefiner attribute), [1] (phenotypic.refine.RefineBySineFit attribute), [1] sentinel_resubmitted_path() (in module phenotypic.sdk_), [1] SeparateObjects (class in phenotypic.refine), [1] separation_threshold (phenotypic.refine.ExtractColonyCore attribute), [1] set_active_set() (phenotypic.tune.CompositeScorer method), [1] set_build() (phenotypic.gui.shell.ToolSession method) set_data_posix (phenotypic.sdk_.HDF attribute), [1], [2], [3] (phenotypic.sdk_.hdf_.HDF attribute), [1] set_filters() (phenotypic.abc_.PrefabPipeline method), [1] (phenotypic.prefab.FilamentousFungiPipeline method), [1] (phenotypic.prefab.GridSectionPipeline method), [1] (phenotypic.prefab.HeavyOtsuPipeline method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1] (phenotypic.prefab.HeavyWatershedPipeline method), [1] (phenotypic.prefab.RoundPeaksPipeline method), [1] (phenotypic.prefab.SpImagerPipeline method), [1] set_meas() (phenotypic.abc_.PrefabPipeline method), [1] (phenotypic.ImagePipeline method) (phenotypic.prefab.FilamentousFungiPipeline method), [1] (phenotypic.prefab.GridSectionPipeline method), [1] (phenotypic.prefab.HeavyOtsuPipeline method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1] (phenotypic.prefab.HeavyWatershedPipeline method), [1] (phenotypic.prefab.RoundPeaksPipeline method), [1] (phenotypic.prefab.SpImagerPipeline method), [1] set_model() (phenotypic.abc_.PrefabPipeline method), [1] (phenotypic.prefab.FilamentousFungiPipeline method), [1] (phenotypic.prefab.GridSectionPipeline method), [1] (phenotypic.prefab.HeavyOtsuPipeline method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1] (phenotypic.prefab.HeavyWatershedPipeline method), [1] (phenotypic.prefab.RoundPeaksPipeline method), [1] (phenotypic.prefab.SpImagerPipeline method), [1] set_ops() (phenotypic.abc_.PrefabPipeline method), [1] (phenotypic.ImagePipeline method) (phenotypic.prefab.FilamentousFungiPipeline method), [1] (phenotypic.prefab.GridSectionPipeline method), [1] (phenotypic.prefab.HeavyOtsuPipeline method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1] (phenotypic.prefab.HeavyWatershedPipeline method), [1] (phenotypic.prefab.RoundPeaksPipeline method), [1] (phenotypic.prefab.SpImagerPipeline method), [1]

