Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z _ __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) (phenotypic.sdk_.constants_.IMAGE_TYPES class method) __copy__() (phenotypic.abc_.BackgroundSubtraction method) (phenotypic.abc_.BaseOperation method) (phenotypic.abc_.ContrastAdjustment method) (phenotypic.abc_.FocusBlob method) (phenotypic.abc_.FocusEdge method) (phenotypic.abc_.GpuDetector method) (phenotypic.abc_.GridCorrector method) (phenotypic.abc_.GridFinder method) (phenotypic.abc_.GridMeasureFeatures method) (phenotypic.abc_.GridObjectDetector method) (phenotypic.abc_.GridObjectRefiner method) (phenotypic.abc_.GridOperation method) (phenotypic.abc_.ImageCorrector method) (phenotypic.abc_.ImageDenoiser method) (phenotypic.abc_.ImageEnhancer method) (phenotypic.abc_.ImageOperation method) (phenotypic.abc_.MeasureFeatures method) (phenotypic.abc_.MorphologicalFiltering method) (phenotypic.abc_.ObjectDetector method) (phenotypic.abc_.ObjectRefiner method) (phenotypic.abc_.PostMeasurement method) (phenotypic.abc_.PrefabPipeline method) (phenotypic.abc_.Smoothing method) (phenotypic.abc_.ThresholdDetector method) (phenotypic.analysis.EdgeCorrector method) (phenotypic.analysis.ErrorCutoffFinder method) (phenotypic.analysis.ExpectedVsDetectedCount method) (phenotypic.analysis.GridOccupancy method) (phenotypic.analysis.ICC method) (phenotypic.analysis.LinearCapAndLagModel method) (phenotypic.analysis.LinearLagModel method) (phenotypic.analysis.LogGrowthModel method) (phenotypic.analysis.MADOutlierRemover method) (phenotypic.analysis.MaxModifiedZScore method) (phenotypic.analysis.RelativeMAD method) (phenotypic.analysis.ReplicateAgreement method) (phenotypic.analysis.TukeyOutlierFraction method) (phenotypic.analysis.TukeyOutlierRemover method) (phenotypic.correction.BayesShrinkCorrector method) (phenotypic.correction.CaptureMetadata method) (phenotypic.correction.ColorCheckerProfile method) (phenotypic.correction.ColorCorrector method) (phenotypic.correction.ColorDenoise method) (phenotypic.correction.DenoiseBlockMatch method) (phenotypic.correction.GridAligner method) (phenotypic.correction.ImageCropper method) (phenotypic.correction.ImagePadder method) (phenotypic.correction.VisuShrinkCorrector method) (phenotypic.detect.CannyDetector method) (phenotypic.detect.ChanVeseDetector method) (phenotypic.detect.CompositeDetector method) (phenotypic.detect.FilamentousFungiDetector method) (phenotypic.detect.HysteresisDetector method) (phenotypic.detect.InoculumDetector method) (phenotypic.detect.IsodataDetector method) (phenotypic.detect.LiDetector method) (phenotypic.detect.MadHysteresisDetector method) (phenotypic.detect.ManualGridPointDetector method) (phenotypic.detect.ManualPointDetector method) (phenotypic.detect.MeanDetector method) (phenotypic.detect.MinimumDetector method) (phenotypic.detect.OtsuDetector method) (phenotypic.detect.RankOtsuDetector method) (phenotypic.detect.RoundPeaksDetector method) (phenotypic.detect.SecondaryOtsuDetector method) (phenotypic.detect.SinePeakDetector method) (phenotypic.detect.TriangleDetector method) (phenotypic.detect.UserThreshold method) (phenotypic.detect.WatershedDetector method) (phenotypic.detect.YenDetector method) (phenotypic.enhance.BayesShrinkEnhancer method) (phenotypic.enhance.CompositeEnhance method) (phenotypic.enhance.ContrastStretching method) (phenotypic.enhance.EnhanceBlockMatch method) (phenotypic.enhance.EnhanceLocalContrast method) (phenotypic.enhance.FlattenIllumination method) (phenotypic.enhance.FocusBlobLoG method) (phenotypic.enhance.FocusEdgeFrangi method) (phenotypic.enhance.FocusEdgeHessian method) (phenotypic.enhance.FocusEdgeLaplace method) (phenotypic.enhance.FocusEdgeMeijering method) (phenotypic.enhance.FocusEdgePhase method) (phenotypic.enhance.FocusEdgeSato method) (phenotypic.enhance.FocusEdgeSobel method) (phenotypic.enhance.GaussianBlur method) (phenotypic.enhance.GrayOpening method) (phenotypic.enhance.ImageInverter method) (phenotypic.enhance.LocalEdgeDenoise method) (phenotypic.enhance.MedianFilter method) (phenotypic.enhance.NonLocalMeansDenoiser method) (phenotypic.enhance.RankMedianEnhancer method) (phenotypic.enhance.SetDetectMode method) (phenotypic.enhance.SharpenEdgeGauss method) (phenotypic.enhance.StructureSmoothing method) (phenotypic.enhance.SubtractGaussian method) (phenotypic.enhance.SubtractOpening method) (phenotypic.enhance.SubtractRollingBall method) (phenotypic.enhance.SubtractWhiteTophat method) (phenotypic.enhance.VisuShrinkEnhancer method) (phenotypic.enhance.WhiteTophatEnhance method) (phenotypic.grid.AutoGridFinder method) (phenotypic.grid.CenteredAutoGridFinder method) (phenotypic.grid.GridApply method) (phenotypic.grid.ManualGridFinder method) (phenotypic.measure.MeasureBounds method) (phenotypic.measure.MeasureColor method) (phenotypic.measure.MeasureGridLinRegStats method) (phenotypic.measure.MeasureGridSpread method) (phenotypic.measure.MeasureIntensity method) (phenotypic.measure.MeasureNeighborDist method) (phenotypic.measure.MeasureOrientationZones method) (phenotypic.measure.MeasureShape method) (phenotypic.measure.MeasureSize method) (phenotypic.measure.MeasureSymmetricZones method) (phenotypic.measure.MeasureTexture method) (phenotypic.prefab.FilamentousFungiPipeline method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.prefab.RoundPeaksPipeline method) (phenotypic.prefab.SpImagerPipeline method) (phenotypic.refine.ExtractColonyCore method) (phenotypic.refine.GridAlignmentRefiner method) (phenotypic.refine.GridOversizedObjectRemover method) (phenotypic.refine.KeepNearestCenter method) (phenotypic.refine.KeepSectionLargest method) (phenotypic.refine.ManualRefine method) (phenotypic.refine.MaskClosing method) (phenotypic.refine.MaskDilation method) (phenotypic.refine.MaskErosion method) (phenotypic.refine.MaskFill method) (phenotypic.refine.MaskGradient method) (phenotypic.refine.MaskOpening method) (phenotypic.refine.MaskWhiteTophat method) (phenotypic.refine.MergeFragmentChains method) (phenotypic.refine.NearestNeighborMerger method) (phenotypic.refine.ReduceSectionsByLine method) (phenotypic.refine.RefineBySineFit method) (phenotypic.refine.RemoveBorderObjects method) (phenotypic.refine.RemoveByFeature method) (phenotypic.refine.RemoveGridOutliers method) (phenotypic.refine.RemoveLowCircularity method) (phenotypic.refine.SeparateObjects method) (phenotypic.refine.Skeletonize method) (phenotypic.refine.SmallObjectRemover method) (phenotypic.refine.SmallToLargeMerger method) (phenotypic.refine.Thinning method) (phenotypic.refine.TrimAsymmetry method) (phenotypic.tune.Budget method) (phenotypic.tune.Categorical method) (phenotypic.tune.EvaluationResult method) (phenotypic.tune.Evaluator method) (phenotypic.tune.Excluded method) (phenotypic.tune.Fixed method) (phenotypic.tune.FloatRange method) (phenotypic.tune.HeldOutConfig method) (phenotypic.tune.ImportanceReport method) (phenotypic.tune.InferredSearchSpace method) (phenotypic.tune.IntRange method) (phenotypic.tune.Knob method) (phenotypic.tune.score.CompositeScorer method) (phenotypic.tune.score.GroundTruthMasks method) (phenotypic.tune.score.QCScorer method) (phenotypic.tune.score.ReferenceFreeScorer method) (phenotypic.tune.score.Scorer method) (phenotypic.tune.score.SupervisedScorer method) (phenotypic.tune.SearchSpace method) (phenotypic.tune.strategy.GridConfig method) (phenotypic.tune.strategy.OptunaConfig method) (phenotypic.tune.strategy.RandomConfig method) (phenotypic.tune.strategy.StrategyConfig method) (phenotypic.tune.Trial method) (phenotypic.tune.TuningSpec method) __deepcopy__() (phenotypic.abc_.BackgroundSubtraction method) (phenotypic.abc_.BaseOperation method) (phenotypic.abc_.ContrastAdjustment method) (phenotypic.abc_.FocusBlob method) (phenotypic.abc_.FocusEdge method) (phenotypic.abc_.GpuDetector method) (phenotypic.abc_.GridCorrector method) (phenotypic.abc_.GridFinder method) (phenotypic.abc_.GridMeasureFeatures method) (phenotypic.abc_.GridObjectDetector method) (phenotypic.abc_.GridObjectRefiner method) (phenotypic.abc_.GridOperation method) (phenotypic.abc_.ImageCorrector method) (phenotypic.abc_.ImageDenoiser method) (phenotypic.abc_.ImageEnhancer method) (phenotypic.abc_.ImageOperation method) (phenotypic.abc_.MeasureFeatures method) (phenotypic.abc_.MorphologicalFiltering method) (phenotypic.abc_.ObjectDetector method) (phenotypic.abc_.ObjectRefiner method) (phenotypic.abc_.PostMeasurement method) (phenotypic.abc_.PrefabPipeline method) (phenotypic.abc_.Smoothing method) (phenotypic.abc_.ThresholdDetector method) (phenotypic.analysis.EdgeCorrector method) (phenotypic.analysis.ErrorCutoffFinder method) (phenotypic.analysis.ExpectedVsDetectedCount method) (phenotypic.analysis.GridOccupancy method) (phenotypic.analysis.ICC method) (phenotypic.analysis.LinearCapAndLagModel method) (phenotypic.analysis.LinearLagModel method) (phenotypic.analysis.LogGrowthModel method) (phenotypic.analysis.MADOutlierRemover method) (phenotypic.analysis.MaxModifiedZScore method) (phenotypic.analysis.RelativeMAD method) (phenotypic.analysis.ReplicateAgreement method) (phenotypic.analysis.TukeyOutlierFraction method) (phenotypic.analysis.TukeyOutlierRemover method) (phenotypic.correction.BayesShrinkCorrector method) (phenotypic.correction.CaptureMetadata method) (phenotypic.correction.ColorCheckerProfile method) (phenotypic.correction.ColorCorrector method) (phenotypic.correction.ColorDenoise method) (phenotypic.correction.DenoiseBlockMatch method) (phenotypic.correction.GridAligner method) (phenotypic.correction.ImageCropper method) (phenotypic.correction.ImagePadder method) (phenotypic.correction.VisuShrinkCorrector method) (phenotypic.detect.CannyDetector method) (phenotypic.detect.ChanVeseDetector method) (phenotypic.detect.CompositeDetector method) (phenotypic.detect.FilamentousFungiDetector method) (phenotypic.detect.HysteresisDetector method) (phenotypic.detect.InoculumDetector method) (phenotypic.detect.IsodataDetector method) (phenotypic.detect.LiDetector method) (phenotypic.detect.MadHysteresisDetector method) (phenotypic.detect.ManualGridPointDetector method) (phenotypic.detect.ManualPointDetector method) (phenotypic.detect.MeanDetector method) (phenotypic.detect.MinimumDetector method) (phenotypic.detect.OtsuDetector method) (phenotypic.detect.RankOtsuDetector method) (phenotypic.detect.RoundPeaksDetector method) (phenotypic.detect.SecondaryOtsuDetector method) (phenotypic.detect.SinePeakDetector method) (phenotypic.detect.TriangleDetector method) (phenotypic.detect.UserThreshold method) (phenotypic.detect.WatershedDetector method) (phenotypic.detect.YenDetector method) (phenotypic.enhance.BayesShrinkEnhancer method) (phenotypic.enhance.CompositeEnhance method) (phenotypic.enhance.ContrastStretching method) (phenotypic.enhance.EnhanceBlockMatch method) (phenotypic.enhance.EnhanceLocalContrast method) (phenotypic.enhance.FlattenIllumination method) (phenotypic.enhance.FocusBlobLoG method) (phenotypic.enhance.FocusEdgeFrangi method) (phenotypic.enhance.FocusEdgeHessian method) (phenotypic.enhance.FocusEdgeLaplace method) (phenotypic.enhance.FocusEdgeMeijering method) (phenotypic.enhance.FocusEdgePhase method) (phenotypic.enhance.FocusEdgeSato method) (phenotypic.enhance.FocusEdgeSobel method) (phenotypic.enhance.GaussianBlur method) (phenotypic.enhance.GrayOpening method) (phenotypic.enhance.ImageInverter method) (phenotypic.enhance.LocalEdgeDenoise method) (phenotypic.enhance.MedianFilter method) (phenotypic.enhance.NonLocalMeansDenoiser method) (phenotypic.enhance.RankMedianEnhancer method) (phenotypic.enhance.SetDetectMode method) (phenotypic.enhance.SharpenEdgeGauss method) (phenotypic.enhance.StructureSmoothing method) (phenotypic.enhance.SubtractGaussian method) (phenotypic.enhance.SubtractOpening method) (phenotypic.enhance.SubtractRollingBall method) (phenotypic.enhance.SubtractWhiteTophat method) (phenotypic.enhance.VisuShrinkEnhancer method) (phenotypic.enhance.WhiteTophatEnhance method) (phenotypic.grid.AutoGridFinder method) (phenotypic.grid.CenteredAutoGridFinder method) (phenotypic.grid.GridApply method) (phenotypic.grid.ManualGridFinder method) (phenotypic.measure.MeasureBounds method) (phenotypic.measure.MeasureColor method) (phenotypic.measure.MeasureGridLinRegStats method) (phenotypic.measure.MeasureGridSpread method) (phenotypic.measure.MeasureIntensity method) (phenotypic.measure.MeasureNeighborDist method) (phenotypic.measure.MeasureOrientationZones method) (phenotypic.measure.MeasureShape method) (phenotypic.measure.MeasureSize method) (phenotypic.measure.MeasureSymmetricZones method) (phenotypic.measure.MeasureTexture method) (phenotypic.prefab.FilamentousFungiPipeline