set_post() (phenotypic.abc_.PrefabPipeline method), [1] (phenotypic.prefab.FilamentousFungiPipeline method), [1] (phenotypic.prefab.GridSectionPipeline method), [1] (phenotypic.prefab.HeavyOtsuPipeline method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1] (phenotypic.prefab.HeavyWatershedPipeline method), [1] (phenotypic.prefab.RoundPeaksPipeline method), [1] (phenotypic.prefab.SpImagerPipeline method), [1] set_qc() (phenotypic.abc_.PrefabPipeline method), [1] (phenotypic.prefab.FilamentousFungiPipeline method), [1] (phenotypic.prefab.GridSectionPipeline method), [1] (phenotypic.prefab.HeavyOtsuPipeline method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1] (phenotypic.prefab.HeavyWatershedPipeline method), [1] (phenotypic.prefab.RoundPeaksPipeline method), [1] (phenotypic.prefab.SpImagerPipeline method), [1] SetAnalyzer (class in phenotypic.analysis.abc_) setdefault() (phenotypic.util.BackgroundMetrics method), [1] (phenotypic.util.ContrastMetrics method), [1] (phenotypic.util.image_metrics.BackgroundMetrics method) (phenotypic.util.image_metrics.ContrastMetrics method) (phenotypic.util.image_metrics.NoiseMetrics method) (phenotypic.util.image_metrics.QualityScores method) (phenotypic.util.image_metrics.StructureMetrics method) (phenotypic.util.NoiseMetrics method), [1] (phenotypic.util.QualityScores method), [1] (phenotypic.util.StructureMetrics method), [1] SetDetectMode (class in phenotypic.enhance), [1] setup_logging() (in module phenotypic.phenotypicCLI) severity (phenotypic.gui.builder._validation.Issue attribute), [1] SHAPE (class in phenotypic.schema) shape (phenotypic._core._image_parts.accessors._detect_mat_accessor.DetectMatAccessor property) (phenotypic._core._image_parts.accessors._grayscale_accessor.Grayscale property) (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap property) (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask property) (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor property) (phenotypic._core._image_parts.accessors._rgb_accessor.ImageRGB property) (phenotypic.detect.ManualGridPointDetector attribute), [1] (phenotypic.detect.ManualPointDetector attribute), [1] (phenotypic.detect.RankOtsuDetector attribute), [1] (phenotypic.enhance.GrayOpening attribute), [1] (phenotypic.enhance.MedianFilter attribute), [1] (phenotypic.enhance.RankMedianEnhancer attribute), [1] (phenotypic.enhance.SubtractOpening attribute), [1] (phenotypic.enhance.SubtractWhiteTophat attribute), [1] (phenotypic.enhance.WhiteTophatEnhance attribute), [1] (phenotypic.refine.ManualRefine attribute), [1] (phenotypic.refine.MaskClosing attribute), [1] (phenotypic.refine.MaskDilation attribute), [1] (phenotypic.refine.MaskErosion attribute), [1] (phenotypic.refine.MaskGradient attribute), [1] (phenotypic.refine.MaskOpening attribute), [1] (phenotypic.refine.MaskWhiteTophat attribute), [1] shard_parquet_filename() (in module phenotypic.sdk_), [1] SharpenEdgeGauss (class in phenotypic.enhance), [1] Sharpness (phenotypic.util.image_metrics.QualityScores attribute) (phenotypic.util.QualityScores attribute), [1] shift_x (phenotypic.enhance.RankMedianEnhancer attribute), [1] shift_y (phenotypic.enhance.RankMedianEnhancer attribute), [1] shoulder_slope_ratio (phenotypic.analysis.DoubleSoftplus attribute), [1] show() (phenotypic._core._image_parts.accessors._detect_mat_accessor.DetectMatAccessor method) (phenotypic._core._image_parts.accessors._grayscale_accessor.Grayscale method) (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap method) (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask method) (phenotypic._core._image_parts.accessors._rgb_accessor.ImageRGB method) (phenotypic.analysis.abc_.ModelFitter method) (phenotypic.analysis.abc_.QualityCheck method) (phenotypic.analysis.abc_.SetAnalyzer method) (phenotypic.analysis.DoubleSoftplus method), [1] (phenotypic.analysis.EdgeCorrector method), [1] (phenotypic.analysis.ExpectedVsDetectedCount method), [1] (phenotypic.analysis.ICC method), [1] (phenotypic.analysis.LinearSoftplus method), [1] (phenotypic.analysis.LogGrowthModel method), [1] (phenotypic.analysis.MADOutlierRemover method), [1] (phenotypic.analysis.MaxModifiedZScore method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount method) (phenotypic.analysis.qc.ICC method) (phenotypic.analysis.qc.MaxModifiedZScore method) (phenotypic.analysis.qc.RelativeMAD method) (phenotypic.analysis.qc.ReplicateAgreement method) (phenotypic.analysis.qc.TukeyOutlierFraction method) (phenotypic.analysis.RelativeMAD method), [1] (phenotypic.analysis.ReplicateAgreement method), [1] (phenotypic.analysis.TukeyOutlierFraction method), [1] (phenotypic.analysis.TukeyOutlierRemover method), [1] (phenotypic.Image method) sigma (phenotypic.correction.BayesShrinkCorrector attribute), [1] (phenotypic.correction.DenoiseBlockMatch attribute), [1] (phenotypic.correction.VisuShrinkCorrector attribute), [1] (phenotypic.detect.CannyDetector attribute), [1] (phenotypic.enhance.BayesShrinkEnhancer attribute), [1] (phenotypic.enhance.FlattenIllumination attribute), [1] (phenotypic.enhance.GaussianBlur attribute), [1] (phenotypic.enhance.NonLocalMeansDenoiser attribute), [1] (phenotypic.enhance.StructureSmoothing attribute), [1] (phenotypic.enhance.SubtractGaussian attribute), [1] (phenotypic.enhance.VisuShrinkEnhancer attribute), [1] sigma_color (phenotypic.enhance.LocalEdgeDenoise attribute), [1] sigma_mad (phenotypic.util.image_metrics.NoiseMetrics attribute) (phenotypic.util.NoiseMetrics attribute), [1] sigma_onf (phenotypic.enhance.FocusEdgePhase attribute), [1] sigma_psd (phenotypic.correction.ColorDenoise attribute), [1] (phenotypic.enhance.EnhanceBlockMatch attribute), [1] sigma_spatial (phenotypic.enhance.LocalEdgeDenoise attribute), [1] sigmas (phenotypic.enhance.FocusEdgeFrangi attribute), [1] (phenotypic.enhance.FocusEdgeHessian attribute), [1] (phenotypic.enhance.FocusEdgeMeijering attribute), [1] (phenotypic.enhance.FocusEdgeSato attribute), [1] SinePeakDetector (class in phenotypic.detect), [1] SINGLE_IMAGE_HDF5_PARENT_GROUP (phenotypic.sdk_.constants_.IO attribute), [1] SINGLE_IMAGE_ROOT_POSIX (phenotypic.sdk_.HDF attribute), [1], [2], [3] (phenotypic.sdk_.hdf_.HDF attribute), [1] SIZE (class in phenotypic.schema) size (phenotypic._core._image_parts.accessors._detect_mat_accessor.DetectMatAccessor property) (phenotypic._core._image_parts.accessors._grayscale_accessor.Grayscale property) (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap property) (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask property) (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor property) (phenotypic._core._image_parts.accessors._rgb_accessor.ImageRGB property) size_distribution() (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) size_scatter() (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) size_threshold (phenotypic.refine.SmallToLargeMerger attribute), [1] size_viewer() (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) Skeletonize (class in phenotypic.refine), [1] slices (phenotypic._core._image_parts.accessors._objects_accessor.ObjectsAccessor property) SLURM_ARRAY_JOB_ID (phenotypic.sdk_.EnvVar attribute), [1] SLURM_ARRAY_TASK_COUNT (phenotypic.sdk_.EnvVar attribute), [1] SLURM_ARRAY_TASK_ID (phenotypic.sdk_.EnvVar attribute), [1] SLURM_CPUS_PER_TASK (phenotypic.sdk_.EnvVar attribute), [1] SLURM_INFO (phenotypic.sdk_.DashboardManifestKey attribute), [1] SLURM_JOB_ID (phenotypic.sdk_.EnvVar attribute), [1] SLURM_JOB_IDS (phenotypic.sdk_.JobMetadataKey attribute), [1] SLURM_MEM_PER_NODE (phenotypic.sdk_.EnvVar attribute), [1] slurm_scripts_dir() (in module phenotypic.sdk_), [1] small_object_min_size (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] SmallObjectRemover (class in phenotypic.refine), [1] SmallToLargeMerger (class in phenotypic.refine), [1] smax (phenotypic.analysis.DoubleSoftplus attribute), [1] (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL attribute) Smoothing (class in phenotypic.abc_), [1] smoothing_sigma (phenotypic.detect.RoundPeaksDetector attribute), [1] (phenotypic.detect.SinePeakDetector attribute), [1] (phenotypic.refine.GridAlignmentRefiner attribute), [1] (phenotypic.refine.RefineBySineFit attribute), [1] smoothing_window (phenotypic.measure.MeasureSymmetricZones attribute), [1] (phenotypic.refine.TrimAsymmetry attribute), [1] snr (phenotypic.util.image_metrics.NoiseMetrics attribute) SNR (phenotypic.util.image_metrics.QualityScores attribute) snr (phenotypic.util.NoiseMetrics attribute), [1] SNR (phenotypic.util.QualityScores attribute), [1] snr_margin (phenotypic.detect.FilamentousFungiDetector attribute), [1] SOLIDITY (phenotypic.schema.SHAPE attribute) source (phenotypic.tune.Knob attribute), [1] source_block_id (phenotypic.gui.builder._state.Edge attribute), [1] SOURCE_PLATE (phenotypic.schema.SAMPLE_METADATA attribute) source_port (phenotypic.gui.builder._state.Edge attribute), [1] SOURCE_WELL (phenotypic.schema.SAMPLE_METADATA attribute) SPAN_PCT_HIGH (phenotypic.grid.CenteredAutoGridFinder attribute), [1] SPAN_PCT_LOW (phenotypic.grid.CenteredAutoGridFinder attribute), [1] SPARSE_AREA (phenotypic.schema.SYMMETRIC_ZONES attribute) SPARSE_END_RADIUS (phenotypic.schema.SYMMETRIC_ZONES attribute) spatial_size_map() (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) specs() (phenotypic.abc_.BoundFigures method), [1] SpImagerPipeline (class in phenotypic.prefab), [1] split() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] split_measurements() (in module phenotypic.util), [1] split_merged (phenotypic.detect.RoundPeaksDetector attribute), [1] (phenotypic.detect.SinePeakDetector attribute), [1] (phenotypic.refine.GridAlignmentRefiner attribute), [1] (phenotypic.refine.RefineBySineFit attribute), [1] splitlines() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] SRGB (phenotypic.sdk_.constants_.GAMMA_ENCODINGS attribute), [1] stability_weight (phenotypic.tune.Evaluator attribute), [1] stage_arg (phenotypic.correction.DenoiseBlockMatch attribute), [1] (phenotypic.enhance.EnhanceBlockMatch attribute), [1] STANDARD_DEVIATION_INTENSITY (phenotypic.schema.INTENSITY attribute) START_TIME (phenotypic.sdk_.DashboardManifestKey attribute), [1] (phenotypic.sdk_.JobMetadataKey attribute), [1] STARTED (phenotypic.sdk_.DashboardManifestKey attribute), [1] (phenotypic.sdk_.ProcessingStateKey attribute), [1] startswith() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] STATUS (phenotypic.schema.MODEL_METRICS attribute) (phenotypic.schema.QUALITY_CHECK attribute) status_col() (phenotypic.analysis.abc_.QualityCheck class method) (phenotypic.analysis.ExpectedVsDetectedCount class method), [1] (phenotypic.analysis.ICC class method), [1] (phenotypic.analysis.MaxModifiedZScore class method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount class method) (phenotypic.analysis.qc.ICC class method) (phenotypic.analysis.qc.MaxModifiedZScore class method) (phenotypic.analysis.qc.RelativeMAD class method) (phenotypic.analysis.qc.ReplicateAgreement class method) (phenotypic.analysis.qc.TukeyOutlierFraction class method) (phenotypic.analysis.RelativeMAD class method), [1] (phenotypic.analysis.ReplicateAgreement class method), [1] (phenotypic.analysis.TukeyOutlierFraction class method), [1] stddev_mag_threshold (phenotypic.correction.ColorCheckerProfile attribute), [1] stderr_label (phenotypic.analysis.DoubleSoftplus attribute), [1] (phenotypic.analysis.LinearSoftplus attribute), [1] step (phenotypic.abc_.Control attribute), [1] (phenotypic.sdk_.typing_.TuneSpec attribute) (phenotypic.tune.FloatRange attribute), [1] (phenotypic.tune.IntRange attribute), [1] (phenotypic.tune.TuneSpec attribute), [1] storage_url (phenotypic.gui.tune.TuneRunRoot attribute) (phenotypic.tune.OptunaConfig attribute), [1] store (phenotypic.tune.TuningEngine property), [1] STRAIN (phenotypic.schema.GENETIC_METADATA attribute) strategy (phenotypic.tune.TuningSpec attribute), [1] StrategyConfig (class in phenotypic.tune), [1] STRESS (phenotypic.schema.CONDITION_METADATA attribute) strict_writer() (phenotypic.sdk_.HDF method), [1] (phenotypic.sdk_.hdf_.HDF method) strip() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] structural_response_curve() (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) structure (phenotypic.refine.MaskFill attribute), [1] StructureMetrics (class in phenotypic.util), [1] (class in phenotypic.util.image_metrics) StructureSmoothing (class in phenotypic.enhance), [1] study_name (phenotypic.gui.tune.TuneRunRoot attribute) StudyStore (in module phenotypic.tune), [1] subject (phenotypic.abc_.BoundFigures property), [1] subject_label (phenotypic.analysis.ICC attribute), [1] (phenotypic.analysis.qc.ICC attribute) subject_param (phenotypic.abc_.FigureSpec attribute), [1], [2], [3] submit_drip_feed_start() (in module phenotypic.sdk_.slurm), [1] submit_script() (in module phenotypic.sdk_.slurm), [1] subtract_background (phenotypic.detect.RoundPeaksDetector attribute), [1] (phenotypic.detect.SinePeakDetector attribute), [1] SubtractGaussian (class in phenotypic.enhance), [1] SubtractOpening (class in phenotypic.enhance), [1] SubtractRollingBall (class in phenotypic.enhance), [1] SubtractWhiteTophat (class in phenotypic.enhance), [1] SUCCESS_RATE (phenotypic.sdk_.DashboardManifestKey attribute), [1] SUFFIX (phenotypic.schema.METADATA attribute) suggested_domain (phenotypic.tune.targets.TunableParam attribute) SUM_AVERAGE (phenotypic.schema.TEXTURE attribute) SUM_ENTROPY (phenotypic.schema.TEXTURE attribute) SUM_VARIANCE (phenotypic.schema.TEXTURE attribute) summary() (phenotypic.analysis.abc_.QualityCheck method) (phenotypic.analysis.ExpectedVsDetectedCount method), [1] (phenotypic.analysis.ICC method), [1] (phenotypic.analysis.MaxModifiedZScore method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount method) (phenotypic.analysis.qc.ICC method) (phenotypic.analysis.qc.MaxModifiedZScore method) (phenotypic.analysis.qc.RelativeMAD method) (phenotypic.analysis.qc.ReplicateAgreement method) (phenotypic.analysis.qc.TukeyOutlierFraction method) (phenotypic.analysis.RelativeMAD method), [1] (phenotypic.analysis.ReplicateAgreement method), [1] (phenotypic.analysis.TukeyOutlierFraction method), [1] SupervisedScorer (class in phenotypic.tune), [1] SUPPLEMENT (phenotypic.schema.CONDITION_METADATA attribute) SUPPORTED_FORMATS (phenotypic.sdk_.constants_.IMAGE_MODE attribute), [1] supports_batching (phenotypic.abc_.GpuDetector attribute), [1] suspicious (phenotypic.tune.EvaluationResult attribute), [1] (phenotypic.tune.Trial attribute), [1] suspicious_count_floor (phenotypic.tune.Evaluator attribute), [1] suspicious_score_floor (phenotypic.tune.Evaluator attribute), [1] swapcase() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] swmr_reader() (phenotypic.sdk_.HDF method), [1] (phenotypic.sdk_.hdf_.HDF method) swmr_writer() (phenotypic.sdk_.HDF method), [1] (phenotypic.sdk_.hdf_.HDF method) SYMMETRIC_RADIUS (phenotypic.schema.SYMMETRIC_ZONES attribute) SYMMETRIC_ZONES (class in phenotypic.schema) symmetry_threshold (phenotypic.measure.MeasureSymmetricZones attribute), [1] (phenotypic.refine.TrimAsymmetry attribute), [1]