method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.prefab.RoundPeaksPipeline method) (phenotypic.prefab.SpImagerPipeline method) (phenotypic.refine.ExtractColonyCore method) (phenotypic.refine.GridAlignmentRefiner method) (phenotypic.refine.GridOversizedObjectRemover method) (phenotypic.refine.KeepNearestCenter method) (phenotypic.refine.KeepSectionLargest method) (phenotypic.refine.ManualRefine method) (phenotypic.refine.MaskClosing method) (phenotypic.refine.MaskDilation method) (phenotypic.refine.MaskErosion method) (phenotypic.refine.MaskFill method) (phenotypic.refine.MaskGradient method) (phenotypic.refine.MaskOpening method) (phenotypic.refine.MaskWhiteTophat method) (phenotypic.refine.MergeFragmentChains method) (phenotypic.refine.NearestNeighborMerger method) (phenotypic.refine.ReduceSectionsByLine method) (phenotypic.refine.RefineBySineFit method) (phenotypic.refine.RemoveBorderObjects method) (phenotypic.refine.RemoveByFeature method) (phenotypic.refine.RemoveGridOutliers method) (phenotypic.refine.RemoveLowCircularity method) (phenotypic.refine.SeparateObjects method) (phenotypic.refine.Skeletonize method) (phenotypic.refine.SmallObjectRemover method) (phenotypic.refine.SmallToLargeMerger method) (phenotypic.refine.Thinning method) (phenotypic.refine.TrimAsymmetry method) (phenotypic.tune.Budget method) (phenotypic.tune.Categorical method) (phenotypic.tune.EvaluationResult method) (phenotypic.tune.Evaluator method) (phenotypic.tune.Excluded method) (phenotypic.tune.Fixed method) (phenotypic.tune.FloatRange method) (phenotypic.tune.HeldOutConfig method) (phenotypic.tune.ImportanceReport method) (phenotypic.tune.InferredSearchSpace method) (phenotypic.tune.IntRange method) (phenotypic.tune.Knob method) (phenotypic.tune.score.CompositeScorer method) (phenotypic.tune.score.GroundTruthMasks method) (phenotypic.tune.score.QCScorer method) (phenotypic.tune.score.ReferenceFreeScorer method) (phenotypic.tune.score.Scorer method) (phenotypic.tune.score.SupervisedScorer method) (phenotypic.tune.SearchSpace method) (phenotypic.tune.strategy.GridConfig method) (phenotypic.tune.strategy.OptunaConfig method) (phenotypic.tune.strategy.RandomConfig method) (phenotypic.tune.strategy.StrategyConfig method) (phenotypic.tune.Trial method) (phenotypic.tune.TuningSpec method) __del__() (phenotypic.abc_.BackgroundSubtraction method) (phenotypic.abc_.BaseOperation method) (phenotypic.abc_.ContrastAdjustment method) (phenotypic.abc_.FocusBlob method) (phenotypic.abc_.FocusEdge method) (phenotypic.abc_.GpuDetector method) (phenotypic.abc_.GridCorrector method) (phenotypic.abc_.GridFinder method) (phenotypic.abc_.GridMeasureFeatures method) (phenotypic.abc_.GridObjectDetector method) (phenotypic.abc_.GridObjectRefiner method) (phenotypic.abc_.GridOperation method) (phenotypic.abc_.ImageCorrector method) (phenotypic.abc_.ImageDenoiser method) (phenotypic.abc_.ImageEnhancer method) (phenotypic.abc_.ImageOperation method) (phenotypic.abc_.MeasureFeatures method) (phenotypic.abc_.MorphologicalFiltering method) (phenotypic.abc_.ObjectDetector method) (phenotypic.abc_.ObjectRefiner method) (phenotypic.abc_.PostMeasurement method) (phenotypic.abc_.PrefabPipeline method) (phenotypic.abc_.Smoothing method) (phenotypic.abc_.ThresholdDetector method) (phenotypic.correction.BayesShrinkCorrector method) (phenotypic.correction.ColorCorrector method) (phenotypic.correction.ColorDenoise method) (phenotypic.correction.DenoiseBlockMatch method) (phenotypic.correction.GridAligner method) (phenotypic.correction.ImageCropper method) (phenotypic.correction.ImagePadder method) (phenotypic.correction.VisuShrinkCorrector method) (phenotypic.detect.CannyDetector method) (phenotypic.detect.ChanVeseDetector method) (phenotypic.detect.CompositeDetector method) (phenotypic.detect.FilamentousFungiDetector method) (phenotypic.detect.HysteresisDetector method) (phenotypic.detect.InoculumDetector method) (phenotypic.detect.IsodataDetector method) (phenotypic.detect.LiDetector method) (phenotypic.detect.MadHysteresisDetector method) (phenotypic.detect.ManualGridPointDetector method) (phenotypic.detect.ManualPointDetector method) (phenotypic.detect.MeanDetector method) (phenotypic.detect.MinimumDetector method) (phenotypic.detect.OtsuDetector method) (phenotypic.detect.RankOtsuDetector method) (phenotypic.detect.RoundPeaksDetector method) (phenotypic.detect.SecondaryOtsuDetector method) (phenotypic.detect.SinePeakDetector method) (phenotypic.detect.TriangleDetector method) (phenotypic.detect.UserThreshold method) (phenotypic.detect.WatershedDetector method) (phenotypic.detect.YenDetector method) (phenotypic.enhance.BayesShrinkEnhancer method) (phenotypic.enhance.CompositeEnhance method) (phenotypic.enhance.ContrastStretching method) (phenotypic.enhance.EnhanceBlockMatch method) (phenotypic.enhance.EnhanceLocalContrast method) (phenotypic.enhance.FlattenIllumination method) (phenotypic.enhance.FocusBlobLoG method) (phenotypic.enhance.FocusEdgeFrangi method) (phenotypic.enhance.FocusEdgeHessian method) (phenotypic.enhance.FocusEdgeLaplace method) (phenotypic.enhance.FocusEdgeMeijering method) (phenotypic.enhance.FocusEdgePhase method) (phenotypic.enhance.FocusEdgeSato method) (phenotypic.enhance.FocusEdgeSobel method) (phenotypic.enhance.GaussianBlur method) (phenotypic.enhance.GrayOpening method) (phenotypic.enhance.ImageInverter method) (phenotypic.enhance.LocalEdgeDenoise method) (phenotypic.enhance.MedianFilter method) (phenotypic.enhance.NonLocalMeansDenoiser method) (phenotypic.enhance.RankMedianEnhancer method) (phenotypic.enhance.SetDetectMode method) (phenotypic.enhance.SharpenEdgeGauss method) (phenotypic.enhance.StructureSmoothing method) (phenotypic.enhance.SubtractGaussian method) (phenotypic.enhance.SubtractOpening method) (phenotypic.enhance.SubtractRollingBall method) (phenotypic.enhance.SubtractWhiteTophat method) (phenotypic.enhance.VisuShrinkEnhancer method) (phenotypic.enhance.WhiteTophatEnhance method) (phenotypic.grid.AutoGridFinder method) (phenotypic.grid.CenteredAutoGridFinder method) (phenotypic.grid.GridApply method) (phenotypic.grid.ManualGridFinder method) (phenotypic.measure.MeasureBounds method) (phenotypic.measure.MeasureColor method) (phenotypic.measure.MeasureGridLinRegStats method) (phenotypic.measure.MeasureGridSpread method) (phenotypic.measure.MeasureIntensity method) (phenotypic.measure.MeasureNeighborDist method) (phenotypic.measure.MeasureOrientationZones method) (phenotypic.measure.MeasureShape method) (phenotypic.measure.MeasureSize method) (phenotypic.measure.MeasureSymmetricZones method) (phenotypic.measure.MeasureTexture method) (phenotypic.prefab.FilamentousFungiPipeline method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.prefab.RoundPeaksPipeline method) (phenotypic.prefab.SpImagerPipeline method) (phenotypic.refine.ExtractColonyCore method) (phenotypic.refine.GridAlignmentRefiner method) (phenotypic.refine.GridOversizedObjectRemover method) (phenotypic.refine.KeepNearestCenter method) (phenotypic.refine.KeepSectionLargest method) (phenotypic.refine.ManualRefine method) (phenotypic.refine.MaskClosing method) (phenotypic.refine.MaskDilation method) (phenotypic.refine.MaskErosion method) (phenotypic.refine.MaskFill method) (phenotypic.refine.MaskGradient method) (phenotypic.refine.MaskOpening method) (phenotypic.refine.MaskWhiteTophat method) (phenotypic.refine.MergeFragmentChains method) (phenotypic.refine.NearestNeighborMerger method) (phenotypic.refine.ReduceSectionsByLine method) (phenotypic.refine.RefineBySineFit method) (phenotypic.refine.RemoveBorderObjects method) (phenotypic.refine.RemoveByFeature method) (phenotypic.refine.RemoveGridOutliers method) (phenotypic.refine.RemoveLowCircularity method) (phenotypic.refine.SeparateObjects method) (phenotypic.refine.Skeletonize method) (phenotypic.refine.SmallObjectRemover method) (phenotypic.refine.SmallToLargeMerger method) (phenotypic.refine.Thinning method) (phenotypic.refine.TrimAsymmetry method) __delitem__() (phenotypic._core._image_parts.accessors._metadata_accessor.MetadataAccessor method) __dir__() (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) __eq__() (phenotypic.Image method) __get_pydantic_json_schema__() (phenotypic.abc_.BackgroundSubtraction class method) (phenotypic.abc_.BaseOperation class method) (phenotypic.abc_.ContrastAdjustment class method) (phenotypic.abc_.FocusBlob class method) (phenotypic.abc_.FocusEdge class method) (phenotypic.abc_.GpuDetector class method) (phenotypic.abc_.GridCorrector class method) (phenotypic.abc_.GridFinder class method) (phenotypic.abc_.GridMeasureFeatures class method) (phenotypic.abc_.GridObjectDetector class method) (phenotypic.abc_.GridObjectRefiner class method) (phenotypic.abc_.GridOperation class method) (phenotypic.abc_.ImageCorrector class method) (phenotypic.abc_.ImageDenoiser class method) (phenotypic.abc_.ImageEnhancer class method) (phenotypic.abc_.ImageOperation class method) (phenotypic.abc_.MeasureFeatures class method) (phenotypic.abc_.MorphologicalFiltering class method) (phenotypic.abc_.ObjectDetector class method) (phenotypic.abc_.ObjectRefiner class method) (phenotypic.abc_.PostMeasurement class method) (phenotypic.abc_.PrefabPipeline class method) (phenotypic.abc_.Smoothing class method) (phenotypic.abc_.ThresholdDetector class method) (phenotypic.analysis.EdgeCorrector class method) (phenotypic.analysis.ErrorCutoffFinder class method) (phenotypic.analysis.ExpectedVsDetectedCount class method) (phenotypic.analysis.GridOccupancy class method) (phenotypic.analysis.ICC class method) (phenotypic.analysis.LinearCapAndLagModel class method) (phenotypic.analysis.LinearLagModel class method) (phenotypic.analysis.LogGrowthModel class method) (phenotypic.analysis.MADOutlierRemover class method) (phenotypic.analysis.MaxModifiedZScore class method) (phenotypic.analysis.RelativeMAD class method) (phenotypic.analysis.ReplicateAgreement class method) (phenotypic.analysis.TukeyOutlierFraction class method) (phenotypic.analysis.TukeyOutlierRemover class method) (phenotypic.correction.BayesShrinkCorrector class method) (phenotypic.correction.CaptureMetadata class method) (phenotypic.correction.ColorCheckerProfile class method) (phenotypic.correction.ColorCorrector class method) (phenotypic.correction.ColorDenoise class method) (phenotypic.correction.DenoiseBlockMatch class method) (phenotypic.correction.GridAligner class method) (phenotypic.correction.ImageCropper class method) (phenotypic.correction.ImagePadder class method) (phenotypic.correction.VisuShrinkCorrector class method) (phenotypic.detect.CannyDetector class method) (phenotypic.detect.ChanVeseDetector class method) (phenotypic.detect.CompositeDetector class method) (phenotypic.detect.FilamentousFungiDetector class method) (phenotypic.detect.HysteresisDetector class method) (phenotypic.detect.InoculumDetector class method) (phenotypic.detect.IsodataDetector class method) (phenotypic.detect.LiDetector class method) (phenotypic.detect.MadHysteresisDetector class method) (phenotypic.detect.ManualGridPointDetector class method) (phenotypic.detect.ManualPointDetector class method) (phenotypic.detect.MeanDetector class method) (phenotypic.detect.MinimumDetector class method) (phenotypic.detect.OtsuDetector class method) (phenotypic.detect.RankOtsuDetector class method) (phenotypic.detect.RoundPeaksDetector class method) (phenotypic.detect.SecondaryOtsuDetector class method) (phenotypic.detect.SinePeakDetector class method) (phenotypic.detect.TriangleDetector class method) (phenotypic.detect.UserThreshold class method) (phenotypic.detect.WatershedDetector class method) (phenotypic.detect.YenDetector class method) (phenotypic.enhance.BayesShrinkEnhancer class method) (phenotypic.enhance.CompositeEnhance class method) (phenotypic.enhance.ContrastStretching class method) (phenotypic.enhance.EnhanceBlockMatch class method) (phenotypic.enhance.EnhanceLocalContrast class method) (phenotypic.enhance.FlattenIllumination class method) (phenotypic.enhance.FocusBlobLoG class method) (phenotypic.enhance.FocusEdgeFrangi class method) (phenotypic.enhance.FocusEdgeHessian class method) (phenotypic.enhance.FocusEdgeLaplace class method) (phenotypic.enhance.FocusEdgeMeijering class method) (phenotypic.enhance.FocusEdgePhase class method) (phenotypic.enhance.FocusEdgeSato class method) (phenotypic.enhance.FocusEdgeSobel class method) (phenotypic.enhance.GaussianBlur class method) (phenotypic.enhance.GrayOpening class method) (phenotypic.enhance.ImageInverter class method) (phenotypic.enhance.LocalEdgeDenoise class method) (phenotypic.enhance.MedianFilter class method) (phenotypic.enhance.NonLocalMeansDenoiser class