T

table() (phenotypic._core._image_parts.accessors._metadata_accessor.MetadataAccessor method) target (phenotypic.tune.Knob attribute), [1] (phenotypic.tune.targets.TunableParam attribute) target_block_id (phenotypic.gui.builder._state.Edge attribute), [1] target_illuminant (phenotypic.correction.ColorCheckerProfile attribute), [1] target_port (phenotypic.gui.builder._state.Edge attribute), [1] target_slot (phenotypic.gui.builder._state.Edge attribute), [1] targets() (phenotypic.tune.SearchSpace method), [1] task_status_filename() (in module phenotypic.sdk_), [1] task_status_path() (in module phenotypic.sdk_), [1] tau_band_variance (phenotypic.sdk_.branch_pathfinding.FilterThresholds attribute), [1] tau_core (phenotypic.measure.MeasureSymmetricZones attribute), [1] tau_dense (phenotypic.measure.MeasureSymmetricZones attribute), [1] tau_gray_snr (phenotypic.sdk_.branch_pathfinding.FilterThresholds attribute), [1] tau_median_cost (phenotypic.sdk_.branch_pathfinding.FilterThresholds attribute), [1] tau_pct_energy_median (phenotypic.sdk_.branch_pathfinding.FilterThresholds attribute), [1] tau_sparse (phenotypic.measure.MeasureSymmetricZones attribute), [1] tau_window_cost (phenotypic.sdk_.branch_pathfinding.FilterThresholds attribute), [1] TECHNICAL_REPLICATE (phenotypic.schema.SAMPLE_METADATA attribute) TEMPERATURE (phenotypic.schema.INCUBATION_METADATA attribute) term_name (phenotypic.tune.QCScorer attribute), [1] terms (phenotypic.tune.EvaluationResult attribute), [1] (phenotypic.tune.Trial attribute), [1] TEXTURE (class in phenotypic.schema) texture_enhance (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] texture_quant_lvl (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] texture_scale (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] texture_warn (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] Thinning (class in phenotypic.refine), [1] thresh_method (phenotypic.detect.InoculumDetector attribute), [1] (phenotypic.detect.RoundPeaksDetector attribute), [1] (phenotypic.detect.SinePeakDetector attribute), [1] threshold (phenotypic.analysis.MADOutlierRemover attribute), [1], [2], [3] (phenotypic.detect.UserThreshold attribute), [1] threshold_used (phenotypic.sdk_.branch_pathfinding.PrescreenResult attribute), [1] ThresholdDetector (class in phenotypic.abc_), [1] thresholds (phenotypic.sdk_.branch_pathfinding.FilterResult attribute), [1] TIFF_EXTENSIONS (phenotypic.sdk_.constants_.IO attribute), [1] tile_overlap (phenotypic.detect.FilamentousFungiDetector attribute), [1] tile_size (phenotypic.detect.FilamentousFungiDetector attribute), [1] TIME (phenotypic.schema.INCUBATION_METADATA attribute) time_label (phenotypic.analysis.abc_.ModelFitter attribute), [1] (phenotypic.analysis.DoubleSoftplus attribute), [1] (phenotypic.analysis.EdgeCorrector attribute), [1] (phenotypic.analysis.LinearSoftplus attribute), [1] (phenotypic.analysis.LogGrowthModel attribute), [1] (phenotypic.analysis.MaxModifiedZScore attribute), [1] (phenotypic.analysis.qc.MaxModifiedZScore attribute) (phenotypic.analysis.qc.RelativeMAD attribute) (phenotypic.analysis.qc.ReplicateAgreement attribute) (phenotypic.analysis.qc.TukeyOutlierFraction attribute) (phenotypic.analysis.RelativeMAD attribute), [1] (phenotypic.analysis.ReplicateAgreement attribute), [1] (phenotypic.analysis.TukeyOutlierFraction attribute), [1] TIME_UNIT (phenotypic.schema.INCUBATION_METADATA attribute) timed_execution() (in module phenotypic.sdk_), [1] (in module phenotypic.sdk_.funcs_) TIMEPOINT (phenotypic.schema.INCUBATION_METADATA attribute) TIMESTAMP (phenotypic.sdk_.ProcessingStateKey attribute), [1] title (phenotypic.abc_.FigureSpec attribute), [1], [2], [3] title() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] to_dataframe() (phenotypic.tune.JournalStudyStore method), [1] to_dict() (phenotypic.tune.GeneralizationReport method), [1] to_json() (phenotypic.abc_.BackgroundSubtraction method), [1] (phenotypic.abc_.BaseOperation method), [1] (phenotypic.abc_.ContrastAdjustment method), [1] (phenotypic.abc_.FocusBlob method), [1] (phenotypic.abc_.FocusEdge method), [1] (phenotypic.abc_.GpuDetector method), [1] (phenotypic.abc_.GridCorrector method), [1] (phenotypic.abc_.GridFinder method), [1] (phenotypic.abc_.GridMeasureFeatures method), [1] (phenotypic.abc_.GridObjectDetector method), [1] (phenotypic.abc_.GridObjectRefiner method), [1] (phenotypic.abc_.GridOperation method), [1] (phenotypic.abc_.ImageCorrector method), [1] (phenotypic.abc_.ImageDenoiser method), [1] (phenotypic.abc_.ImageEnhancer method), [1] (phenotypic.abc_.ImageOperation method), [1] (phenotypic.abc_.MeasureFeatures method), [1] (phenotypic.abc_.MorphologicalFiltering method), [1] (phenotypic.abc_.ObjectDetector method), [1] (phenotypic.abc_.ObjectRefiner method), [1] (phenotypic.abc_.PostMeasurement method), [1] (phenotypic.abc_.PrefabPipeline method), [1] (phenotypic.abc_.Smoothing method), [1] (phenotypic.abc_.ThresholdDetector method), [1] (phenotypic.correction.BayesShrinkCorrector method), [1] (phenotypic.correction.ColorCheckerProfile method), [1] (phenotypic.correction.ColorCorrector method), [1] (phenotypic.correction.ColorDenoise method), [1] (phenotypic.correction.DenoiseBlockMatch method), [1] (phenotypic.correction.GridAligner method), [1] (phenotypic.correction.ImageCropper method), [1] (phenotypic.correction.ImagePadder method), [1] (phenotypic.correction.VisuShrinkCorrector method), [1] (phenotypic.detect.CannyDetector method), [1] (phenotypic.detect.ChanVeseDetector method), [1] (phenotypic.detect.CompositeDetector method), [1] (phenotypic.detect.FilamentousFungiDetector method), [1] (phenotypic.detect.HysteresisDetector method), [1] (phenotypic.detect.InoculumDetector method), [1] (phenotypic.detect.IsodataDetector method), [1] (phenotypic.detect.LiDetector method), [1] (phenotypic.detect.MadHysteresisDetector method), [1] (phenotypic.detect.ManualGridPointDetector method), [1] (phenotypic.detect.ManualPointDetector method), [1] (phenotypic.detect.MeanDetector method), [1] (phenotypic.detect.MinimumDetector method), [1] (phenotypic.detect.OtsuDetector method), [1] (phenotypic.detect.RankOtsuDetector method), [1] (phenotypic.detect.RoundPeaksDetector method), [1] (phenotypic.detect.SecondaryOtsuDetector method), [1] (phenotypic.detect.SinePeakDetector method), [1] (phenotypic.detect.TriangleDetector method), [1] (phenotypic.detect.UserThreshold method), [1] (phenotypic.detect.WatershedDetector method), [1] (phenotypic.detect.YenDetector method), [1] (phenotypic.enhance.BayesShrinkEnhancer method), [1] (phenotypic.enhance.ContrastStretching method), [1] (phenotypic.enhance.EnhanceBlockMatch method), [1] (phenotypic.enhance.EnhanceLocalContrast method), [1] (phenotypic.enhance.FlattenIllumination method), [1] (phenotypic.enhance.FocusBlobLoG method), [1] (phenotypic.enhance.FocusEdgeFrangi method), [1] (phenotypic.enhance.FocusEdgeHessian method), [1] (phenotypic.enhance.FocusEdgeLaplace method), [1] (phenotypic.enhance.FocusEdgeMeijering method), [1] (phenotypic.enhance.FocusEdgePhase method), [1] (phenotypic.enhance.FocusEdgeSato method), [1] (phenotypic.enhance.FocusEdgeSobel method), [1] (phenotypic.enhance.GaussianBlur method), [1] (phenotypic.enhance.GrayOpening method), [1] (phenotypic.enhance.ImageInverter method), [1] (phenotypic.enhance.LocalEdgeDenoise method), [1] (phenotypic.enhance.MedianFilter method), [1] (phenotypic.enhance.NonLocalMeansDenoiser method), [1] (phenotypic.enhance.RankMedianEnhancer method), [1] (phenotypic.enhance.SetDetectMode method), [1] (phenotypic.enhance.SharpenEdgeGauss method), [1] (phenotypic.enhance.StructureSmoothing method), [1] (phenotypic.enhance.SubtractGaussian method), [1] (phenotypic.enhance.SubtractOpening method), [1] (phenotypic.enhance.SubtractRollingBall method), [1] (phenotypic.enhance.SubtractWhiteTophat method), [1] (phenotypic.enhance.VisuShrinkEnhancer method), [1] (phenotypic.enhance.WhiteTophatEnhance method), [1] (phenotypic.grid.AutoGridFinder method), [1] (phenotypic.grid.CenteredAutoGridFinder method), [1] (phenotypic.grid.GridApply method), [1] (phenotypic.grid.ManualGridFinder method), [1] (phenotypic.ImagePipeline method) (phenotypic.measure.MeasureBounds method), [1] (phenotypic.measure.MeasureColor method), [1] (phenotypic.measure.MeasureGridLinRegStats method), [1] (phenotypic.measure.MeasureGridSpatial method), [1] (phenotypic.measure.MeasureGridSpread method), [1] (phenotypic.measure.MeasureIntensity method), [1] (phenotypic.measure.MeasureShape method), [1] (phenotypic.measure.MeasureSize method), [1] (phenotypic.measure.MeasureSymmetricZones method), [1] (phenotypic.measure.MeasureTexture method), [1] (phenotypic.post.AppendString method) (phenotypic.post.ExpandMetadata method) (phenotypic.post.MergeMetadata method) (phenotypic.post.PrependString method) (phenotypic.prefab.FilamentousFungiPipeline method), [1] (phenotypic.prefab.GridSectionPipeline method), [1] (phenotypic.prefab.HeavyOtsuPipeline method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1] (phenotypic.prefab.HeavyWatershedPipeline method), [1] (phenotypic.prefab.RoundPeaksPipeline method), [1] (phenotypic.prefab.SpImagerPipeline method), [1] (phenotypic.refine.ExtractColonyCore method), [1] (phenotypic.refine.GridAlignmentRefiner method), [1] (phenotypic.refine.GridOversizedObjectRemover method), [1] (phenotypic.refine.KeepNearestCenter method), [1] (phenotypic.refine.KeepSectionLargest method), [1] (phenotypic.refine.ManualRefine method), [1] (phenotypic.refine.MaskClosing method), [1] (phenotypic.refine.MaskDilation method), [1] (phenotypic.refine.MaskErosion method), [1] (phenotypic.refine.MaskFill method), [1] (phenotypic.refine.MaskGradient method), [1] (phenotypic.refine.MaskOpening method), [1] (phenotypic.refine.MaskWhiteTophat method), [1] (phenotypic.refine.MergeFragmentChains method), [1] (phenotypic.refine.NearestNeighborMerger method), [1] (phenotypic.refine.ReduceSectionsByLine method), [1] (phenotypic.refine.RefineBySineFit method), [1] (phenotypic.refine.RemoveBorderObjects method), [1] (phenotypic.refine.RemoveByFeature method), [1] (phenotypic.refine.RemoveGridOutliers method), [1] (phenotypic.refine.RemoveLowCircularity method), [1] (phenotypic.refine.SeparateObjects method), [1] (phenotypic.refine.Skeletonize method), [1] (phenotypic.refine.SmallObjectRemover method), [1] (phenotypic.refine.SmallToLargeMerger method), [1] (phenotypic.refine.Thinning method), [1] (phenotypic.refine.TrimAsymmetry method), [1] (phenotypic.tune.TuningSpec method), [1]

to_parquet() (phenotypic.tune.JournalStudyStore method), [1] to_pipeline_dag() (in module phenotypic.gui.builder._conversion_dag) to_search_space() (phenotypic.tune.InferredSearchSpace method), [1] toast_queue (phenotypic.gui.builder._state._DagBuilderState attribute), [1] tol (phenotypic.detect.ChanVeseDetector attribute), [1] (phenotypic.grid.AutoGridFinder attribute), [1] ToolSession (class in phenotypic.gui.shell) top (phenotypic.correction.ImageCropper attribute), [1] (phenotypic.correction.ImagePadder attribute), [1] top_k (phenotypic.tune.ScreeningConfig attribute), [1] top_n (phenotypic.analysis.EdgeCorrector attribute), [1] TOTAL_CHUNKS (phenotypic.sdk_.DashboardManifestSlurmInfoKey attribute), [1] total_cost (phenotypic.sdk_.branch_pathfinding.FragmentPath attribute), [1] TOTAL_IMAGES (phenotypic.sdk_.DashboardManifestKey attribute), [1] TOTAL_ROWS (phenotypic.sdk_.ChunkManifestKey attribute), [1] touch() (phenotypic.gui.shell.ToolSession method) translate() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] TREATMENT (phenotypic.schema.CONDITION_METADATA attribute) Trial (class in phenotypic.tune), [1] trials (phenotypic.tune.JournalStudyStore property), [1] trials_parquet_path() (in module phenotypic.sdk_), [1] trials_path (phenotypic.gui.tune.TuneRunRoot attribute) TriangleDetector (class in phenotypic.detect), [1] TrimAsymmetry (class in phenotypic.refine), [1] truncate (phenotypic.enhance.GaussianBlur attribute), [1] (phenotypic.enhance.SubtractGaussian attribute), [1] try_thresh() (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) TukeyOutlierFraction (class in phenotypic.analysis), [1] (class in phenotypic.analysis.qc) TukeyOutlierRemover (class in phenotypic.analysis), [1] tunable (phenotypic.sdk_.typing_.TuneSpec attribute) (phenotypic.tune.TuneSpec attribute), [1] TunableParam (class in phenotypic.tune.targets) tune_cache_dir() (in module phenotypic.sdk_), [1] tune_cache_run_marker_path() (in module phenotypic.sdk_), [1] tune_cache_split_assignment_path() (in module phenotypic.sdk_), [1] tune_cache_splits_dir() (in module phenotypic.sdk_), [1] tune_cache_study_db_path() (in module phenotypic.sdk_), [1] TuneRunRoot (class in phenotypic.gui.tune) TuneRunRootError TuneSpec (class in phenotypic.sdk_.typing_) (class in phenotypic.tune), [1] tuning_spec_path() (in module phenotypic.sdk_), [1] TuningEngine (class in phenotypic.tune), [1] TuningSpec (class in phenotypic.tune), [1]