method) (phenotypic.enhance.RankMedianEnhancer class method) (phenotypic.enhance.SetDetectMode class method) (phenotypic.enhance.SharpenEdgeGauss class method) (phenotypic.enhance.StructureSmoothing class method) (phenotypic.enhance.SubtractGaussian class method) (phenotypic.enhance.SubtractOpening class method) (phenotypic.enhance.SubtractRollingBall class method) (phenotypic.enhance.SubtractWhiteTophat class method) (phenotypic.enhance.VisuShrinkEnhancer class method) (phenotypic.enhance.WhiteTophatEnhance class method) (phenotypic.grid.AutoGridFinder class method) (phenotypic.grid.CenteredAutoGridFinder class method) (phenotypic.grid.GridApply class method) (phenotypic.grid.ManualGridFinder class method) (phenotypic.measure.MeasureBounds class method) (phenotypic.measure.MeasureColor class method) (phenotypic.measure.MeasureGridLinRegStats class method) (phenotypic.measure.MeasureGridSpread class method) (phenotypic.measure.MeasureIntensity class method) (phenotypic.measure.MeasureNeighborDist class method) (phenotypic.measure.MeasureOrientationZones class method) (phenotypic.measure.MeasureShape class method) (phenotypic.measure.MeasureSize class method) (phenotypic.measure.MeasureSymmetricZones class method) (phenotypic.measure.MeasureTexture class method) (phenotypic.prefab.FilamentousFungiPipeline class method) (phenotypic.prefab.GridSectionPipeline class method) (phenotypic.prefab.HeavyOtsuPipeline class method) (phenotypic.prefab.HeavyRoundPeaksPipeline class method) (phenotypic.prefab.HeavyWatershedPipeline class method) (phenotypic.prefab.RoundPeaksPipeline class method) (phenotypic.prefab.SpImagerPipeline class method) (phenotypic.refine.ExtractColonyCore class method) (phenotypic.refine.GridAlignmentRefiner class method) (phenotypic.refine.GridOversizedObjectRemover class method) (phenotypic.refine.KeepNearestCenter class method) (phenotypic.refine.KeepSectionLargest class method) (phenotypic.refine.ManualRefine class method) (phenotypic.refine.MaskClosing class method) (phenotypic.refine.MaskDilation class method) (phenotypic.refine.MaskErosion class method) (phenotypic.refine.MaskFill class method) (phenotypic.refine.MaskGradient class method) (phenotypic.refine.MaskOpening class method) (phenotypic.refine.MaskWhiteTophat class method) (phenotypic.refine.MergeFragmentChains class method) (phenotypic.refine.NearestNeighborMerger class method) (phenotypic.refine.ReduceSectionsByLine class method) (phenotypic.refine.RefineBySineFit class method) (phenotypic.refine.RemoveBorderObjects class method) (phenotypic.refine.RemoveByFeature class method) (phenotypic.refine.RemoveGridOutliers class method) (phenotypic.refine.RemoveLowCircularity class method) (phenotypic.refine.SeparateObjects class method) (phenotypic.refine.Skeletonize class method) (phenotypic.refine.SmallObjectRemover class method) (phenotypic.refine.SmallToLargeMerger class method) (phenotypic.refine.Thinning class method) (phenotypic.refine.TrimAsymmetry class method) (phenotypic.tune.Budget class method) (phenotypic.tune.Categorical class method) (phenotypic.tune.EvaluationResult class method) (phenotypic.tune.Evaluator class method) (phenotypic.tune.Excluded class method) (phenotypic.tune.Fixed class method) (phenotypic.tune.FloatRange class method) (phenotypic.tune.HeldOutConfig class method) (phenotypic.tune.ImportanceReport class method) (phenotypic.tune.InferredSearchSpace class method) (phenotypic.tune.IntRange class method) (phenotypic.tune.Knob class method) (phenotypic.tune.score.CompositeScorer class method) (phenotypic.tune.score.GroundTruthMasks class method) (phenotypic.tune.score.QCScorer class method) (phenotypic.tune.score.ReferenceFreeScorer class method) (phenotypic.tune.score.Scorer class method) (phenotypic.tune.score.SupervisedScorer class method) (phenotypic.tune.SearchSpace class method) (phenotypic.tune.strategy.GridConfig class method) (phenotypic.tune.strategy.OptunaConfig class method) (phenotypic.tune.strategy.RandomConfig class method) (phenotypic.tune.strategy.StrategyConfig class method) (phenotypic.tune.Trial class method) (phenotypic.tune.TuningSpec class method) __getattr__() (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) (phenotypic.sdk_.constants_.IMAGE_TYPES class method) __getstate__() (phenotypic.sdk_.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) (phenotypic.abc_.BaseOperation method) (phenotypic.abc_.ContrastAdjustment method) (phenotypic.abc_.FocusBlob method) (phenotypic.abc_.FocusEdge method) (phenotypic.abc_.GpuDetector method) (phenotypic.abc_.GridCorrector method) (phenotypic.abc_.GridFinder method) (phenotypic.abc_.GridMeasureFeatures method) (phenotypic.abc_.GridObjectDetector method) (phenotypic.abc_.GridObjectRefiner method) (phenotypic.abc_.GridOperation method) (phenotypic.abc_.ImageCorrector method) (phenotypic.abc_.ImageDenoiser method) (phenotypic.abc_.ImageEnhancer method) (phenotypic.abc_.ImageOperation method) (phenotypic.abc_.MeasureFeatures method) (phenotypic.abc_.MorphologicalFiltering method) (phenotypic.abc_.ObjectDetector method) (phenotypic.abc_.ObjectRefiner method) (phenotypic.abc_.PostMeasurement method) (phenotypic.abc_.PrefabPipeline method) (phenotypic.abc_.Smoothing method) (phenotypic.abc_.ThresholdDetector method) (phenotypic.analysis.EdgeCorrector method) (phenotypic.analysis.ErrorCutoffFinder method) (phenotypic.analysis.ExpectedVsDetectedCount method) (phenotypic.analysis.GridOccupancy method) (phenotypic.analysis.ICC method) (phenotypic.analysis.LinearCapAndLagModel method) (phenotypic.analysis.LinearLagModel method) (phenotypic.analysis.LogGrowthModel method) (phenotypic.analysis.MADOutlierRemover method) (phenotypic.analysis.MaxModifiedZScore method) (phenotypic.analysis.RelativeMAD method) (phenotypic.analysis.ReplicateAgreement method) (phenotypic.analysis.TukeyOutlierFraction method) (phenotypic.analysis.TukeyOutlierRemover method) (phenotypic.correction.BayesShrinkCorrector method) (phenotypic.correction.CaptureMetadata method) (phenotypic.correction.ColorCheckerProfile method) (phenotypic.correction.ColorCorrector method) (phenotypic.correction.ColorDenoise method) (phenotypic.correction.DenoiseBlockMatch method) (phenotypic.correction.GridAligner method) (phenotypic.correction.ImageCropper method) (phenotypic.correction.ImagePadder method) (phenotypic.correction.VisuShrinkCorrector method) (phenotypic.detect.CannyDetector method) (phenotypic.detect.ChanVeseDetector method) (phenotypic.detect.CompositeDetector method) (phenotypic.detect.FilamentousFungiDetector method) (phenotypic.detect.HysteresisDetector method) (phenotypic.detect.InoculumDetector method) (phenotypic.detect.IsodataDetector method) (phenotypic.detect.LiDetector method) (phenotypic.detect.MadHysteresisDetector method) (phenotypic.detect.ManualGridPointDetector method) (phenotypic.detect.ManualPointDetector method) (phenotypic.detect.MeanDetector method) (phenotypic.detect.MinimumDetector method) (phenotypic.detect.OtsuDetector method) (phenotypic.detect.RankOtsuDetector method) (phenotypic.detect.RoundPeaksDetector method) (phenotypic.detect.SecondaryOtsuDetector method) (phenotypic.detect.SinePeakDetector method) (phenotypic.detect.TriangleDetector method) (phenotypic.detect.UserThreshold method) (phenotypic.detect.WatershedDetector method) (phenotypic.detect.YenDetector method) (phenotypic.enhance.BayesShrinkEnhancer method) (phenotypic.enhance.CompositeEnhance method) (phenotypic.enhance.ContrastStretching method) (phenotypic.enhance.EnhanceBlockMatch method) (phenotypic.enhance.EnhanceLocalContrast method) (phenotypic.enhance.FlattenIllumination method) (phenotypic.enhance.FocusBlobLoG method) (phenotypic.enhance.FocusEdgeFrangi method) (phenotypic.enhance.FocusEdgeHessian method) (phenotypic.enhance.FocusEdgeLaplace method) (phenotypic.enhance.FocusEdgeMeijering method) (phenotypic.enhance.FocusEdgePhase method) (phenotypic.enhance.FocusEdgeSato method) (phenotypic.enhance.FocusEdgeSobel method) (phenotypic.enhance.GaussianBlur method) (phenotypic.enhance.GrayOpening method) (phenotypic.enhance.ImageInverter method) (phenotypic.enhance.LocalEdgeDenoise method) (phenotypic.enhance.MedianFilter method) (phenotypic.enhance.NonLocalMeansDenoiser method) (phenotypic.enhance.RankMedianEnhancer method) (phenotypic.enhance.SetDetectMode method) (phenotypic.enhance.SharpenEdgeGauss method) (phenotypic.enhance.StructureSmoothing method) (phenotypic.enhance.SubtractGaussian method) (phenotypic.enhance.SubtractOpening method) (phenotypic.enhance.SubtractRollingBall method) (phenotypic.enhance.SubtractWhiteTophat method) (phenotypic.enhance.VisuShrinkEnhancer method) (phenotypic.enhance.WhiteTophatEnhance method) (phenotypic.grid.AutoGridFinder method) (phenotypic.grid.CenteredAutoGridFinder method) (phenotypic.grid.GridApply method) (phenotypic.grid.ManualGridFinder method) (phenotypic.GridImage method) (phenotypic.Image method) (phenotypic.ImagePipeline method) (phenotypic.measure.MeasureBounds method) (phenotypic.measure.MeasureColor method) (phenotypic.measure.MeasureGridLinRegStats method) (phenotypic.measure.MeasureGridSpread method) (phenotypic.measure.MeasureIntensity method) (phenotypic.measure.MeasureNeighborDist method) (phenotypic.measure.MeasureOrientationZones method) (phenotypic.measure.MeasureShape method) (phenotypic.measure.MeasureSize method) (phenotypic.measure.MeasureSymmetricZones method) (phenotypic.measure.MeasureTexture method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.refine.ExtractColonyCore method) (phenotypic.refine.GridAlignmentRefiner method) (phenotypic.refine.GridOversizedObjectRemover method) (phenotypic.refine.KeepNearestCenter method) (phenotypic.refine.KeepSectionLargest method) (phenotypic.refine.ManualRefine method) (phenotypic.refine.MaskClosing method) (phenotypic.refine.MaskDilation method) (phenotypic.refine.MaskErosion method) (phenotypic.refine.MaskFill method) (phenotypic.refine.MaskGradient method) (phenotypic.refine.MaskOpening method) (phenotypic.refine.MaskWhiteTophat method) (phenotypic.refine.MergeFragmentChains method) (phenotypic.refine.NearestNeighborMerger method) (phenotypic.refine.ReduceSectionsByLine method) (phenotypic.refine.RefineBySineFit method) (phenotypic.refine.RemoveBorderObjects method) (phenotypic.refine.RemoveByFeature method) (phenotypic.refine.RemoveGridOutliers method) (phenotypic.refine.RemoveLowCircularity method) (phenotypic.refine.SeparateObjects method) (phenotypic.refine.Skeletonize method) (phenotypic.refine.SmallObjectRemover method) (phenotypic.refine.SmallToLargeMerger method) (phenotypic.refine.Thinning method) (phenotypic.refine.TrimAsymmetry method) (phenotypic.sdk_.HDF method) (phenotypic.tune.Budget method) (phenotypic.tune.Categorical method) (phenotypic.tune.EvaluationResult method) (phenotypic.tune.Evaluator method) (phenotypic.tune.Excluded method) (phenotypic.tune.Fixed method) (phenotypic.tune.FloatRange method) (phenotypic.tune.HeldOutConfig method) (phenotypic.tune.ImportanceReport method) (phenotypic.tune.InferredSearchSpace method) (phenotypic.tune.IntRange method) (phenotypic.tune.JournalStudyStore method) (phenotypic.tune.Knob method) (phenotypic.tune.score.CompositeScorer method) (phenotypic.tune.score.GroundTruthMasks method) (phenotypic.tune.score.QCScorer method) (phenotypic.tune.score.ReferenceFreeScorer method) (phenotypic.tune.score.Scorer method) (phenotypic.tune.score.SupervisedScorer method) (phenotypic.tune.SearchSpace method) (phenotypic.tune.strategy.GridConfig method) (phenotypic.tune.strategy.OptunaConfig method) (phenotypic.tune.strategy.RandomConfig method) (phenotypic.tune.strategy.StrategyConfig method) (phenotypic.tune.Trial method) (phenotypic.tune.TuningEngine method) (phenotypic.tune.TuningSpec method) __init_subclass__() (phenotypic.analysis.ExpectedVsDetectedCount class method) (phenotypic.analysis.GridOccupancy class method) (phenotypic.analysis.ICC class method) (phenotypic.analysis.MaxModifiedZScore class method) (phenotypic.analysis.RelativeMAD class method) (phenotypic.analysis.ReplicateAgreement class method) (phenotypic.analysis.TukeyOutlierFraction class method) __invert__() (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask method) __ior__() (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask method) __iter__() (phenotypic._core._image_parts.accessors._objects_accessor.ObjectsAccessor method) (phenotypic.abc_.BackgroundSubtraction method) (phenotypic.abc_.BaseOperation method) (phenotypic.abc_.ContrastAdjustment method) (phenotypic.abc_.FocusBlob method) (phenotypic.abc_.FocusEdge method) (phenotypic.abc_.GpuDetector method) (phenotypic.abc_.GridCorrector method) (phenotypic.abc_.GridFinder