U

UNDER_DISTANCE (phenotypic.schema.GRID_SPATIAL attribute) UNDER_NEIGHBOR_OBJ_LABEL (phenotypic.schema.GRID_SPATIAL attribute) UNDERSEGMENTED (phenotypic.schema.ErrorCategory attribute) Uniformity (phenotypic.util.image_metrics.QualityScores attribute) (phenotypic.util.QualityScores attribute), [1] UnknownError, [1] unmatched_groups (phenotypic.analysis.abc_.QualityCheck attribute), [1] (phenotypic.analysis.ExpectedVsDetectedCount attribute), [1] (phenotypic.analysis.ICC attribute), [1] (phenotypic.analysis.MaxModifiedZScore attribute), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount attribute) (phenotypic.analysis.qc.ICC attribute) (phenotypic.analysis.qc.MaxModifiedZScore attribute) (phenotypic.analysis.qc.RelativeMAD attribute) (phenotypic.analysis.qc.ReplicateAgreement attribute) (phenotypic.analysis.qc.TukeyOutlierFraction attribute) (phenotypic.analysis.RelativeMAD attribute), [1] (phenotypic.analysis.ReplicateAgreement attribute), [1] (phenotypic.analysis.TukeyOutlierFraction attribute), [1] UnsupportedFileTypeError, [1] UnsupportedImageFormat, [1] update() (phenotypic.util.BackgroundMetrics method), [1] (phenotypic.util.ContrastMetrics method), [1] (phenotypic.util.image_metrics.BackgroundMetrics method) (phenotypic.util.image_metrics.ContrastMetrics method) (phenotypic.util.image_metrics.NoiseMetrics method) (phenotypic.util.image_metrics.QualityScores method) (phenotypic.util.image_metrics.StructureMetrics method) (phenotypic.util.NoiseMetrics method), [1] (phenotypic.util.QualityScores method), [1] (phenotypic.util.StructureMetrics method), [1] update_forward_refs() (phenotypic.abc_.BackgroundSubtraction class method), [1] (phenotypic.abc_.BaseOperation class method), [1] (phenotypic.abc_.ContrastAdjustment class method), [1] (phenotypic.abc_.FocusBlob class method), [1] (phenotypic.abc_.FocusEdge class method), [1] (phenotypic.abc_.GpuDetector class method), [1] (phenotypic.abc_.GridCorrector class method), [1] (phenotypic.abc_.GridFinder class method), [1] (phenotypic.abc_.GridMeasureFeatures class method), [1] (phenotypic.abc_.GridObjectDetector class method), [1] (phenotypic.abc_.GridObjectRefiner class method), [1] (phenotypic.abc_.GridOperation class method), [1] (phenotypic.abc_.ImageCorrector class method), [1] (phenotypic.abc_.ImageDenoiser class method), [1] (phenotypic.abc_.ImageEnhancer class method), [1] (phenotypic.abc_.ImageOperation class method), [1] (phenotypic.abc_.MeasureFeatures class method), [1] (phenotypic.abc_.MorphologicalFiltering class method), [1] (phenotypic.abc_.ObjectDetector class method), [1] (phenotypic.abc_.ObjectRefiner class method), [1] (phenotypic.abc_.PostMeasurement class method), [1] (phenotypic.abc_.PrefabPipeline class method), [1] (phenotypic.abc_.Smoothing class method), [1] (phenotypic.abc_.ThresholdDetector class method), [1] (phenotypic.analysis.abc_.ModelFitter class method) (phenotypic.analysis.abc_.QualityCheck class method) (phenotypic.analysis.abc_.SetAnalyzer class method) (phenotypic.analysis.DoubleSoftplus class method), [1] (phenotypic.analysis.EdgeCorrector class method), [1] (phenotypic.analysis.ErrorCutoffFinder class method), [1] (phenotypic.analysis.ExpectedVsDetectedCount class method), [1] (phenotypic.analysis.ICC class method), [1] (phenotypic.analysis.LinearSoftplus class method), [1] (phenotypic.analysis.LogGrowthModel class method), [1] (phenotypic.analysis.MADOutlierRemover class method), [1] (phenotypic.analysis.MaxModifiedZScore class method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount class method) (phenotypic.analysis.qc.ICC class method) (phenotypic.analysis.qc.MaxModifiedZScore class method) (phenotypic.analysis.qc.RelativeMAD class method) (phenotypic.analysis.qc.ReplicateAgreement class method) (phenotypic.analysis.qc.TukeyOutlierFraction class method) (phenotypic.analysis.RelativeMAD class method), [1] (phenotypic.analysis.ReplicateAgreement class method), [1] (phenotypic.analysis.TukeyOutlierFraction class method), [1] (phenotypic.analysis.TukeyOutlierRemover class method), [1] (phenotypic.correction.BayesShrinkCorrector class method), [1] (phenotypic.correction.CaptureMetadata class method), [1] (phenotypic.correction.ColorCheckerProfile class method), [1] (phenotypic.correction.ColorCorrector class method), [1] (phenotypic.correction.ColorDenoise class method), [1] (phenotypic.correction.DenoiseBlockMatch class method), [1] (phenotypic.correction.GridAligner class method), [1] (phenotypic.correction.ImageCropper class method), [1] (phenotypic.correction.ImagePadder class method), [1] (phenotypic.correction.VisuShrinkCorrector class method), [1] (phenotypic.detect.CannyDetector class method), [1] (phenotypic.detect.ChanVeseDetector class method), [1] (phenotypic.detect.CompositeDetector class method), [1] (phenotypic.detect.FilamentousFungiDetector class method), [1] (phenotypic.detect.HysteresisDetector class method), [1] (phenotypic.detect.InoculumDetector class method), [1] (phenotypic.detect.IsodataDetector class method), [1] (phenotypic.detect.LiDetector class method), [1] (phenotypic.detect.MadHysteresisDetector class method), [1] (phenotypic.detect.ManualGridPointDetector class method), [1] (phenotypic.detect.ManualPointDetector class method), [1] (phenotypic.detect.MeanDetector class method), [1] (phenotypic.detect.MinimumDetector class method), [1] (phenotypic.detect.OtsuDetector class method), [1] (phenotypic.detect.RankOtsuDetector class method), [1] (phenotypic.detect.RoundPeaksDetector class method), [1] (phenotypic.detect.SecondaryOtsuDetector class method), [1] (phenotypic.detect.SinePeakDetector class method), [1] (phenotypic.detect.TriangleDetector class method), [1] (phenotypic.detect.UserThreshold class method), [1] (phenotypic.detect.WatershedDetector class method), [1] (phenotypic.detect.YenDetector class method), [1] (phenotypic.enhance.BayesShrinkEnhancer class method), [1] (phenotypic.enhance.ContrastStretching class method), [1] (phenotypic.enhance.EnhanceBlockMatch class method), [1] (phenotypic.enhance.EnhanceLocalContrast class method), [1] (phenotypic.enhance.FlattenIllumination class method), [1] (phenotypic.enhance.FocusBlobLoG class method), [1] (phenotypic.enhance.FocusEdgeFrangi class method), [1] (phenotypic.enhance.FocusEdgeHessian class method), [1] (phenotypic.enhance.FocusEdgeLaplace class method), [1] (phenotypic.enhance.FocusEdgeMeijering class method), [1] (phenotypic.enhance.FocusEdgePhase class method), [1] (phenotypic.enhance.FocusEdgeSato class method), [1] (phenotypic.enhance.FocusEdgeSobel class method), [1] (phenotypic.enhance.GaussianBlur class method), [1] (phenotypic.enhance.GrayOpening class method), [1] (phenotypic.enhance.ImageInverter class method), [1] (phenotypic.enhance.LocalEdgeDenoise class method), [1] (phenotypic.enhance.MedianFilter class method), [1] (phenotypic.enhance.NonLocalMeansDenoiser class method), [1] (phenotypic.enhance.RankMedianEnhancer class method), [1] (phenotypic.enhance.SetDetectMode class method), [1] (phenotypic.enhance.SharpenEdgeGauss class method), [1] (phenotypic.enhance.StructureSmoothing class method), [1] (phenotypic.enhance.SubtractGaussian class method), [1] (phenotypic.enhance.SubtractOpening class method), [1] (phenotypic.enhance.SubtractRollingBall class method), [1] (phenotypic.enhance.SubtractWhiteTophat class method), [1] (phenotypic.enhance.VisuShrinkEnhancer class method), [1] (phenotypic.enhance.WhiteTophatEnhance class method), [1] (phenotypic.grid.AutoGridFinder class method), [1] (phenotypic.grid.CenteredAutoGridFinder class method), [1] (phenotypic.grid.GridApply class method), [1] (phenotypic.grid.ManualGridFinder class method), [1] (phenotypic.measure.MeasureBounds class method), [1] (phenotypic.measure.MeasureColor class method), [1] (phenotypic.measure.MeasureGridLinRegStats class method), [1] (phenotypic.measure.MeasureGridSpatial class method), [1] (phenotypic.measure.MeasureGridSpread class method), [1] (phenotypic.measure.MeasureIntensity class method), [1] (phenotypic.measure.MeasureShape class method), [1] (phenotypic.measure.MeasureSize class method), [1] (phenotypic.measure.MeasureSymmetricZones class method), [1] (phenotypic.measure.MeasureTexture class method), [1] (phenotypic.post.AppendString class method) (phenotypic.post.ExpandMetadata class method) (phenotypic.post.MergeMetadata class method) (phenotypic.post.PrependString class method) (phenotypic.prefab.FilamentousFungiPipeline class method), [1] (phenotypic.prefab.GridSectionPipeline class method), [1] (phenotypic.prefab.HeavyOtsuPipeline class method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline class method), [1] (phenotypic.prefab.HeavyWatershedPipeline class method), [1] (phenotypic.prefab.RoundPeaksPipeline class method), [1] (phenotypic.prefab.SpImagerPipeline class method), [1] (phenotypic.refine.ExtractColonyCore class method), [1] (phenotypic.refine.GridAlignmentRefiner class method), [1] (phenotypic.refine.GridOversizedObjectRemover class method), [1] (phenotypic.refine.KeepNearestCenter class method), [1] (phenotypic.refine.KeepSectionLargest class method), [1] (phenotypic.refine.ManualRefine class method), [1] (phenotypic.refine.MaskClosing class method), [1] (phenotypic.refine.MaskDilation class method), [1] (phenotypic.refine.MaskErosion class method), [1] (phenotypic.refine.MaskFill class method), [1] (phenotypic.refine.MaskGradient class method), [1] (phenotypic.refine.MaskOpening class method), [1] (phenotypic.refine.MaskWhiteTophat class method), [1] (phenotypic.refine.MergeFragmentChains class method), [1] (phenotypic.refine.NearestNeighborMerger class method), [1] (phenotypic.refine.ReduceSectionsByLine class method), [1] (phenotypic.refine.RefineBySineFit class method), [1] (phenotypic.refine.RemoveBorderObjects class method), [1] (phenotypic.refine.RemoveByFeature class method), [1] (phenotypic.refine.RemoveGridOutliers class method), [1] (phenotypic.refine.RemoveLowCircularity class method), [1] (phenotypic.refine.SeparateObjects class method), [1] (phenotypic.refine.Skeletonize class method), [1] (phenotypic.refine.SmallObjectRemover class method), [1] (phenotypic.refine.SmallToLargeMerger class method), [1] (phenotypic.refine.Thinning class method), [1] (phenotypic.refine.TrimAsymmetry class method), [1] (phenotypic.tune.Budget class method), [1] (phenotypic.tune.Categorical class method), [1] (phenotypic.tune.CompositeScorer class method), [1] (phenotypic.tune.EvaluationResult class method), [1] (phenotypic.tune.Evaluator class method), [1] (phenotypic.tune.Excluded class method), [1] (phenotypic.tune.Fixed class method), [1] (phenotypic.tune.FloatRange class method), [1] (phenotypic.tune.GridConfig class method), [1] (phenotypic.tune.GroundTruthMasks class method), [1] (phenotypic.tune.HeldOutConfig class method), [1] (phenotypic.tune.ImportanceReport class method), [1] (phenotypic.tune.InferredSearchSpace class method), [1] (phenotypic.tune.IntRange class method), [1] (phenotypic.tune.Knob class method), [1] (phenotypic.tune.OptunaConfig class method), [1] (phenotypic.tune.QCScorer class method), [1] (phenotypic.tune.RandomConfig class method), [1] (phenotypic.tune.ReferenceFreeScorer class method), [1] (phenotypic.tune.Scorer class method), [1] (phenotypic.tune.SearchSpace class method), [1] (phenotypic.tune.StrategyConfig class method), [1] (phenotypic.tune.SupervisedScorer class method), [1] (phenotypic.tune.targets.Nested class method) (phenotypic.tune.targets.Param class method) (phenotypic.tune.targets.Presence class method) (phenotypic.tune.targets.TunableParam class method) (phenotypic.tune.Trial class method), [1] (phenotypic.tune.TuningSpec class method), [1]

upper() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1] UPPER_FENCE (phenotypic.schema.QUALITY_TUKEY attribute) upper_percentile (phenotypic.enhance.ContrastStretching attribute), [1] use_gat (phenotypic.correction.BayesShrinkCorrector attribute), [1] (phenotypic.correction.ColorDenoise attribute), [1] (phenotypic.correction.VisuShrinkCorrector attribute), [1] (phenotypic.enhance.BayesShrinkEnhancer attribute), [1] (phenotypic.enhance.EnhanceBlockMatch attribute), [1] (phenotypic.enhance.LocalEdgeDenoise attribute), [1] (phenotypic.enhance.NonLocalMeansDenoiser attribute), [1] (phenotypic.enhance.VisuShrinkEnhancer attribute), [1] use_quantiles (phenotypic.detect.CannyDetector attribute), [1] UserThreshold (class in phenotypic.detect), [1] UUID (phenotypic.schema.METADATA attribute) UuidAssignmentError, [1] UUIDReassignmentError, [1]