method) (phenotypic.abc_.GridMeasureFeatures method) (phenotypic.abc_.GridObjectDetector method) (phenotypic.abc_.GridObjectRefiner method) (phenotypic.abc_.GridOperation method) (phenotypic.abc_.ImageCorrector method) (phenotypic.abc_.ImageDenoiser method) (phenotypic.abc_.ImageEnhancer method) (phenotypic.abc_.ImageOperation method) (phenotypic.abc_.MeasureFeatures method) (phenotypic.abc_.MorphologicalFiltering method) (phenotypic.abc_.ObjectDetector method) (phenotypic.abc_.ObjectRefiner method) (phenotypic.abc_.PostMeasurement method) (phenotypic.abc_.PrefabPipeline method) (phenotypic.abc_.Smoothing method) (phenotypic.abc_.ThresholdDetector method) (phenotypic.analysis.EdgeCorrector method) (phenotypic.analysis.ErrorCutoffFinder method) (phenotypic.analysis.ExpectedVsDetectedCount method) (phenotypic.analysis.GridOccupancy method) (phenotypic.analysis.ICC method) (phenotypic.analysis.LinearCapAndLagModel method) (phenotypic.analysis.LinearLagModel method) (phenotypic.analysis.LogGrowthModel method) (phenotypic.analysis.MADOutlierRemover method) (phenotypic.analysis.MaxModifiedZScore method) (phenotypic.analysis.RelativeMAD method) (phenotypic.analysis.ReplicateAgreement method) (phenotypic.analysis.TukeyOutlierFraction method) (phenotypic.analysis.TukeyOutlierRemover method) (phenotypic.correction.BayesShrinkCorrector method) (phenotypic.correction.CaptureMetadata method) (phenotypic.correction.ColorCheckerProfile method) (phenotypic.correction.ColorCorrector method) (phenotypic.correction.ColorDenoise method) (phenotypic.correction.DenoiseBlockMatch method) (phenotypic.correction.GridAligner method) (phenotypic.correction.ImageCropper method) (phenotypic.correction.ImagePadder method) (phenotypic.correction.VisuShrinkCorrector method) (phenotypic.detect.CannyDetector method) (phenotypic.detect.ChanVeseDetector method) (phenotypic.detect.CompositeDetector method) (phenotypic.detect.FilamentousFungiDetector method) (phenotypic.detect.HysteresisDetector method) (phenotypic.detect.InoculumDetector method) (phenotypic.detect.IsodataDetector method) (phenotypic.detect.LiDetector method) (phenotypic.detect.MadHysteresisDetector method) (phenotypic.detect.ManualGridPointDetector method) (phenotypic.detect.ManualPointDetector method) (phenotypic.detect.MeanDetector method) (phenotypic.detect.MinimumDetector method) (phenotypic.detect.OtsuDetector method) (phenotypic.detect.RankOtsuDetector method) (phenotypic.detect.RoundPeaksDetector method) (phenotypic.detect.SecondaryOtsuDetector method) (phenotypic.detect.SinePeakDetector method) (phenotypic.detect.TriangleDetector method) (phenotypic.detect.UserThreshold method) (phenotypic.detect.WatershedDetector method) (phenotypic.detect.YenDetector method) (phenotypic.enhance.BayesShrinkEnhancer method) (phenotypic.enhance.CompositeEnhance method) (phenotypic.enhance.ContrastStretching method) (phenotypic.enhance.EnhanceBlockMatch method) (phenotypic.enhance.EnhanceLocalContrast method) (phenotypic.enhance.FlattenIllumination method) (phenotypic.enhance.FocusBlobLoG method) (phenotypic.enhance.FocusEdgeFrangi method) (phenotypic.enhance.FocusEdgeHessian method) (phenotypic.enhance.FocusEdgeLaplace method) (phenotypic.enhance.FocusEdgeMeijering method) (phenotypic.enhance.FocusEdgePhase method) (phenotypic.enhance.FocusEdgeSato method) (phenotypic.enhance.FocusEdgeSobel method) (phenotypic.enhance.GaussianBlur method) (phenotypic.enhance.GrayOpening method) (phenotypic.enhance.ImageInverter method) (phenotypic.enhance.LocalEdgeDenoise method) (phenotypic.enhance.MedianFilter method) (phenotypic.enhance.NonLocalMeansDenoiser method) (phenotypic.enhance.RankMedianEnhancer method) (phenotypic.enhance.SetDetectMode method) (phenotypic.enhance.SharpenEdgeGauss method) (phenotypic.enhance.StructureSmoothing method) (phenotypic.enhance.SubtractGaussian method) (phenotypic.enhance.SubtractOpening method) (phenotypic.enhance.SubtractRollingBall method) (phenotypic.enhance.SubtractWhiteTophat method) (phenotypic.enhance.VisuShrinkEnhancer method) (phenotypic.enhance.WhiteTophatEnhance method) (phenotypic.grid.AutoGridFinder method) (phenotypic.grid.CenteredAutoGridFinder method) (phenotypic.grid.GridApply method) (phenotypic.grid.ManualGridFinder method) (phenotypic.measure.MeasureBounds method) (phenotypic.measure.MeasureColor method) (phenotypic.measure.MeasureGridLinRegStats method) (phenotypic.measure.MeasureGridSpread method) (phenotypic.measure.MeasureIntensity method) (phenotypic.measure.MeasureNeighborDist method) (phenotypic.measure.MeasureOrientationZones method) (phenotypic.measure.MeasureShape method) (phenotypic.measure.MeasureSize method) (phenotypic.measure.MeasureSymmetricZones method) (phenotypic.measure.MeasureTexture method) (phenotypic.prefab.FilamentousFungiPipeline method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.prefab.RoundPeaksPipeline method) (phenotypic.prefab.SpImagerPipeline method) (phenotypic.refine.ExtractColonyCore method) (phenotypic.refine.GridAlignmentRefiner method) (phenotypic.refine.GridOversizedObjectRemover method) (phenotypic.refine.KeepNearestCenter method) (phenotypic.refine.KeepSectionLargest method) (phenotypic.refine.ManualRefine method) (phenotypic.refine.MaskClosing method) (phenotypic.refine.MaskDilation method) (phenotypic.refine.MaskErosion method) (phenotypic.refine.MaskFill method) (phenotypic.refine.MaskGradient method) (phenotypic.refine.MaskOpening method) (phenotypic.refine.MaskWhiteTophat method) (phenotypic.refine.MergeFragmentChains method) (phenotypic.refine.NearestNeighborMerger method) (phenotypic.refine.ReduceSectionsByLine method) (phenotypic.refine.RefineBySineFit method) (phenotypic.refine.RemoveBorderObjects method) (phenotypic.refine.RemoveByFeature method) (phenotypic.refine.RemoveGridOutliers method) (phenotypic.refine.RemoveLowCircularity method) (phenotypic.refine.SeparateObjects method) (phenotypic.refine.Skeletonize method) (phenotypic.refine.SmallObjectRemover method) (phenotypic.refine.SmallToLargeMerger method) (phenotypic.refine.Thinning method) (phenotypic.refine.TrimAsymmetry method) (phenotypic.sdk_.constants_.IMAGE_MODE class method) (phenotypic.sdk_.constants_.IMAGE_TYPES class method) (phenotypic.tune.Budget method) (phenotypic.tune.Categorical method) (phenotypic.tune.EvaluationResult method) (phenotypic.tune.Evaluator method) (phenotypic.tune.Excluded method) (phenotypic.tune.Fixed method) (phenotypic.tune.FloatRange method) (phenotypic.tune.HeldOutConfig method) (phenotypic.tune.ImportanceReport method) (phenotypic.tune.InferredSearchSpace method) (phenotypic.tune.IntRange method) (phenotypic.tune.Knob method) (phenotypic.tune.score.CompositeScorer method) (phenotypic.tune.score.GroundTruthMasks method) (phenotypic.tune.score.QCScorer method) (phenotypic.tune.score.ReferenceFreeScorer method) (phenotypic.tune.score.Scorer method) (phenotypic.tune.score.SupervisedScorer method) (phenotypic.tune.strategy.GridConfig method) (phenotypic.tune.strategy.OptunaConfig method) (phenotypic.tune.strategy.RandomConfig method) (phenotypic.tune.strategy.StrategyConfig method) (phenotypic.tune.Trial method) (phenotypic.tune.TuningSpec method) __ixor__() (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask method) __len__() (phenotypic._core._image_parts.accessors._detect_mat_accessor.DetectMatAccessor method) (phenotypic._core._image_parts.accessors._grayscale_accessor.Grayscale 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._plot_accessor.PlotAccessor method) (phenotypic._core._image_parts.accessors._rgb_accessor.ImageRGB method) (phenotypic.sdk_.constants_.IMAGE_MODE class method) (phenotypic.sdk_.constants_.IMAGE_TYPES class method) __new_member__() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) __or__() (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask method) __pretty__() (phenotypic.abc_.BackgroundSubtraction method) (phenotypic.abc_.BaseOperation method) (phenotypic.abc_.ContrastAdjustment method) (phenotypic.abc_.FocusBlob method) (phenotypic.abc_.FocusEdge method) (phenotypic.abc_.GpuDetector method) (phenotypic.abc_.GridCorrector method) (phenotypic.abc_.GridFinder method) (phenotypic.abc_.GridMeasureFeatures method) (phenotypic.abc_.GridObjectDetector method) (phenotypic.abc_.GridObjectRefiner method) (phenotypic.abc_.GridOperation method) (phenotypic.abc_.ImageCorrector method) (phenotypic.abc_.ImageDenoiser method) (phenotypic.abc_.ImageEnhancer method) (phenotypic.abc_.ImageOperation method) (phenotypic.abc_.MeasureFeatures method) (phenotypic.abc_.MorphologicalFiltering method) (phenotypic.abc_.ObjectDetector method) (phenotypic.abc_.ObjectRefiner method) (phenotypic.abc_.PostMeasurement method) (phenotypic.abc_.PrefabPipeline method) (phenotypic.abc_.Smoothing method) (phenotypic.abc_.ThresholdDetector method) (phenotypic.analysis.EdgeCorrector method) (phenotypic.analysis.ErrorCutoffFinder method) (phenotypic.analysis.ExpectedVsDetectedCount method) (phenotypic.analysis.GridOccupancy method) (phenotypic.analysis.ICC method) (phenotypic.analysis.LinearCapAndLagModel method) (phenotypic.analysis.LinearLagModel method) (phenotypic.analysis.LogGrowthModel method) (phenotypic.analysis.MADOutlierRemover method) (phenotypic.analysis.MaxModifiedZScore method) (phenotypic.analysis.RelativeMAD method) (phenotypic.analysis.ReplicateAgreement method) (phenotypic.analysis.TukeyOutlierFraction method) (phenotypic.analysis.TukeyOutlierRemover method) (phenotypic.correction.BayesShrinkCorrector method) (phenotypic.correction.CaptureMetadata method) (phenotypic.correction.ColorCheckerProfile method) (phenotypic.correction.ColorCorrector method) (phenotypic.correction.ColorDenoise method) (phenotypic.correction.DenoiseBlockMatch method) (phenotypic.correction.GridAligner method) (phenotypic.correction.ImageCropper method) (phenotypic.correction.ImagePadder method) (phenotypic.correction.VisuShrinkCorrector method) (phenotypic.detect.CannyDetector method) (phenotypic.detect.ChanVeseDetector method) (phenotypic.detect.CompositeDetector method) (phenotypic.detect.FilamentousFungiDetector method) (phenotypic.detect.HysteresisDetector method) (phenotypic.detect.InoculumDetector method) (phenotypic.detect.IsodataDetector method) (phenotypic.detect.LiDetector method) (phenotypic.detect.MadHysteresisDetector method) (phenotypic.detect.ManualGridPointDetector method) (phenotypic.detect.ManualPointDetector method) (phenotypic.detect.MeanDetector method) (phenotypic.detect.MinimumDetector method) (phenotypic.detect.OtsuDetector method) (phenotypic.detect.RankOtsuDetector method) (phenotypic.detect.RoundPeaksDetector method) (phenotypic.detect.SecondaryOtsuDetector method) (phenotypic.detect.SinePeakDetector method) (phenotypic.detect.TriangleDetector method) (phenotypic.detect.UserThreshold method) (phenotypic.detect.WatershedDetector method) (phenotypic.detect.YenDetector method) (phenotypic.enhance.BayesShrinkEnhancer method) (phenotypic.enhance.CompositeEnhance method) (phenotypic.enhance.ContrastStretching method) (phenotypic.enhance.EnhanceBlockMatch method) (phenotypic.enhance.EnhanceLocalContrast method) (phenotypic.enhance.FlattenIllumination method) (phenotypic.enhance.FocusBlobLoG method) (phenotypic.enhance.FocusEdgeFrangi method) (phenotypic.enhance.FocusEdgeHessian method) (phenotypic.enhance.FocusEdgeLaplace method) (phenotypic.enhance.FocusEdgeMeijering method) (phenotypic.enhance.FocusEdgePhase method) (phenotypic.enhance.FocusEdgeSato method) (phenotypic.enhance.FocusEdgeSobel method) (phenotypic.enhance.GaussianBlur method) (phenotypic.enhance.GrayOpening method) (phenotypic.enhance.ImageInverter method) (phenotypic.enhance.LocalEdgeDenoise method) (phenotypic.enhance.MedianFilter method) (phenotypic.enhance.NonLocalMeansDenoiser method) (phenotypic.enhance.RankMedianEnhancer method) (phenotypic.enhance.SetDetectMode method) (phenotypic.enhance.SharpenEdgeGauss method) (phenotypic.enhance.StructureSmoothing method) (phenotypic.enhance.SubtractGaussian method) (phenotypic.enhance.SubtractOpening method) (phenotypic.enhance.SubtractRollingBall method) (phenotypic.enhance.SubtractWhiteTophat method) (phenotypic.enhance.VisuShrinkEnhancer method) (phenotypic.enhance.WhiteTophatEnhance method) (phenotypic.grid.AutoGridFinder method) (phenotypic.grid.CenteredAutoGridFinder method) (phenotypic.grid.GridApply method) (phenotypic.grid.ManualGridFinder method) (phenotypic.measure.MeasureBounds method) (phenotypic.measure.MeasureColor method) (phenotypic.measure.MeasureGridLinRegStats method) (phenotypic.measure.MeasureGridSpread method) (phenotypic.measure.MeasureIntensity method) (phenotypic.measure.MeasureNeighborDist method) (phenotypic.measure.MeasureOrientationZones method) (phenotypic.measure.MeasureShape method) (phenotypic.measure.MeasureSize method) (phenotypic.measure.MeasureSymmetricZones method) (phenotypic.measure.MeasureTexture method) (phenotypic.prefab.FilamentousFungiPipeline method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.prefab.RoundPeaksPipeline method) (phenotypic.prefab.SpImagerPipeline method) (phenotypic.refine.ExtractColonyCore method) (phenotypic.refine.GridAlignmentRefiner method) (phenotypic.refine.GridOversizedObjectRemover method) (phenotypic.refine.KeepNearestCenter method) (phenotypic.refine.KeepSectionLargest method) (phenotypic.refine.ManualRefine method) (phenotypic.refine.MaskClosing method) (phenotypic.refine.MaskDilation method) (phenotypic.refine.MaskErosion method) (phenotypic.refine.MaskFill method) (phenotypic.refine.MaskGradient method) (phenotypic.refine.MaskOpening method) (phenotypic.refine.MaskWhiteTophat method) (phenotypic.refine.MergeFragmentChains method) (phenotypic.refine.NearestNeighborMerger method) (phenotypic.refine.ReduceSectionsByLine method) (phenotypic.refine.RefineBySineFit method) (phenotypic.refine.RemoveBorderObjects method) (phenotypic.refine.RemoveByFeature method) (phenotypic.refine.RemoveGridOutliers method) (phenotypic.refine.RemoveLowCircularity method) (phenotypic.refine.SeparateObjects method) (phenotypic.refine.Skeletonize method) (phenotypic.refine.SmallObjectRemover method) (phenotypic.refine.SmallToLargeMerger method) (phenotypic.refine.Thinning method) (phenotypic.refine.TrimAsymmetry method) (phenotypic.tune.Budget method) (phenotypic.tune.Categorical method) (phenotypic.tune.EvaluationResult method) (phenotypic.tune.Evaluator method) (phenotypic.tune.Excluded method) (phenotypic.tune.Fixed method) (phenotypic.tune.FloatRange method) (phenotypic.tune.HeldOutConfig method) (phenotypic.tune.ImportanceReport method) (phenotypic.tune.InferredSearchSpace method) (phenotypic.tune.IntRange method) (phenotypic.tune.Knob method) (phenotypic.tune.score.CompositeScorer method) (phenotypic.tune.score.GroundTruthMasks method) (phenotypic.tune.score.QCScorer method) (phenotypic.tune.score.ReferenceFreeScorer method) (phenotypic.tune.score.Scorer method) (phenotypic.tune.score.SupervisedScorer method) (phenotypic.tune.SearchSpace method) (phenotypic.tune.strategy.GridConfig method) (phenotypic.tune.strategy.OptunaConfig method) (phenotypic.tune.strategy.RandomConfig method) (phenotypic.tune.strategy.StrategyConfig method) (phenotypic.tune.Trial method) (phenotypic.tune.TuningSpec method) __pydantic_init_subclass__() (phenotypic.abc_.BackgroundSubtraction class method) (phenotypic.abc_.BaseOperation class method) (phenotypic.abc_.ContrastAdjustment class method) (phenotypic.abc_.FocusBlob class method) (phenotypic.abc_.FocusEdge class method) (phenotypic.abc_.GpuDetector class method) (phenotypic.abc_.GridCorrector class method) (phenotypic.abc_.GridFinder class method) (phenotypic.abc_.GridMeasureFeatures class method) (phenotypic.abc_.GridObjectDetector class method) (phenotypic.abc_.GridObjectRefiner class method) (phenotypic.abc_.GridOperation class method) (phenotypic.abc_.ImageCorrector class method) (phenotypic.abc_.ImageDenoiser class method) (phenotypic.abc_.ImageEnhancer class method) (phenotypic.abc_.ImageOperation class method) (phenotypic.abc_.MeasureFeatures class method) (phenotypic.abc_.MorphologicalFiltering class method) (phenotypic.abc_.ObjectDetector class method) (phenotypic.abc_.ObjectRefiner class method) (phenotypic.abc_.PostMeasurement class method) (phenotypic.abc_.PrefabPipeline class method) (phenotypic.abc_.Smoothing class method) (phenotypic.abc_.ThresholdDetector class method) (phenotypic.analysis.EdgeCorrector class method) (phenotypic.analysis.ErrorCutoffFinder class method) (phenotypic.analysis.ExpectedVsDetectedCount class method) (phenotypic.analysis.GridOccupancy class method) (phenotypic.analysis.ICC class method) (phenotypic.analysis.LinearCapAndLagModel class method) (phenotypic.analysis.LinearLagModel class method) (phenotypic.analysis.LogGrowthModel class method) (phenotypic.analysis.MADOutlierRemover class method) (phenotypic.analysis.MaxModifiedZScore class method) (phenotypic.analysis.RelativeMAD class method) (phenotypic.analysis.ReplicateAgreement class method) (phenotypic.analysis.TukeyOutlierFraction class method) (phenotypic.analysis.TukeyOutlierRemover class method) (phenotypic.correction.BayesShrinkCorrector class method) (phenotypic.correction.CaptureMetadata class method) (phenotypic.correction.ColorCheckerProfile class method) (phenotypic.correction.ColorCorrector class method) (phenotypic.correction.ColorDenoise class method) (phenotypic.correction.DenoiseBlockMatch class method) (phenotypic.correction.GridAligner class method) (phenotypic.correction.ImageCropper class method) (phenotypic.correction.ImagePadder class method) (phenotypic.correction.VisuShrinkCorrector class method) (phenotypic.detect.CannyDetector class method) (phenotypic.detect.ChanVeseDetector class method) (phenotypic.detect.CompositeDetector class method) (phenotypic.detect.FilamentousFungiDetector class method) (phenotypic.detect.HysteresisDetector class method) (phenotypic.detect.InoculumDetector class method) (phenotypic.detect.IsodataDetector class method) (phenotypic.detect.LiDetector class method) (phenotypic.detect.MadHysteresisDetector class method) (phenotypic.detect.ManualGridPointDetector class method) (phenotypic.detect.ManualPointDetector class method) (phenotypic.detect.MeanDetector class method) (phenotypic.detect.MinimumDetector class method) (phenotypic.detect.OtsuDetector class method) (phenotypic.detect.RankOtsuDetector class method) (phenotypic.detect.RoundPeaksDetector class method) (phenotypic.detect.SecondaryOtsuDetector class method) (phenotypic.detect.SinePeakDetector class method) (phenotypic.detect.TriangleDetector class method) (phenotypic.detect.UserThreshold class method) (phenotypic.detect.WatershedDetector class method) (phenotypic.detect.YenDetector class method) (phenotypic.enhance.BayesShrinkEnhancer class method) (phenotypic.enhance.CompositeEnhance class method) (phenotypic.enhance.ContrastStretching class method) (phenotypic.enhance.EnhanceBlockMatch class method) (phenotypic.enhance.EnhanceLocalContrast class method) (phenotypic.enhance.FlattenIllumination class method) (phenotypic.enhance.FocusBlobLoG class method) (phenotypic.enhance.FocusEdgeFrangi class method) (phenotypic.enhance.FocusEdgeHessian class method) (phenotypic.enhance.FocusEdgeLaplace class method) (phenotypic.enhance.FocusEdgeMeijering class method) (phenotypic.enhance.FocusEdgePhase class method) (phenotypic.enhance.FocusEdgeSato class method) (phenotypic.enhance.FocusEdgeSobel class method) (phenotypic.enhance.GaussianBlur class method) (phenotypic.enhance.GrayOpening class method) (phenotypic.enhance.ImageInverter class method) (phenotypic.enhance.LocalEdgeDenoise class method) (phenotypic.enhance.MedianFilter class method) (phenotypic.enhance.NonLocalMeansDenoiser class method) (phenotypic.enhance.RankMedianEnhancer class method) (phenotypic.enhance.SetDetectMode class method) (phenotypic.enhance.SharpenEdgeGauss class method) (phenotypic.enhance.StructureSmoothing class method) (phenotypic.enhance.SubtractGaussian class method) (phenotypic.enhance.SubtractOpening class method) (phenotypic.enhance.SubtractRollingBall class method) (phenotypic.enhance.SubtractWhiteTophat class method) (phenotypic.enhance.VisuShrinkEnhancer class method) (phenotypic.enhance.WhiteTophatEnhance class method) (phenotypic.grid.AutoGridFinder class method) (phenotypic.grid.CenteredAutoGridFinder class method) (phenotypic.grid.GridApply class method) (phenotypic.grid.ManualGridFinder class method) (phenotypic.measure.MeasureBounds class method) (phenotypic.measure.MeasureColor class method) (phenotypic.measure.MeasureGridLinRegStats class method) (phenotypic.measure.MeasureGridSpread class method) (phenotypic.measure.MeasureIntensity class method) (phenotypic.measure.MeasureNeighborDist class method) (phenotypic.measure.MeasureOrientationZones class method) (phenotypic.measure.MeasureShape class method) (phenotypic.measure.MeasureSize class method) (phenotypic.measure.MeasureSymmetricZones class method) (phenotypic.measure.MeasureTexture class method) (phenotypic.prefab.FilamentousFungiPipeline class method) (phenotypic.prefab.GridSectionPipeline class method) (phenotypic.prefab.HeavyOtsuPipeline class method) (phenotypic.prefab.HeavyRoundPeaksPipeline class method) (phenotypic.prefab.HeavyWatershedPipeline class method) (phenotypic.prefab.RoundPeaksPipeline class method) (phenotypic.prefab.SpImagerPipeline class method) (phenotypic.refine.ExtractColonyCore class method) (phenotypic.refine.GridAlignmentRefiner class method) (phenotypic.refine.GridOversizedObjectRemover class method) (phenotypic.refine.KeepNearestCenter class method) (phenotypic.refine.KeepSectionLargest class method) (phenotypic.refine.ManualRefine class method) (phenotypic.refine.MaskClosing class method) (phenotypic.refine.MaskDilation class method) (phenotypic.refine.MaskErosion class method) (phenotypic.refine.MaskFill class method) (phenotypic.refine.MaskGradient class method) (phenotypic.refine.MaskOpening class method) (phenotypic.refine.MaskWhiteTophat class method) (phenotypic.refine.MergeFragmentChains class method) (phenotypic.refine.NearestNeighborMerger class method) (phenotypic.refine.ReduceSectionsByLine class method) (phenotypic.refine.RefineBySineFit class method) (phenotypic.refine.RemoveBorderObjects class method) (phenotypic.refine.RemoveByFeature class method) (phenotypic.refine.RemoveGridOutliers class method) (phenotypic.refine.RemoveLowCircularity class method) (phenotypic.refine.SeparateObjects class method) (phenotypic.refine.Skeletonize class method) (phenotypic.refine.SmallObjectRemover class method) (phenotypic.refine.SmallToLargeMerger class method) (phenotypic.refine.Thinning class method) (phenotypic.refine.TrimAsymmetry class method) (phenotypic.tune.Budget class method) (phenotypic.tune.Categorical class method) (phenotypic.tune.EvaluationResult class method) (phenotypic.tune.Evaluator class method) (phenotypic.tune.Excluded class method) (phenotypic.tune.Fixed class method) (phenotypic.tune.FloatRange class method) (phenotypic.tune.HeldOutConfig class method) (phenotypic.tune.ImportanceReport class method) (phenotypic.tune.InferredSearchSpace class method) (phenotypic.tune.IntRange class method) (phenotypic.tune.Knob class method) (phenotypic.tune.score.CompositeScorer class method) (phenotypic.tune.score.GroundTruthMasks class method) (phenotypic.tune.score.QCScorer class method) (phenotypic.tune.score.ReferenceFreeScorer class method) (phenotypic.tune.score.Scorer class method) (phenotypic.tune.score.SupervisedScorer class method) (phenotypic.tune.SearchSpace class method) (phenotypic.tune.strategy.GridConfig class method) (phenotypic.tune.strategy.OptunaConfig class method) (phenotypic.tune.strategy.RandomConfig class method) (phenotypic.tune.strategy.StrategyConfig class method) (phenotypic.tune.Trial class method) (phenotypic.tune.TuningSpec class method) __pydantic_on_complete__() (phenotypic.abc_.BackgroundSubtraction class method) (phenotypic.abc_.BaseOperation class method) (phenotypic.abc_.ContrastAdjustment class method) (phenotypic.abc_.FocusBlob class method) (phenotypic.abc_.FocusEdge class method) (phenotypic.abc_.GpuDetector class method) (phenotypic.abc_.GridCorrector class method) (phenotypic.abc_.GridFinder class method) (phenotypic.abc_.GridMeasureFeatures class method) (phenotypic.abc_.GridObjectDetector class method) (phenotypic.abc_.GridObjectRefiner class method) (phenotypic.abc_.GridOperation class method) (phenotypic.abc_.ImageCorrector class method) (phenotypic.abc_.ImageDenoiser class method) (phenotypic.abc_.ImageEnhancer class method) (phenotypic.abc_.ImageOperation class method) (phenotypic.abc_.MeasureFeatures class method) (phenotypic.abc_.MorphologicalFiltering class method) (phenotypic.abc_.ObjectDetector class method) (phenotypic.abc_.ObjectRefiner class method) (phenotypic.abc_.PostMeasurement class method) (phenotypic.abc_.PrefabPipeline class method) (phenotypic.abc_.Smoothing class method) (phenotypic.abc_.ThresholdDetector class method) (phenotypic.analysis.EdgeCorrector class method) (phenotypic.analysis.ErrorCutoffFinder class method) (phenotypic.analysis.ExpectedVsDetectedCount class method) (phenotypic.analysis.GridOccupancy class method) (phenotypic.analysis.ICC class method) (phenotypic.analysis.LinearCapAndLagModel class method) (phenotypic.analysis.LinearLagModel class method) (phenotypic.analysis.LogGrowthModel class