V

v (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL attribute) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL attribute) val_range() (phenotypic._core._image_parts.accessors._detect_mat_accessor.DetectMatAccessor method) (phenotypic._core._image_parts.accessors._grayscale_accessor.Grayscale method) (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap method) (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask method) (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) (phenotypic._core._image_parts.accessors._rgb_accessor.ImageRGB method) validate() (in module phenotypic.gui.builder._validation) (phenotypic.abc_.BackgroundSubtraction class method), [1] (phenotypic.abc_.BaseOperation class method), [1] (phenotypic.abc_.ContrastAdjustment class method), [1] (phenotypic.abc_.FocusBlob class method), [1] (phenotypic.abc_.FocusEdge class method), [1] (phenotypic.abc_.GpuDetector class method), [1] (phenotypic.abc_.GridCorrector class method), [1] (phenotypic.abc_.GridFinder class method), [1] (phenotypic.abc_.GridMeasureFeatures class method), [1] (phenotypic.abc_.GridObjectDetector class method), [1] (phenotypic.abc_.GridObjectRefiner class method), [1] (phenotypic.abc_.GridOperation class method), [1] (phenotypic.abc_.ImageCorrector class method), [1] (phenotypic.abc_.ImageDenoiser class method), [1] (phenotypic.abc_.ImageEnhancer class method), [1] (phenotypic.abc_.ImageOperation class method), [1] (phenotypic.abc_.MeasureFeatures class method), [1] (phenotypic.abc_.MorphologicalFiltering class method), [1] (phenotypic.abc_.ObjectDetector class method), [1] (phenotypic.abc_.ObjectRefiner class method), [1] (phenotypic.abc_.PostMeasurement class method), [1] (phenotypic.abc_.PrefabPipeline class method), [1] (phenotypic.abc_.Smoothing class method), [1] (phenotypic.abc_.ThresholdDetector class method), [1] (phenotypic.analysis.abc_.ModelFitter class method) (phenotypic.analysis.abc_.QualityCheck class method) (phenotypic.analysis.abc_.SetAnalyzer class method) (phenotypic.analysis.DoubleSoftplus class method), [1] (phenotypic.analysis.EdgeCorrector class method), [1] (phenotypic.analysis.ErrorCutoffFinder class method), [1] (phenotypic.analysis.ExpectedVsDetectedCount class method), [1] (phenotypic.analysis.ICC class method), [1] (phenotypic.analysis.LinearSoftplus class method), [1] (phenotypic.analysis.LogGrowthModel class method), [1] (phenotypic.analysis.MADOutlierRemover class method), [1] (phenotypic.analysis.MaxModifiedZScore class method), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount class method) (phenotypic.analysis.qc.ICC class method) (phenotypic.analysis.qc.MaxModifiedZScore class method) (phenotypic.analysis.qc.RelativeMAD class method) (phenotypic.analysis.qc.ReplicateAgreement class method) (phenotypic.analysis.qc.TukeyOutlierFraction class method) (phenotypic.analysis.RelativeMAD class method), [1] (phenotypic.analysis.ReplicateAgreement class method), [1] (phenotypic.analysis.TukeyOutlierFraction class method), [1] (phenotypic.analysis.TukeyOutlierRemover class method), [1] (phenotypic.correction.BayesShrinkCorrector class method), [1] (phenotypic.correction.CaptureMetadata class method), [1] (phenotypic.correction.ColorCheckerProfile class method), [1] (phenotypic.correction.ColorCorrector class method), [1] (phenotypic.correction.ColorDenoise class method), [1] (phenotypic.correction.DenoiseBlockMatch class method), [1] (phenotypic.correction.GridAligner class method), [1] (phenotypic.correction.ImageCropper class method), [1] (phenotypic.correction.ImagePadder class method), [1] (phenotypic.correction.VisuShrinkCorrector class method), [1] (phenotypic.detect.CannyDetector class method), [1] (phenotypic.detect.ChanVeseDetector class method), [1] (phenotypic.detect.CompositeDetector class method), [1] (phenotypic.detect.FilamentousFungiDetector class method), [1] (phenotypic.detect.HysteresisDetector class method), [1] (phenotypic.detect.InoculumDetector class method), [1] (phenotypic.detect.IsodataDetector class method), [1] (phenotypic.detect.LiDetector class method), [1] (phenotypic.detect.MadHysteresisDetector class method), [1] (phenotypic.detect.ManualGridPointDetector class method), [1] (phenotypic.detect.ManualPointDetector class method), [1] (phenotypic.detect.MeanDetector class method), [1] (phenotypic.detect.MinimumDetector class method), [1] (phenotypic.detect.OtsuDetector class method), [1] (phenotypic.detect.RankOtsuDetector class method), [1] (phenotypic.detect.RoundPeaksDetector class method), [1] (phenotypic.detect.SecondaryOtsuDetector class method), [1] (phenotypic.detect.SinePeakDetector class method), [1] (phenotypic.detect.TriangleDetector class method), [1] (phenotypic.detect.UserThreshold class method), [1] (phenotypic.detect.WatershedDetector class method), [1] (phenotypic.detect.YenDetector class method), [1] (phenotypic.enhance.BayesShrinkEnhancer class method), [1] (phenotypic.enhance.ContrastStretching class method), [1] (phenotypic.enhance.EnhanceBlockMatch class method), [1] (phenotypic.enhance.EnhanceLocalContrast class method), [1] (phenotypic.enhance.FlattenIllumination class method), [1] (phenotypic.enhance.FocusBlobLoG class method), [1] (phenotypic.enhance.FocusEdgeFrangi class method), [1] (phenotypic.enhance.FocusEdgeHessian class method), [1] (phenotypic.enhance.FocusEdgeLaplace class method), [1] (phenotypic.enhance.FocusEdgeMeijering class method), [1] (phenotypic.enhance.FocusEdgePhase class method), [1] (phenotypic.enhance.FocusEdgeSato class method), [1] (phenotypic.enhance.FocusEdgeSobel class method), [1] (phenotypic.enhance.GaussianBlur class method), [1] (phenotypic.enhance.GrayOpening class method), [1] (phenotypic.enhance.ImageInverter class method), [1] (phenotypic.enhance.LocalEdgeDenoise class method), [1] (phenotypic.enhance.MedianFilter class method), [1] (phenotypic.enhance.NonLocalMeansDenoiser class method), [1] (phenotypic.enhance.RankMedianEnhancer class method), [1] (phenotypic.enhance.SetDetectMode class method), [1] (phenotypic.enhance.SharpenEdgeGauss class method), [1] (phenotypic.enhance.StructureSmoothing class method), [1] (phenotypic.enhance.SubtractGaussian class method), [1] (phenotypic.enhance.SubtractOpening class method), [1] (phenotypic.enhance.SubtractRollingBall class method), [1] (phenotypic.enhance.SubtractWhiteTophat class method), [1] (phenotypic.enhance.VisuShrinkEnhancer class method), [1] (phenotypic.enhance.WhiteTophatEnhance class method), [1] (phenotypic.grid.AutoGridFinder class method), [1] (phenotypic.grid.CenteredAutoGridFinder class method), [1] (phenotypic.grid.GridApply class method), [1] (phenotypic.grid.ManualGridFinder class method), [1] (phenotypic.measure.MeasureBounds class method), [1] (phenotypic.measure.MeasureColor class method), [1] (phenotypic.measure.MeasureGridLinRegStats class method), [1] (phenotypic.measure.MeasureGridSpatial class method), [1] (phenotypic.measure.MeasureGridSpread class method), [1] (phenotypic.measure.MeasureIntensity class method), [1] (phenotypic.measure.MeasureShape class method), [1] (phenotypic.measure.MeasureSize class method), [1] (phenotypic.measure.MeasureSymmetricZones class method), [1] (phenotypic.measure.MeasureTexture class method), [1] (phenotypic.post.AppendString class method) (phenotypic.post.ExpandMetadata class method) (phenotypic.post.MergeMetadata class method) (phenotypic.post.PrependString class method) (phenotypic.prefab.FilamentousFungiPipeline class method), [1] (phenotypic.prefab.GridSectionPipeline class method), [1] (phenotypic.prefab.HeavyOtsuPipeline class method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline class method), [1] (phenotypic.prefab.HeavyWatershedPipeline class method), [1] (phenotypic.prefab.RoundPeaksPipeline class method), [1] (phenotypic.prefab.SpImagerPipeline class method), [1] (phenotypic.refine.ExtractColonyCore class method), [1] (phenotypic.refine.GridAlignmentRefiner class method), [1] (phenotypic.refine.GridOversizedObjectRemover class method), [1] (phenotypic.refine.KeepNearestCenter class method), [1] (phenotypic.refine.KeepSectionLargest class method), [1] (phenotypic.refine.ManualRefine class method), [1] (phenotypic.refine.MaskClosing class method), [1] (phenotypic.refine.MaskDilation class method), [1] (phenotypic.refine.MaskErosion class method), [1] (phenotypic.refine.MaskFill class method), [1] (phenotypic.refine.MaskGradient class method), [1] (phenotypic.refine.MaskOpening class method), [1] (phenotypic.refine.MaskWhiteTophat class method), [1] (phenotypic.refine.MergeFragmentChains class method), [1] (phenotypic.refine.NearestNeighborMerger class method), [1] (phenotypic.refine.ReduceSectionsByLine class method), [1] (phenotypic.refine.RefineBySineFit class method), [1] (phenotypic.refine.RemoveBorderObjects class method), [1] (phenotypic.refine.RemoveByFeature class method), [1] (phenotypic.refine.RemoveGridOutliers class method), [1] (phenotypic.refine.RemoveLowCircularity class method), [1] (phenotypic.refine.SeparateObjects class method), [1] (phenotypic.refine.Skeletonize class method), [1] (phenotypic.refine.SmallObjectRemover class method), [1] (phenotypic.refine.SmallToLargeMerger class method), [1] (phenotypic.refine.Thinning class method), [1] (phenotypic.refine.TrimAsymmetry class method), [1] (phenotypic.tune.Budget class method), [1] (phenotypic.tune.Categorical class method), [1] (phenotypic.tune.CompositeScorer class method), [1] (phenotypic.tune.EvaluationResult class method), [1] (phenotypic.tune.Evaluator class method), [1] (phenotypic.tune.Excluded class method), [1] (phenotypic.tune.Fixed class method), [1] (phenotypic.tune.FloatRange class method), [1] (phenotypic.tune.GridConfig class method), [1] (phenotypic.tune.GroundTruthMasks class method), [1] (phenotypic.tune.HeldOutConfig class method), [1] (phenotypic.tune.ImportanceReport class method), [1] (phenotypic.tune.InferredSearchSpace class method), [1] (phenotypic.tune.IntRange class method), [1] (phenotypic.tune.Knob class method), [1] (phenotypic.tune.OptunaConfig class method), [1] (phenotypic.tune.QCScorer class method), [1] (phenotypic.tune.RandomConfig class method), [1] (phenotypic.tune.ReferenceFreeScorer class method), [1] (phenotypic.tune.Scorer class method), [1] (phenotypic.tune.SearchSpace class method), [1] (phenotypic.tune.StrategyConfig class method), [1] (phenotypic.tune.SupervisedScorer class method), [1] (phenotypic.tune.targets.Nested class method) (phenotypic.tune.targets.Param class method) (phenotypic.tune.targets.Presence class method) (phenotypic.tune.targets.TunableParam class method) (phenotypic.tune.Trial class method), [1] (phenotypic.tune.TuningSpec class method), [1]