method) (phenotypic.analysis.MADOutlierRemover class method) (phenotypic.analysis.MaxModifiedZScore class method) (phenotypic.analysis.RelativeMAD class method) (phenotypic.analysis.ReplicateAgreement class method) (phenotypic.analysis.TukeyOutlierFraction class method) (phenotypic.analysis.TukeyOutlierRemover class method) (phenotypic.correction.BayesShrinkCorrector class method) (phenotypic.correction.CaptureMetadata class method) (phenotypic.correction.ColorCheckerProfile class method) (phenotypic.correction.ColorCorrector class method) (phenotypic.correction.ColorDenoise class method) (phenotypic.correction.DenoiseBlockMatch class method) (phenotypic.correction.GridAligner class method) (phenotypic.correction.ImageCropper class method) (phenotypic.correction.ImagePadder class method) (phenotypic.correction.VisuShrinkCorrector class method) (phenotypic.detect.CannyDetector class method) (phenotypic.detect.ChanVeseDetector class method) (phenotypic.detect.CompositeDetector class method) (phenotypic.detect.FilamentousFungiDetector class method) (phenotypic.detect.HysteresisDetector class method) (phenotypic.detect.InoculumDetector class method) (phenotypic.detect.IsodataDetector class method) (phenotypic.detect.LiDetector class method) (phenotypic.detect.MadHysteresisDetector class method) (phenotypic.detect.ManualGridPointDetector class method) (phenotypic.detect.ManualPointDetector class method) (phenotypic.detect.MeanDetector class method) (phenotypic.detect.MinimumDetector class method) (phenotypic.detect.OtsuDetector class method) (phenotypic.detect.RankOtsuDetector class method) (phenotypic.detect.RoundPeaksDetector class method) (phenotypic.detect.SecondaryOtsuDetector class method) (phenotypic.detect.SinePeakDetector class method) (phenotypic.detect.TriangleDetector class method) (phenotypic.detect.UserThreshold class method) (phenotypic.detect.WatershedDetector class method) (phenotypic.detect.YenDetector class method) (phenotypic.enhance.BayesShrinkEnhancer class method) (phenotypic.enhance.CompositeEnhance class method) (phenotypic.enhance.ContrastStretching class method) (phenotypic.enhance.EnhanceBlockMatch class method) (phenotypic.enhance.EnhanceLocalContrast class method) (phenotypic.enhance.FlattenIllumination class method) (phenotypic.enhance.FocusBlobLoG class method) (phenotypic.enhance.FocusEdgeFrangi class method) (phenotypic.enhance.FocusEdgeHessian class method) (phenotypic.enhance.FocusEdgeLaplace class method) (phenotypic.enhance.FocusEdgeMeijering class method) (phenotypic.enhance.FocusEdgePhase class method) (phenotypic.enhance.FocusEdgeSato class method) (phenotypic.enhance.FocusEdgeSobel class method) (phenotypic.enhance.GaussianBlur class method) (phenotypic.enhance.GrayOpening class method) (phenotypic.enhance.ImageInverter class method) (phenotypic.enhance.LocalEdgeDenoise class method) (phenotypic.enhance.MedianFilter class method) (phenotypic.enhance.NonLocalMeansDenoiser class method) (phenotypic.enhance.RankMedianEnhancer class method) (phenotypic.enhance.SetDetectMode class method) (phenotypic.enhance.SharpenEdgeGauss class method) (phenotypic.enhance.StructureSmoothing class method) (phenotypic.enhance.SubtractGaussian class method) (phenotypic.enhance.SubtractOpening class method) (phenotypic.enhance.SubtractRollingBall class method) (phenotypic.enhance.SubtractWhiteTophat class method) (phenotypic.enhance.VisuShrinkEnhancer class method) (phenotypic.enhance.WhiteTophatEnhance class method) (phenotypic.grid.AutoGridFinder class method) (phenotypic.grid.CenteredAutoGridFinder class method) (phenotypic.grid.GridApply class method) (phenotypic.grid.ManualGridFinder class method) (phenotypic.measure.MeasureBounds class method) (phenotypic.measure.MeasureColor class method) (phenotypic.measure.MeasureGridLinRegStats class method) (phenotypic.measure.MeasureGridSpread class method) (phenotypic.measure.MeasureIntensity class method) (phenotypic.measure.MeasureNeighborDist class method) (phenotypic.measure.MeasureOrientationZones class method) (phenotypic.measure.MeasureShape class method) (phenotypic.measure.MeasureSize class method) (phenotypic.measure.MeasureSymmetricZones class method) (phenotypic.measure.MeasureTexture class method) (phenotypic.prefab.FilamentousFungiPipeline class method) (phenotypic.prefab.GridSectionPipeline class method) (phenotypic.prefab.HeavyOtsuPipeline class method) (phenotypic.prefab.HeavyRoundPeaksPipeline class method) (phenotypic.prefab.HeavyWatershedPipeline class method) (phenotypic.prefab.RoundPeaksPipeline class method) (phenotypic.prefab.SpImagerPipeline class method) (phenotypic.refine.ExtractColonyCore class method) (phenotypic.refine.GridAlignmentRefiner class method) (phenotypic.refine.GridOversizedObjectRemover class method) (phenotypic.refine.KeepNearestCenter class method) (phenotypic.refine.KeepSectionLargest class method) (phenotypic.refine.ManualRefine class method) (phenotypic.refine.MaskClosing class method) (phenotypic.refine.MaskDilation class method) (phenotypic.refine.MaskErosion class method) (phenotypic.refine.MaskFill class method) (phenotypic.refine.MaskGradient class method) (phenotypic.refine.MaskOpening class method) (phenotypic.refine.MaskWhiteTophat class method) (phenotypic.refine.MergeFragmentChains class method) (phenotypic.refine.NearestNeighborMerger class method) (phenotypic.refine.ReduceSectionsByLine class method) (phenotypic.refine.RefineBySineFit class method) (phenotypic.refine.RemoveBorderObjects class method) (phenotypic.refine.RemoveByFeature class method) (phenotypic.refine.RemoveGridOutliers class method) (phenotypic.refine.RemoveLowCircularity class method) (phenotypic.refine.SeparateObjects class method) (phenotypic.refine.Skeletonize class method) (phenotypic.refine.SmallObjectRemover class method) (phenotypic.refine.SmallToLargeMerger class method) (phenotypic.refine.Thinning class method) (phenotypic.refine.TrimAsymmetry class method) (phenotypic.tune.Budget class method) (phenotypic.tune.Categorical class method) (phenotypic.tune.EvaluationResult class method) (phenotypic.tune.Evaluator class method) (phenotypic.tune.Excluded class method) (phenotypic.tune.Fixed class method) (phenotypic.tune.FloatRange class method) (phenotypic.tune.HeldOutConfig class method) (phenotypic.tune.ImportanceReport class method) (phenotypic.tune.InferredSearchSpace class method) (phenotypic.tune.IntRange class method) (phenotypic.tune.Knob class method) (phenotypic.tune.score.CompositeScorer class method) (phenotypic.tune.score.GroundTruthMasks class method) (phenotypic.tune.score.QCScorer class method) (phenotypic.tune.score.ReferenceFreeScorer class method) (phenotypic.tune.score.Scorer class method) (phenotypic.tune.score.SupervisedScorer class method) (phenotypic.tune.SearchSpace class method) (phenotypic.tune.strategy.GridConfig class method) (phenotypic.tune.strategy.OptunaConfig class method) (phenotypic.tune.strategy.RandomConfig class method) (phenotypic.tune.strategy.StrategyConfig class method) (phenotypic.tune.Trial class method) (phenotypic.tune.TuningSpec class method) __repr__() (phenotypic.Image method) __repr_name__() (phenotypic.abc_.BackgroundSubtraction method) (phenotypic.abc_.BaseOperation method) (phenotypic.abc_.ContrastAdjustment method) (phenotypic.abc_.FocusBlob method) (phenotypic.abc_.FocusEdge method) (phenotypic.abc_.GpuDetector method) (phenotypic.abc_.GridCorrector method) (phenotypic.abc_.GridFinder method) (phenotypic.abc_.GridMeasureFeatures method) (phenotypic.abc_.GridObjectDetector method) (phenotypic.abc_.GridObjectRefiner method) (phenotypic.abc_.GridOperation method) (phenotypic.abc_.ImageCorrector method) (phenotypic.abc_.ImageDenoiser method) (phenotypic.abc_.ImageEnhancer method) (phenotypic.abc_.ImageOperation method) (phenotypic.abc_.MeasureFeatures method) (phenotypic.abc_.MorphologicalFiltering method) (phenotypic.abc_.ObjectDetector method) (phenotypic.abc_.ObjectRefiner method) (phenotypic.abc_.PostMeasurement method) (phenotypic.abc_.PrefabPipeline method) (phenotypic.abc_.Smoothing method) (phenotypic.abc_.ThresholdDetector method) (phenotypic.analysis.EdgeCorrector method) (phenotypic.analysis.ErrorCutoffFinder method) (phenotypic.analysis.ExpectedVsDetectedCount method) (phenotypic.analysis.GridOccupancy method) (phenotypic.analysis.ICC method) (phenotypic.analysis.LinearCapAndLagModel method) (phenotypic.analysis.LinearLagModel method) (phenotypic.analysis.LogGrowthModel method) (phenotypic.analysis.MADOutlierRemover method) (phenotypic.analysis.MaxModifiedZScore method) (phenotypic.analysis.RelativeMAD method) (phenotypic.analysis.ReplicateAgreement method) (phenotypic.analysis.TukeyOutlierFraction method) (phenotypic.analysis.TukeyOutlierRemover method) (phenotypic.correction.BayesShrinkCorrector method) (phenotypic.correction.CaptureMetadata method) (phenotypic.correction.ColorCheckerProfile method) (phenotypic.correction.ColorCorrector method) (phenotypic.correction.ColorDenoise method) (phenotypic.correction.DenoiseBlockMatch method) (phenotypic.correction.GridAligner method) (phenotypic.correction.ImageCropper method) (phenotypic.correction.ImagePadder method) (phenotypic.correction.VisuShrinkCorrector method) (phenotypic.detect.CannyDetector method) (phenotypic.detect.ChanVeseDetector method) (phenotypic.detect.CompositeDetector method) (phenotypic.detect.FilamentousFungiDetector method) (phenotypic.detect.HysteresisDetector method) (phenotypic.detect.InoculumDetector method) (phenotypic.detect.IsodataDetector method) (phenotypic.detect.LiDetector method) (phenotypic.detect.MadHysteresisDetector method) (phenotypic.detect.ManualGridPointDetector method) (phenotypic.detect.ManualPointDetector method) (phenotypic.detect.MeanDetector method) (phenotypic.detect.MinimumDetector method) (phenotypic.detect.OtsuDetector method) (phenotypic.detect.RankOtsuDetector method) (phenotypic.detect.RoundPeaksDetector method) (phenotypic.detect.SecondaryOtsuDetector method) (phenotypic.detect.SinePeakDetector method) (phenotypic.detect.TriangleDetector method) (phenotypic.detect.UserThreshold method) (phenotypic.detect.WatershedDetector method) (phenotypic.detect.YenDetector method) (phenotypic.enhance.BayesShrinkEnhancer method) (phenotypic.enhance.CompositeEnhance method) (phenotypic.enhance.ContrastStretching method) (phenotypic.enhance.EnhanceBlockMatch method) (phenotypic.enhance.EnhanceLocalContrast method) (phenotypic.enhance.FlattenIllumination method) (phenotypic.enhance.FocusBlobLoG method) (phenotypic.enhance.FocusEdgeFrangi method) (phenotypic.enhance.FocusEdgeHessian method) (phenotypic.enhance.FocusEdgeLaplace method) (phenotypic.enhance.FocusEdgeMeijering method) (phenotypic.enhance.FocusEdgePhase method) (phenotypic.enhance.FocusEdgeSato method) (phenotypic.enhance.FocusEdgeSobel method) (phenotypic.enhance.GaussianBlur method) (phenotypic.enhance.GrayOpening method) (phenotypic.enhance.ImageInverter method) (phenotypic.enhance.LocalEdgeDenoise method) (phenotypic.enhance.MedianFilter method) (phenotypic.enhance.NonLocalMeansDenoiser method) (phenotypic.enhance.RankMedianEnhancer method) (phenotypic.enhance.SetDetectMode method) (phenotypic.enhance.SharpenEdgeGauss method) (phenotypic.enhance.StructureSmoothing method) (phenotypic.enhance.SubtractGaussian method) (phenotypic.enhance.SubtractOpening method) (phenotypic.enhance.SubtractRollingBall method) (phenotypic.enhance.SubtractWhiteTophat method) (phenotypic.enhance.VisuShrinkEnhancer method) (phenotypic.enhance.WhiteTophatEnhance method) (phenotypic.grid.AutoGridFinder method) (phenotypic.grid.CenteredAutoGridFinder method) (phenotypic.grid.GridApply method) (phenotypic.grid.ManualGridFinder method) (phenotypic.measure.MeasureBounds method) (phenotypic.measure.MeasureColor method) (phenotypic.measure.MeasureGridLinRegStats method) (phenotypic.measure.MeasureGridSpread method) (phenotypic.measure.MeasureIntensity method) (phenotypic.measure.MeasureNeighborDist method) (phenotypic.measure.MeasureOrientationZones method) (phenotypic.measure.MeasureShape method) (phenotypic.measure.MeasureSize method) (phenotypic.measure.MeasureSymmetricZones method) (phenotypic.measure.MeasureTexture method) (phenotypic.prefab.FilamentousFungiPipeline method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.prefab.RoundPeaksPipeline method) (phenotypic.prefab.SpImagerPipeline method) (phenotypic.refine.ExtractColonyCore method) (phenotypic.refine.GridAlignmentRefiner method) (phenotypic.refine.GridOversizedObjectRemover method) (phenotypic.refine.KeepNearestCenter method) (phenotypic.refine.KeepSectionLargest method) (phenotypic.refine.ManualRefine method) (phenotypic.refine.MaskClosing method) (phenotypic.refine.MaskDilation method) (phenotypic.refine.MaskErosion method) (phenotypic.refine.MaskFill method) (phenotypic.refine.MaskGradient method) (phenotypic.refine.MaskOpening method) (phenotypic.refine.MaskWhiteTophat method) (phenotypic.refine.MergeFragmentChains method) (phenotypic.refine.NearestNeighborMerger method) (phenotypic.refine.ReduceSectionsByLine method) (phenotypic.refine.RefineBySineFit method) (phenotypic.refine.RemoveBorderObjects method) (phenotypic.refine.RemoveByFeature method) (phenotypic.refine.RemoveGridOutliers method) (phenotypic.refine.RemoveLowCircularity method) (phenotypic.refine.SeparateObjects method) (phenotypic.refine.Skeletonize method) (phenotypic.refine.SmallObjectRemover method) (phenotypic.refine.SmallToLargeMerger method) (phenotypic.refine.Thinning method) (phenotypic.refine.TrimAsymmetry method) (phenotypic.tune.Budget method) (phenotypic.tune.Categorical method) (phenotypic.tune.EvaluationResult method) (phenotypic.tune.Evaluator method) (phenotypic.tune.Excluded method) (phenotypic.tune.Fixed method) (phenotypic.tune.FloatRange method) (phenotypic.tune.HeldOutConfig method) (phenotypic.tune.ImportanceReport method) (phenotypic.tune.InferredSearchSpace method) (phenotypic.tune.IntRange method) (phenotypic.tune.Knob method) (phenotypic.tune.score.CompositeScorer method) (phenotypic.tune.score.GroundTruthMasks method) (phenotypic.tune.score.QCScorer method) (phenotypic.tune.score.ReferenceFreeScorer method) (phenotypic.tune.score.Scorer method) (phenotypic.tune.score.SupervisedScorer method) (phenotypic.tune.SearchSpace method) (phenotypic.tune.strategy.GridConfig method) (phenotypic.tune.strategy.OptunaConfig method) (phenotypic.tune.strategy.RandomConfig method) (phenotypic.tune.strategy.StrategyConfig method) (phenotypic.tune.Trial method) (phenotypic.tune.TuningSpec method) __repr_recursion__() (phenotypic.abc_.BackgroundSubtraction method) (phenotypic.abc_.BaseOperation method) (phenotypic.abc_.ContrastAdjustment method) (phenotypic.abc_.FocusBlob method) (phenotypic.abc_.FocusEdge method) (phenotypic.abc_.GpuDetector method) (phenotypic.abc_.GridCorrector method) (phenotypic.abc_.GridFinder method) (phenotypic.abc_.GridMeasureFeatures method) (phenotypic.abc_.GridObjectDetector method) (phenotypic.abc_.GridObjectRefiner method) (phenotypic.abc_.GridOperation method) (phenotypic.abc_.ImageCorrector method) (phenotypic.abc_.ImageDenoiser method) (phenotypic.abc_.ImageEnhancer method) (phenotypic.abc_.ImageOperation method) (phenotypic.abc_.MeasureFeatures method) (phenotypic.abc_.MorphologicalFiltering method) (phenotypic.abc_.ObjectDetector method) (phenotypic.abc_.ObjectRefiner method) (phenotypic.abc_.PostMeasurement method) (phenotypic.abc_.PrefabPipeline method) (phenotypic.abc_.Smoothing method) (phenotypic.abc_.ThresholdDetector method) (phenotypic.analysis.EdgeCorrector method) (phenotypic.analysis.ErrorCutoffFinder method) (phenotypic.analysis.ExpectedVsDetectedCount method) (phenotypic.analysis.GridOccupancy method) (phenotypic.analysis.ICC method) (phenotypic.analysis.LinearCapAndLagModel method) (phenotypic.analysis.LinearLagModel method) (phenotypic.analysis.LogGrowthModel method) (phenotypic.analysis.MADOutlierRemover method) (phenotypic.analysis.MaxModifiedZScore method) (phenotypic.analysis.RelativeMAD method) (phenotypic.analysis.ReplicateAgreement method) (phenotypic.analysis.TukeyOutlierFraction method) (phenotypic.analysis.TukeyOutlierRemover method) (phenotypic.correction.BayesShrinkCorrector method) (phenotypic.correction.CaptureMetadata method) (phenotypic.correction.ColorCheckerProfile method) (phenotypic.correction.ColorCorrector method) (phenotypic.correction.ColorDenoise method) (phenotypic.correction.DenoiseBlockMatch method) (phenotypic.correction.GridAligner method) (phenotypic.correction.ImageCropper method) (phenotypic.correction.ImagePadder method) (phenotypic.correction.VisuShrinkCorrector method) (phenotypic.detect.CannyDetector method) (phenotypic.detect.ChanVeseDetector method) (phenotypic.detect.CompositeDetector method) (phenotypic.detect.FilamentousFungiDetector method) (phenotypic.detect.HysteresisDetector method) (phenotypic.detect.InoculumDetector method) (phenotypic.detect.IsodataDetector method) (phenotypic.detect.LiDetector method) (phenotypic.detect.MadHysteresisDetector method) (phenotypic.detect.ManualGridPointDetector method) (phenotypic.detect.ManualPointDetector method) (phenotypic.detect.MeanDetector method) (phenotypic.detect.MinimumDetector method) (phenotypic.detect.OtsuDetector method) (phenotypic.detect.RankOtsuDetector method) (phenotypic.detect.RoundPeaksDetector method) (phenotypic.detect.SecondaryOtsuDetector method) (phenotypic.detect.SinePeakDetector method) (phenotypic.detect.TriangleDetector method) (phenotypic.detect.UserThreshold method) (phenotypic.detect.WatershedDetector method) (phenotypic.detect.YenDetector method) (phenotypic.enhance.BayesShrinkEnhancer method) (phenotypic.enhance.CompositeEnhance method) (phenotypic.enhance.ContrastStretching method) (phenotypic.enhance.EnhanceBlockMatch method) (phenotypic.enhance.EnhanceLocalContrast method) (phenotypic.enhance.FlattenIllumination method) (phenotypic.enhance.FocusBlobLoG method) (phenotypic.enhance.FocusEdgeFrangi method) (phenotypic.enhance.FocusEdgeHessian method) (phenotypic.enhance.FocusEdgeLaplace method) (phenotypic.enhance.FocusEdgeMeijering method) (phenotypic.enhance.FocusEdgePhase method) (phenotypic.enhance.FocusEdgeSato method) (phenotypic.enhance.FocusEdgeSobel method) (phenotypic.enhance.GaussianBlur method) (phenotypic.enhance.GrayOpening method) (phenotypic.enhance.ImageInverter method) (phenotypic.enhance.LocalEdgeDenoise method) (phenotypic.enhance.MedianFilter method) (phenotypic.enhance.NonLocalMeansDenoiser method) (phenotypic.enhance.RankMedianEnhancer method) (phenotypic.enhance.SetDetectMode method) (phenotypic.enhance.SharpenEdgeGauss method) (phenotypic.enhance.StructureSmoothing method) (phenotypic.enhance.SubtractGaussian method) (phenotypic.enhance.SubtractOpening method) (phenotypic.enhance.SubtractRollingBall method) (phenotypic.enhance.SubtractWhiteTophat method) (phenotypic.enhance.VisuShrinkEnhancer method) (phenotypic.enhance.WhiteTophatEnhance method) (phenotypic.grid.AutoGridFinder method) (phenotypic.grid.CenteredAutoGridFinder method) (phenotypic.grid.GridApply method) (phenotypic.grid.ManualGridFinder method) (phenotypic.measure.MeasureBounds method) (phenotypic.measure.MeasureColor method) (phenotypic.measure.MeasureGridLinRegStats method) (phenotypic.measure.MeasureGridSpread method) (phenotypic.measure.MeasureIntensity method) (phenotypic.measure.MeasureNeighborDist method) (phenotypic.measure.MeasureOrientationZones method) (phenotypic.measure.MeasureShape method) (phenotypic.measure.MeasureSize method) (phenotypic.measure.MeasureSymmetricZones method) (phenotypic.measure.MeasureTexture method) (phenotypic.prefab.FilamentousFungiPipeline method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.prefab.RoundPeaksPipeline method) (phenotypic.prefab.SpImagerPipeline method) (phenotypic.refine.ExtractColonyCore method) (phenotypic.refine.GridAlignmentRefiner method) (phenotypic.refine.GridOversizedObjectRemover method) (phenotypic.refine.KeepNearestCenter method) (phenotypic.refine.KeepSectionLargest method) (phenotypic.refine.ManualRefine method) (phenotypic.refine.MaskClosing method) (phenotypic.refine.MaskDilation method) (phenotypic.refine.MaskErosion method) (phenotypic.refine.MaskFill method) (phenotypic.refine.MaskGradient method) (phenotypic.refine.MaskOpening method) (phenotypic.refine.MaskWhiteTophat method) (phenotypic.refine.MergeFragmentChains method) (phenotypic.refine.NearestNeighborMerger method) (phenotypic.refine.ReduceSectionsByLine method) (phenotypic.refine.RefineBySineFit method) (phenotypic.refine.RemoveBorderObjects method) (phenotypic.refine.RemoveByFeature method) (phenotypic.refine.RemoveGridOutliers method) (phenotypic.refine.RemoveLowCircularity method) (phenotypic.refine.SeparateObjects method) (phenotypic.refine.Skeletonize method) (phenotypic.refine.SmallObjectRemover method) (phenotypic.refine.SmallToLargeMerger method) (phenotypic.refine.Thinning method) (phenotypic.refine.TrimAsymmetry method) (phenotypic.tune.Budget method) (phenotypic.tune.Categorical method) (phenotypic.tune.EvaluationResult method) (phenotypic.tune.Evaluator method) (phenotypic.tune.Excluded method) (phenotypic.tune.Fixed method) (phenotypic.tune.FloatRange method) (phenotypic.tune.HeldOutConfig method) (phenotypic.tune.ImportanceReport method) (phenotypic.tune.InferredSearchSpace method) (phenotypic.tune.IntRange method) (phenotypic.tune.Knob method) (phenotypic.tune.score.CompositeScorer method) (phenotypic.tune.score.GroundTruthMasks method) (phenotypic.tune.score.QCScorer method) (phenotypic.tune.score.ReferenceFreeScorer method) (phenotypic.tune.score.Scorer method) (phenotypic.tune.score.SupervisedScorer method) (phenotypic.tune.SearchSpace method) (phenotypic.tune.strategy.GridConfig method) (phenotypic.tune.strategy.OptunaConfig method) (phenotypic.tune.strategy.RandomConfig method) (phenotypic.tune.strategy.StrategyConfig method) (phenotypic.tune.Trial method) (phenotypic.tune.TuningSpec method) __rich_repr__() (phenotypic.abc_.BackgroundSubtraction method) (phenotypic.abc_.BaseOperation method) (phenotypic.abc_.ContrastAdjustment method) (phenotypic.abc_.FocusBlob method) (phenotypic.abc_.FocusEdge method) (phenotypic.abc_.GpuDetector method) (phenotypic.abc_.GridCorrector method) (phenotypic.abc_.GridFinder method) (phenotypic.abc_.GridMeasureFeatures method) (phenotypic.abc_.GridObjectDetector method) (phenotypic.abc_.GridObjectRefiner method) (phenotypic.abc_.GridOperation method) (phenotypic.abc_.ImageCorrector method) (phenotypic.abc_.ImageDenoiser method) (phenotypic.abc_.ImageEnhancer method) (phenotypic.abc_.ImageOperation method) (phenotypic.abc_.MeasureFeatures method) (phenotypic.abc_.MorphologicalFiltering method) (phenotypic.abc_.ObjectDetector method) (phenotypic.abc_.ObjectRefiner method) (phenotypic.abc_.PostMeasurement method) (phenotypic.abc_.PrefabPipeline method) (phenotypic.abc_.Smoothing method) (phenotypic.abc_.ThresholdDetector method) (phenotypic.analysis.EdgeCorrector method) (phenotypic.analysis.ErrorCutoffFinder method) (phenotypic.analysis.ExpectedVsDetectedCount method) (phenotypic.analysis.GridOccupancy method) (phenotypic.analysis.ICC method) (phenotypic.analysis.LinearCapAndLagModel method) (phenotypic.analysis.LinearLagModel method) (phenotypic.analysis.LogGrowthModel method) (phenotypic.analysis.MADOutlierRemover method) (phenotypic.analysis.MaxModifiedZScore method) (phenotypic.analysis.RelativeMAD method) (phenotypic.analysis.ReplicateAgreement method) (phenotypic.analysis.TukeyOutlierFraction method) (phenotypic.analysis.TukeyOutlierRemover method) (phenotypic.correction.BayesShrinkCorrector method) (phenotypic.correction.CaptureMetadata method) (phenotypic.correction.ColorCheckerProfile method) (phenotypic.correction.ColorCorrector method) (phenotypic.correction.ColorDenoise method) (phenotypic.correction.DenoiseBlockMatch method) (phenotypic.correction.GridAligner method) (phenotypic.correction.ImageCropper method) (phenotypic.correction.ImagePadder method) (phenotypic.correction.VisuShrinkCorrector method) (phenotypic.detect.CannyDetector method) (phenotypic.detect.ChanVeseDetector method) (phenotypic.detect.CompositeDetector method) (phenotypic.detect.FilamentousFungiDetector method) (phenotypic.detect.HysteresisDetector method) (phenotypic.detect.InoculumDetector method) (phenotypic.detect.IsodataDetector method) (phenotypic.detect.LiDetector method) (phenotypic.detect.MadHysteresisDetector method) (phenotypic.detect.ManualGridPointDetector method) (phenotypic.detect.ManualPointDetector method) (phenotypic.detect.MeanDetector method) (phenotypic.detect.MinimumDetector method) (phenotypic.detect.OtsuDetector method) (phenotypic.detect.RankOtsuDetector method) (phenotypic.detect.RoundPeaksDetector method) (phenotypic.detect.SecondaryOtsuDetector method) (phenotypic.detect.SinePeakDetector method) (phenotypic.detect.TriangleDetector method) (phenotypic.detect.UserThreshold method) (phenotypic.detect.WatershedDetector method) (phenotypic.detect.YenDetector method) (phenotypic.enhance.BayesShrinkEnhancer method) (phenotypic.enhance.CompositeEnhance method) (phenotypic.enhance.ContrastStretching method) (phenotypic.enhance.EnhanceBlockMatch method) (phenotypic.enhance.EnhanceLocalContrast method) (phenotypic.enhance.FlattenIllumination method) (phenotypic.enhance.FocusBlobLoG method) (phenotypic.enhance.FocusEdgeFrangi