validate_array_chunk() (in module phenotypic.sdk_.slurm), [1] validate_measure_integrity() (in module phenotypic.sdk_.funcs_) validate_obj_count (phenotypic.detect.InoculumDetector attribute), [1] validate_operation_integrity() (in module phenotypic.sdk_.funcs_) value (phenotypic.post.AppendString attribute) (phenotypic.post.PrependString attribute) (phenotypic.refine.RemoveByFeature attribute), [1] VALUE (phenotypic.schema.QUALITY_SE attribute) value (phenotypic.tune.Fixed attribute), [1] VALUE_ROBUST_MEAN (phenotypic.schema.ColorHSV attribute) value_type (phenotypic.tune.targets.TunableParam attribute) values() (phenotypic._core._image_parts.accessors._metadata_accessor.MetadataAccessor method) (phenotypic.tune.FloatRange method), [1] (phenotypic.tune.IntRange method), [1] (phenotypic.util.BackgroundMetrics method), [1] (phenotypic.util.ContrastMetrics method), [1] (phenotypic.util.image_metrics.BackgroundMetrics method) (phenotypic.util.image_metrics.ContrastMetrics method) (phenotypic.util.image_metrics.NoiseMetrics method) (phenotypic.util.image_metrics.QualityScores method) (phenotypic.util.image_metrics.StructureMetrics method) (phenotypic.util.NoiseMetrics method), [1] (phenotypic.util.QualityScores method), [1] (phenotypic.util.StructureMetrics method), [1] VARIANCE (phenotypic.schema.TEXTURE attribute) verbose (phenotypic.abc_.PrefabPipeline attribute), [1] (phenotypic.analysis.abc_.ModelFitter attribute), [1] (phenotypic.analysis.DoubleSoftplus attribute), [1] (phenotypic.analysis.LinearSoftplus attribute), [1] (phenotypic.analysis.LogGrowthModel attribute), [1] (phenotypic.prefab.FilamentousFungiPipeline attribute), [1] (phenotypic.prefab.GridSectionPipeline attribute), [1] (phenotypic.prefab.HeavyOtsuPipeline attribute), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1], [2], [3] (phenotypic.prefab.HeavyWatershedPipeline attribute), [1] (phenotypic.prefab.RoundPeaksPipeline attribute), [1] (phenotypic.prefab.SpImagerPipeline attribute), [1] verified_parquet_path() (in module phenotypic.sdk_), [1] VERSION (phenotypic.sdk_.DashboardManifestKey attribute), [1] (phenotypic.sdk_.ProcessingStateKey attribute), [1] VisuShrinkCorrector (class in phenotypic.correction), [1] VisuShrinkEnhancer (class in phenotypic.enhance), [1] vmax() (phenotypic._core._image_parts.accessors._detect_mat_accessor.DetectMatAccessor method) (phenotypic._core._image_parts.accessors._grayscale_accessor.Grayscale method) (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap method) (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask method) (phenotypic._core._image_parts.accessors._rgb_accessor.ImageRGB method) vmin() (phenotypic._core._image_parts.accessors._detect_mat_accessor.DetectMatAccessor method) (phenotypic._core._image_parts.accessors._grayscale_accessor.Grayscale method) (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap method) (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask method) (phenotypic._core._image_parts.accessors._rgb_accessor.ImageRGB method)

W

wants_subject (phenotypic.abc_.FigureSpec attribute), [1], [2], [3] warmup_c (phenotypic.tune.ScreeningConfig attribute), [1] warmup_floor (phenotypic.tune.ScreeningConfig attribute), [1] warn (phenotypic.grid.AutoGridFinder attribute), [1] (phenotypic.grid.CenteredAutoGridFinder attribute), [1] (phenotypic.measure.MeasureTexture attribute), [1] warn_threshold (phenotypic.analysis.abc_.QualityCheck attribute), [1] (phenotypic.analysis.ExpectedVsDetectedCount attribute), [1] (phenotypic.analysis.ICC attribute), [1] (phenotypic.analysis.MaxModifiedZScore attribute), [1] (phenotypic.analysis.qc.ExpectedVsDetectedCount attribute) (phenotypic.analysis.qc.ICC attribute) (phenotypic.analysis.qc.MaxModifiedZScore attribute) (phenotypic.analysis.qc.RelativeMAD attribute) (phenotypic.analysis.qc.ReplicateAgreement attribute) (phenotypic.analysis.qc.TukeyOutlierFraction attribute) (phenotypic.analysis.RelativeMAD attribute), [1] (phenotypic.analysis.ReplicateAgreement attribute), [1] (phenotypic.analysis.TukeyOutlierFraction attribute), [1] warning (phenotypic.tune.GeneralizationReport attribute), [1] WatershedDetector (class in phenotypic.detect), [1] wavelet (phenotypic.correction.BayesShrinkCorrector attribute), [1] (phenotypic.correction.VisuShrinkCorrector attribute), [1] (phenotypic.enhance.BayesShrinkEnhancer attribute), [1] (phenotypic.enhance.VisuShrinkEnhancer attribute), [1] wavelet_levels (phenotypic.correction.BayesShrinkCorrector attribute), [1] (phenotypic.correction.VisuShrinkCorrector attribute), [1] (phenotypic.enhance.BayesShrinkEnhancer attribute), [1] (phenotypic.enhance.VisuShrinkEnhancer attribute), [1] weights (phenotypic.tune.CompositeScorer attribute), [1] well WHITE_PCT (phenotypic.schema.ColorComposition attribute) WhiteTophatEnhance (class in phenotypic.enhance), [1] widget() (phenotypic.abc_.BackgroundSubtraction method), [1] (phenotypic.abc_.ContrastAdjustment method), [1] (phenotypic.abc_.FocusBlob method), [1] (phenotypic.abc_.FocusEdge method), [1] (phenotypic.abc_.GpuDetector method), [1] (phenotypic.abc_.GridCorrector method), [1] (phenotypic.abc_.GridObjectDetector method), [1] (phenotypic.abc_.GridObjectRefiner method), [1] (phenotypic.abc_.GridOperation method), [1] (phenotypic.abc_.ImageCorrector method), [1] (phenotypic.abc_.ImageDenoiser method), [1] (phenotypic.abc_.ImageEnhancer method), [1] (phenotypic.abc_.ImageOperation method), [1] (phenotypic.abc_.MorphologicalFiltering method), [1] (phenotypic.abc_.ObjectDetector method), [1] (phenotypic.abc_.ObjectRefiner method), [1] (phenotypic.abc_.PrefabPipeline method), [1] (phenotypic.abc_.Smoothing method), [1] (phenotypic.abc_.ThresholdDetector method), [1] (phenotypic.correction.BayesShrinkCorrector method), [1] (phenotypic.correction.ColorCorrector method), [1] (phenotypic.correction.ColorDenoise method), [1] (phenotypic.correction.DenoiseBlockMatch method), [1] (phenotypic.correction.GridAligner method), [1] (phenotypic.correction.ImageCropper method), [1] (phenotypic.correction.ImagePadder method), [1] (phenotypic.correction.VisuShrinkCorrector method), [1] (phenotypic.detect.CannyDetector method), [1] (phenotypic.detect.ChanVeseDetector method), [1] (phenotypic.detect.CompositeDetector method), [1] (phenotypic.detect.FilamentousFungiDetector method), [1] (phenotypic.detect.HysteresisDetector method), [1] (phenotypic.detect.InoculumDetector method), [1] (phenotypic.detect.IsodataDetector method), [1] (phenotypic.detect.LiDetector method), [1] (phenotypic.detect.MadHysteresisDetector method), [1] (phenotypic.detect.ManualGridPointDetector method), [1] (phenotypic.detect.ManualPointDetector method), [1] (phenotypic.detect.MeanDetector method), [1] (phenotypic.detect.MinimumDetector method), [1] (phenotypic.detect.OtsuDetector method), [1] (phenotypic.detect.RankOtsuDetector method), [1] (phenotypic.detect.RoundPeaksDetector method), [1] (phenotypic.detect.SecondaryOtsuDetector method), [1] (phenotypic.detect.SinePeakDetector method), [1] (phenotypic.detect.TriangleDetector method), [1] (phenotypic.detect.UserThreshold method), [1] (phenotypic.detect.WatershedDetector method), [1] (phenotypic.detect.YenDetector method), [1] (phenotypic.enhance.BayesShrinkEnhancer method), [1] (phenotypic.enhance.ContrastStretching method), [1] (phenotypic.enhance.EnhanceBlockMatch method), [1] (phenotypic.enhance.EnhanceLocalContrast method), [1] (phenotypic.enhance.FlattenIllumination method), [1] (phenotypic.enhance.FocusBlobLoG method), [1] (phenotypic.enhance.FocusEdgeFrangi method), [1] (phenotypic.enhance.FocusEdgeHessian method), [1] (phenotypic.enhance.FocusEdgeLaplace method), [1] (phenotypic.enhance.FocusEdgeMeijering method), [1] (phenotypic.enhance.FocusEdgePhase method), [1] (phenotypic.enhance.FocusEdgeSato method), [1] (phenotypic.enhance.FocusEdgeSobel method), [1] (phenotypic.enhance.GaussianBlur method), [1] (phenotypic.enhance.GrayOpening method), [1] (phenotypic.enhance.ImageInverter method), [1] (phenotypic.enhance.LocalEdgeDenoise method), [1] (phenotypic.enhance.MedianFilter method), [1] (phenotypic.enhance.NonLocalMeansDenoiser method), [1] (phenotypic.enhance.RankMedianEnhancer method), [1] (phenotypic.enhance.SetDetectMode method), [1] (phenotypic.enhance.SharpenEdgeGauss method), [1] (phenotypic.enhance.StructureSmoothing method), [1] (phenotypic.enhance.SubtractGaussian method), [1] (phenotypic.enhance.SubtractOpening method), [1] (phenotypic.enhance.SubtractRollingBall method), [1] (phenotypic.enhance.SubtractWhiteTophat method), [1] (phenotypic.enhance.VisuShrinkEnhancer method), [1] (phenotypic.enhance.WhiteTophatEnhance method), [1] (phenotypic.grid.GridApply method), [1] (phenotypic.prefab.FilamentousFungiPipeline method), [1] (phenotypic.prefab.GridSectionPipeline method), [1] (phenotypic.prefab.HeavyOtsuPipeline method), [1] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1] (phenotypic.prefab.HeavyWatershedPipeline method), [1] (phenotypic.prefab.RoundPeaksPipeline method), [1] (phenotypic.prefab.SpImagerPipeline method), [1] (phenotypic.refine.ExtractColonyCore method), [1] (phenotypic.refine.GridAlignmentRefiner method), [1] (phenotypic.refine.GridOversizedObjectRemover method), [1] (phenotypic.refine.KeepNearestCenter method), [1] (phenotypic.refine.KeepSectionLargest method), [1] (phenotypic.refine.ManualRefine method), [1] (phenotypic.refine.MaskClosing method), [1] (phenotypic.refine.MaskDilation method), [1] (phenotypic.refine.MaskErosion method), [1] (phenotypic.refine.MaskFill method), [1] (phenotypic.refine.MaskGradient method), [1] (phenotypic.refine.MaskOpening method), [1] (phenotypic.refine.MaskWhiteTophat method), [1] (phenotypic.refine.MergeFragmentChains method), [1] (phenotypic.refine.NearestNeighborMerger method), [1] (phenotypic.refine.ReduceSectionsByLine method), [1] (phenotypic.refine.RefineBySineFit method), [1] (phenotypic.refine.RemoveBorderObjects method), [1] (phenotypic.refine.RemoveByFeature method), [1] (phenotypic.refine.RemoveGridOutliers method), [1] (phenotypic.refine.RemoveLowCircularity method), [1] (phenotypic.refine.SeparateObjects method), [1] (phenotypic.refine.Skeletonize method), [1] (phenotypic.refine.SmallObjectRemover method), [1] (phenotypic.refine.SmallToLargeMerger method), [1] (phenotypic.refine.Thinning method), [1] (phenotypic.refine.TrimAsymmetry method), [1] (phenotypic.sdk_.LazyWidgetMixin method), [1] (phenotypic.sdk_.mixin.LazyWidgetMixin method)

width (phenotypic.detect.ManualGridPointDetector attribute), [1] (phenotypic.detect.ManualPointDetector attribute), [1] (phenotypic.detect.RankOtsuDetector attribute), [1] (phenotypic.enhance.GrayOpening attribute), [1] (phenotypic.enhance.MedianFilter attribute), [1] (phenotypic.enhance.RankMedianEnhancer attribute), [1] (phenotypic.enhance.SubtractOpening attribute), [1] (phenotypic.enhance.SubtractWhiteTophat attribute), [1] (phenotypic.enhance.WhiteTophatEnhance attribute), [1] (phenotypic.refine.ManualRefine attribute), [1] (phenotypic.refine.MaskClosing attribute), [1] (phenotypic.refine.MaskDilation attribute), [1] (phenotypic.refine.MaskErosion attribute), [1] (phenotypic.refine.MaskGradient attribute), [1] (phenotypic.refine.MaskOpening attribute), [1] (phenotypic.refine.MaskWhiteTophat attribute), [1] win_size (phenotypic.enhance.LocalEdgeDenoise attribute), [1] winner (phenotypic.tune.ScreeningResult attribute), [1] with_traceback() (phenotypic.grid.CenteredAutoGridFinderFallbackWarning method), [1] (phenotypic.gui.tune.TuneRunRootError method) (phenotypic.sdk_.exceptions_.ArrayKeyValueShapeMismatchError method), [1] (phenotypic.sdk_.exceptions_.DataIntegrityError method), [1] (phenotypic.sdk_.exceptions_.EmptyImageError method), [1] (phenotypic.sdk_.exceptions_.GrayscaleOutOfRangeError method), [1] (phenotypic.sdk_.exceptions_.GridImageInputError method), [1] (phenotypic.sdk_.exceptions_.IllegalAssignmentError method), [1] (phenotypic.sdk_.exceptions_.IllegalElementAssignmentError method), [1] (phenotypic.sdk_.exceptions_.ImageOperationError method), [1] (phenotypic.sdk_.exceptions_.ImmutableComponentError method), [1] (phenotypic.sdk_.exceptions_.InputShapeMismatchError method), [1] (phenotypic.sdk_.exceptions_.InterfaceError method), [1] (phenotypic.sdk_.exceptions_.InvalidHsvSchemaError method), [1] (phenotypic.sdk_.exceptions_.InvalidMapValueError method), [1] (phenotypic.sdk_.exceptions_.InvalidMaskScalarValueError method), [1] (phenotypic.sdk_.exceptions_.InvalidMaskValueError method), [1] (phenotypic.sdk_.exceptions_.InvalidShapeError method), [1] (phenotypic.sdk_.exceptions_.MetadataKeySpacesError method), [1] (phenotypic.sdk_.exceptions_.MetadataKeyValueError method), [1] (phenotypic.sdk_.exceptions_.MetadataValueNonScalarError method), [1] (phenotypic.sdk_.exceptions_.NoArrayError method), [1] (phenotypic.sdk_.exceptions_.NoComponentError method), [1] (phenotypic.sdk_.exceptions_.NoImageDataError method), [1] (phenotypic.sdk_.exceptions_.NoObjectsError method), [1] (phenotypic.sdk_.exceptions_.NoOutputError method), [1] (phenotypic.sdk_.exceptions_.ObjectNotFoundError method), [1] (phenotypic.sdk_.exceptions_.OperationFailedError method), [1] (phenotypic.sdk_.exceptions_.OperationIntegrityError method), [1] (phenotypic.sdk_.exceptions_.OutputValueError method), [1] (phenotypic.sdk_.exceptions_.PhenoTypicError method), [1] (phenotypic.sdk_.exceptions_.UnknownError method), [1] (phenotypic.sdk_.exceptions_.UnsupportedFileTypeError method), [1] (phenotypic.sdk_.exceptions_.UnsupportedImageFormat method), [1] (phenotypic.sdk_.exceptions_.UuidAssignmentError method), [1] (phenotypic.sdk_.exceptions_.UUIDReassignmentError method), [1] within_group_caveat (phenotypic.tune.GeneralizationReport attribute), [1]

X

x_COEFF_VARIANCE (phenotypic.schema.Colorxy attribute) X_COEFF_VARIANCE (phenotypic.schema.ColorXYZ attribute) x_headers() (phenotypic.schema.Colorxy class method) x_MAXIMUM (phenotypic.schema.Colorxy attribute) X_MAXIMUM (phenotypic.schema.ColorXYZ attribute) x_MEAN (phenotypic.schema.Colorxy attribute) X_MEAN (phenotypic.schema.ColorXYZ attribute) x_MEDIAN (phenotypic.schema.Colorxy attribute) X_MEDIAN (phenotypic.schema.ColorXYZ attribute) x_MINIMUM (phenotypic.schema.Colorxy attribute)

X_MINIMUM (phenotypic.schema.ColorXYZ attribute) x_Q1 (phenotypic.schema.Colorxy attribute) X_Q1 (phenotypic.schema.ColorXYZ attribute) x_Q3 (phenotypic.schema.Colorxy attribute) X_Q3 (phenotypic.schema.ColorXYZ attribute) x_STDDEV (phenotypic.schema.Colorxy attribute) X_STDDEV (phenotypic.schema.ColorXYZ attribute) xy (phenotypic._core._image_parts.accessors._color_accessor.ColorAccessor property) XYZ (phenotypic._core._image_parts.accessors._color_accessor.ColorAccessor property) XYZ_D65 (phenotypic._core._image_parts.accessors._color_accessor.ColorAccessor property)

Y

y_COEFF_VARIANCE (phenotypic.schema.Colorxy attribute) Y_COEFF_VARIANCE (phenotypic.schema.ColorXYZ attribute) y_headers() (phenotypic.schema.Colorxy class method) y_MAXIMUM (phenotypic.schema.Colorxy attribute) Y_MAXIMUM (phenotypic.schema.ColorXYZ attribute) y_MEAN (phenotypic.schema.Colorxy attribute) Y_MEAN (phenotypic.schema.ColorXYZ attribute) y_MEDIAN (phenotypic.schema.Colorxy attribute) Y_MEDIAN (phenotypic.schema.ColorXYZ attribute)

y_MINIMUM (phenotypic.schema.Colorxy attribute) Y_MINIMUM (phenotypic.schema.ColorXYZ attribute) y_Q1 (phenotypic.schema.Colorxy attribute) Y_Q1 (phenotypic.schema.ColorXYZ attribute) y_Q3 (phenotypic.schema.Colorxy attribute) Y_Q3 (phenotypic.schema.ColorXYZ attribute) y_STDDEV (phenotypic.schema.Colorxy attribute) Y_STDDEV (phenotypic.schema.ColorXYZ attribute) YELLOW_PCT (phenotypic.schema.ColorComposition attribute) YenDetector (class in phenotypic.detect), [1]

Z

Z_COEFF_VARIANCE (phenotypic.schema.ColorXYZ attribute) Z_MAXIMUM (phenotypic.schema.ColorXYZ attribute) Z_MEAN (phenotypic.schema.ColorXYZ attribute) Z_MEDIAN (phenotypic.schema.ColorXYZ attribute) Z_MINIMUM (phenotypic.schema.ColorXYZ attribute) Z_Q1 (phenotypic.schema.ColorXYZ attribute) Z_Q3 (phenotypic.schema.ColorXYZ attribute) Z_STDDEV (phenotypic.schema.ColorXYZ attribute) zfill() (phenotypic.abc_.MeasurementInfo method), [1] (phenotypic.schema.ACQUISITION_METADATA method) (phenotypic.schema.BBOX method) (phenotypic.schema.ColorComposition method) (phenotypic.schema.ColorHSV method) (phenotypic.schema.ColorLab method) (phenotypic.schema.Colorxy method) (phenotypic.schema.ColorXYZ method) (phenotypic.schema.CONDITION_METADATA method) (phenotypic.schema.CURATION method) (phenotypic.schema.DOUBLE_SOFTPLUS_MODEL method) (phenotypic.schema.EDGE_CORRECTION method) (phenotypic.schema.ErrorCategory method) (phenotypic.schema.EXPERIMENT_METADATA method) (phenotypic.schema.GENETIC_METADATA method) (phenotypic.schema.GRID method) (phenotypic.schema.GRID_LINREG_STATS method) (phenotypic.schema.GRID_SPATIAL method) (phenotypic.schema.GRID_SPREAD method) (phenotypic.schema.INCUBATION_METADATA method) (phenotypic.schema.INTENSITY method) (phenotypic.schema.LINEAR_SOFTPLUS_MODEL method) (phenotypic.schema.LOG_GROWTH_MODEL method) (phenotypic.schema.MeasurementInfo method) (phenotypic.schema.METADATA method) (phenotypic.schema.MODEL_METRICS method) (phenotypic.schema.OBJECT method) (phenotypic.schema.PLATE_METADATA method) (phenotypic.schema.QUALITY_CHECK method) (phenotypic.schema.QUALITY_COUNT method) (phenotypic.schema.QUALITY_ICC method) (phenotypic.schema.QUALITY_MAD method) (phenotypic.schema.QUALITY_SE method) (phenotypic.schema.QUALITY_TUKEY method) (phenotypic.schema.QUALITY_ZMAX method) (phenotypic.schema.RADIAL_EXPANSION method) (phenotypic.schema.SAMPLE_METADATA method) (phenotypic.schema.SHAPE method) (phenotypic.schema.SIZE method) (phenotypic.schema.SYMMETRIC_ZONES method) (phenotypic.schema.TEXTURE method) (phenotypic.sdk_.constants_.ConstantLabels method), [1] (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method), [1] (phenotypic.sdk_.constants_.PIPE_STATUS method), [1]