method) (phenotypic.enhance.FocusEdgeHessian method) (phenotypic.enhance.FocusEdgeLaplace method) (phenotypic.enhance.FocusEdgeMeijering method) (phenotypic.enhance.FocusEdgePhase method) (phenotypic.enhance.FocusEdgeSato method) (phenotypic.enhance.FocusEdgeSobel method) (phenotypic.enhance.GaussianBlur method) (phenotypic.enhance.GrayOpening method) (phenotypic.enhance.ImageInverter method) (phenotypic.enhance.LocalEdgeDenoise method) (phenotypic.enhance.MedianFilter method) (phenotypic.enhance.NonLocalMeansDenoiser method) (phenotypic.enhance.RankMedianEnhancer method) (phenotypic.enhance.SetDetectMode method) (phenotypic.enhance.SharpenEdgeGauss method) (phenotypic.enhance.StructureSmoothing method) (phenotypic.enhance.SubtractGaussian method) (phenotypic.enhance.SubtractOpening method) (phenotypic.enhance.SubtractRollingBall method) (phenotypic.enhance.SubtractWhiteTophat method) (phenotypic.enhance.VisuShrinkEnhancer method) (phenotypic.enhance.WhiteTophatEnhance method) (phenotypic.grid.AutoGridFinder method) (phenotypic.grid.CenteredAutoGridFinder method) (phenotypic.grid.GridApply method) (phenotypic.grid.ManualGridFinder method) (phenotypic.measure.MeasureBounds method) (phenotypic.measure.MeasureColor method) (phenotypic.measure.MeasureGridLinRegStats method) (phenotypic.measure.MeasureGridSpread method) (phenotypic.measure.MeasureIntensity method) (phenotypic.measure.MeasureNeighborDist method) (phenotypic.measure.MeasureOrientationZones method) (phenotypic.measure.MeasureShape method) (phenotypic.measure.MeasureSize method) (phenotypic.measure.MeasureSymmetricZones method) (phenotypic.measure.MeasureTexture method) (phenotypic.prefab.FilamentousFungiPipeline method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.prefab.RoundPeaksPipeline method) (phenotypic.prefab.SpImagerPipeline method) (phenotypic.refine.ExtractColonyCore method) (phenotypic.refine.GridAlignmentRefiner method) (phenotypic.refine.GridOversizedObjectRemover method) (phenotypic.refine.KeepNearestCenter method) (phenotypic.refine.KeepSectionLargest method) (phenotypic.refine.ManualRefine method) (phenotypic.refine.MaskClosing method) (phenotypic.refine.MaskDilation method) (phenotypic.refine.MaskErosion method) (phenotypic.refine.MaskFill method) (phenotypic.refine.MaskGradient method) (phenotypic.refine.MaskOpening method) (phenotypic.refine.MaskWhiteTophat method) (phenotypic.refine.MergeFragmentChains method) (phenotypic.refine.NearestNeighborMerger method) (phenotypic.refine.ReduceSectionsByLine method) (phenotypic.refine.RefineBySineFit method) (phenotypic.refine.RemoveBorderObjects method) (phenotypic.refine.RemoveByFeature method) (phenotypic.refine.RemoveGridOutliers method) (phenotypic.refine.RemoveLowCircularity method) (phenotypic.refine.SeparateObjects method) (phenotypic.refine.Skeletonize method) (phenotypic.refine.SmallObjectRemover method) (phenotypic.refine.SmallToLargeMerger method) (phenotypic.refine.Thinning method) (phenotypic.refine.TrimAsymmetry method) (phenotypic.tune.Budget method) (phenotypic.tune.Categorical method) (phenotypic.tune.EvaluationResult method) (phenotypic.tune.Evaluator method) (phenotypic.tune.Excluded method) (phenotypic.tune.Fixed method) (phenotypic.tune.FloatRange method) (phenotypic.tune.HeldOutConfig method) (phenotypic.tune.ImportanceReport method) (phenotypic.tune.InferredSearchSpace method) (phenotypic.tune.IntRange method) (phenotypic.tune.Knob method) (phenotypic.tune.score.CompositeScorer method) (phenotypic.tune.score.GroundTruthMasks method) (phenotypic.tune.score.QCScorer method) (phenotypic.tune.score.ReferenceFreeScorer method) (phenotypic.tune.score.Scorer method) (phenotypic.tune.score.SupervisedScorer method) (phenotypic.tune.SearchSpace method) (phenotypic.tune.strategy.GridConfig method) (phenotypic.tune.strategy.OptunaConfig method) (phenotypic.tune.strategy.RandomConfig method) (phenotypic.tune.strategy.StrategyConfig method) (phenotypic.tune.Trial method) (phenotypic.tune.TuningSpec method) __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) (phenotypic.abc_.PrefabPipeline method) (phenotypic.Image method) (phenotypic.prefab.FilamentousFungiPipeline method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.prefab.RoundPeaksPipeline method) (phenotypic.prefab.SpImagerPipeline method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) __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) _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) _make_footprint() (phenotypic.abc_.ImageEnhancer method) (phenotypic.abc_.ObjectRefiner method) _operate() (phenotypic.abc_.ImageEnhancer method) (phenotypic.abc_.ImageOperation method) (phenotypic.abc_.ObjectDetector method) (phenotypic.abc_.ObjectRefiner method) _parent_image (phenotypic._core._image_parts.accessors._metadata_accessor.MetadataAccessor 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) _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 absolute_drop (phenotypic.tune.GeneralizationReport attribute) ABSOLUTE_FLOOR (phenotypic.grid.CenteredAutoGridFinder attribute) ACCEPTED_FILE_EXTENSIONS (phenotypic.sdk_.constants_.IO attribute) accessor ACTIVE_CHUNKS (phenotypic.sdk_.DashboardManifestSlurmInfoKey attribute) add_image_layer() (in module phenotypic.sdk_.napari_) add_note() (phenotypic.grid.CenteredAutoGridFinderFallbackWarning method) (phenotypic.sdk_.exceptions_.ArrayKeyValueShapeMismatchError method) (phenotypic.sdk_.exceptions_.DataIntegrityError method) (phenotypic.sdk_.exceptions_.EmptyImageError method) (phenotypic.sdk_.exceptions_.GrayscaleOutOfRangeError method) (phenotypic.sdk_.exceptions_.GridImageInputError method) (phenotypic.sdk_.exceptions_.IllegalAssignmentError method) (phenotypic.sdk_.exceptions_.IllegalElementAssignmentError method) (phenotypic.sdk_.exceptions_.ImageOperationError method) (phenotypic.sdk_.exceptions_.ImmutableComponentError method) (phenotypic.sdk_.exceptions_.InputShapeMismatchError method) (phenotypic.sdk_.exceptions_.InterfaceError method) (phenotypic.sdk_.exceptions_.InvalidHsvSchemaError method) (phenotypic.sdk_.exceptions_.InvalidMapValueError method) (phenotypic.sdk_.exceptions_.InvalidMaskScalarValueError method) (phenotypic.sdk_.exceptions_.InvalidMaskValueError method) (phenotypic.sdk_.exceptions_.InvalidShapeError method) (phenotypic.sdk_.exceptions_.MetadataKeySpacesError method) (phenotypic.sdk_.exceptions_.MetadataKeyValueError method) (phenotypic.sdk_.exceptions_.MetadataValueNonScalarError method) (phenotypic.sdk_.exceptions_.NoArrayError method) (phenotypic.sdk_.exceptions_.NoComponentError method) (phenotypic.sdk_.exceptions_.NoImageDataError method) (phenotypic.sdk_.exceptions_.NoObjectsError method) (phenotypic.sdk_.exceptions_.NoOutputError method) (phenotypic.sdk_.exceptions_.ObjectNotFoundError method) (phenotypic.sdk_.exceptions_.OperationFailedError method) (phenotypic.sdk_.exceptions_.OperationIntegrityError method) (phenotypic.sdk_.exceptions_.OutputValueError method) (phenotypic.sdk_.exceptions_.PhenoTypicError method) (phenotypic.sdk_.exceptions_.UnknownError method) (phenotypic.sdk_.exceptions_.UnsupportedFileTypeError method) (phenotypic.sdk_.exceptions_.UnsupportedImageFormat method) (phenotypic.sdk_.exceptions_.UuidAssignmentError method) (phenotypic.sdk_.exceptions_.UUIDReassignmentError method) agg_func (phenotypic.analysis.EdgeCorrector attribute) (phenotypic.analysis.ExpectedVsDetectedCount attribute) (phenotypic.analysis.GridOccupancy attribute) (phenotypic.analysis.ICC attribute) (phenotypic.analysis.LinearCapAndLagModel attribute) (phenotypic.analysis.LinearLagModel attribute) (phenotypic.analysis.LogGrowthModel attribute) (phenotypic.analysis.MADOutlierRemover attribute) (phenotypic.analysis.MaxModifiedZScore attribute) (phenotypic.analysis.RelativeMAD attribute) (phenotypic.analysis.ReplicateAgreement attribute) (phenotypic.analysis.TukeyOutlierFraction attribute) (phenotypic.analysis.TukeyOutlierRemover attribute) all() (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) alpha (phenotypic.enhance.FocusEdgeFrangi attribute) (phenotypic.enhance.FocusEdgeHessian attribute) (phenotypic.enhance.FocusEdgeMeijering attribute) (phenotypic.enhance.StructureSmoothing attribute) AMBIGUOUS_FORMATS (phenotypic.sdk_.constants_.IMAGE_MODE attribute) amount (phenotypic.enhance.SharpenEdgeGauss attribute) ANALYSIS (phenotypic.sdk_.ModulePath attribute) analysis_csv (phenotypic.sdk_.BundleLayout property) analysis_csv_path() (in module phenotypic.sdk_) ANALYSIS_DATA_VERSION (phenotypic.sdk_.DashboardManifestKey attribute) analysis_full_parquet_path() (in module phenotypic.sdk_) analysis_html_path() (in module phenotypic.sdk_) analysis_parquet (phenotypic.sdk_.BundleLayout property) analysis_parquet_path() (in module phenotypic.sdk_) analysis_scatter_json_path() (in module phenotypic.sdk_) AnalysisPluginRegistry (class in phenotypic.sdk_.register) analyze() (phenotypic.abc_.PrefabPipeline method) (phenotypic.analysis.EdgeCorrector method) (phenotypic.analysis.ErrorCutoffFinder method) (phenotypic.analysis.ExpectedVsDetectedCount method) (phenotypic.analysis.GridOccupancy method) (phenotypic.analysis.ICC method) (phenotypic.analysis.LinearCapAndLagModel method) (phenotypic.analysis.LinearLagModel method) (phenotypic.analysis.LogGrowthModel method) (phenotypic.analysis.MADOutlierRemover method) (phenotypic.analysis.MaxModifiedZScore method) (phenotypic.analysis.RelativeMAD method) (phenotypic.analysis.ReplicateAgreement method) (phenotypic.analysis.TukeyOutlierFraction method) (phenotypic.analysis.TukeyOutlierRemover method) (phenotypic.prefab.FilamentousFungiPipeline method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.prefab.RoundPeaksPipeline method) (phenotypic.prefab.SpImagerPipeline method) append() (phenotypic.tune.JournalStudyStore method) append_rst_to_doc() (phenotypic.abc_.MeasurementInfo class method) (phenotypic.sdk_.constants_.ConstantLabels class method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS class method) (phenotypic.sdk_.constants_.PIPE_STATUS class method) apply() (phenotypic.abc_.BackgroundSubtraction method) (phenotypic.abc_.ContrastAdjustment method) (phenotypic.abc_.FocusBlob method) (phenotypic.abc_.FocusEdge method) (phenotypic.abc_.GpuDetector method) (phenotypic.abc_.GridCorrector method) (phenotypic.abc_.GridObjectDetector method) (phenotypic.abc_.GridObjectRefiner method) (phenotypic.abc_.GridOperation method) (phenotypic.abc_.ImageCorrector method) (phenotypic.abc_.ImageDenoiser method) (phenotypic.abc_.ImageEnhancer method), [1] (phenotypic.abc_.ImageOperation method), [1] (phenotypic.abc_.MorphologicalFiltering method) (phenotypic.abc_.ObjectDetector method), [1] (phenotypic.abc_.ObjectRefiner method), [1] (phenotypic.abc_.PostMeasurement method) (phenotypic.abc_.PrefabPipeline method) (phenotypic.abc_.Smoothing method) (phenotypic.abc_.ThresholdDetector method) (phenotypic.correction.BayesShrinkCorrector method) (phenotypic.correction.ColorCorrector method) (phenotypic.correction.ColorDenoise method) (phenotypic.correction.DenoiseBlockMatch method) (phenotypic.correction.GridAligner method) (phenotypic.correction.ImageCropper method) (phenotypic.correction.ImagePadder method) (phenotypic.correction.VisuShrinkCorrector method) (phenotypic.detect.CannyDetector method) (phenotypic.detect.ChanVeseDetector method) (phenotypic.detect.CompositeDetector method) (phenotypic.detect.FilamentousFungiDetector method) (phenotypic.detect.HysteresisDetector method) (phenotypic.detect.InoculumDetector method) (phenotypic.detect.IsodataDetector method) (phenotypic.detect.LiDetector method) (phenotypic.detect.MadHysteresisDetector method) (phenotypic.detect.ManualGridPointDetector method) (phenotypic.detect.ManualPointDetector method) (phenotypic.detect.MeanDetector method) (phenotypic.detect.MinimumDetector method) (phenotypic.detect.OtsuDetector method) (phenotypic.detect.RankOtsuDetector method) (phenotypic.detect.RoundPeaksDetector method) (phenotypic.detect.SecondaryOtsuDetector method) (phenotypic.detect.SinePeakDetector method) (phenotypic.detect.TriangleDetector method) (phenotypic.detect.UserThreshold method) (phenotypic.detect.WatershedDetector method) (phenotypic.detect.YenDetector method) (phenotypic.enhance.BayesShrinkEnhancer method) (phenotypic.enhance.CompositeEnhance method) (phenotypic.enhance.ContrastStretching method) (phenotypic.enhance.EnhanceBlockMatch method) (phenotypic.enhance.EnhanceLocalContrast method) (phenotypic.enhance.FlattenIllumination method) (phenotypic.enhance.FocusBlobLoG method) (phenotypic.enhance.FocusEdgeFrangi method) (phenotypic.enhance.FocusEdgeHessian method) (phenotypic.enhance.FocusEdgeLaplace method) (phenotypic.enhance.FocusEdgeMeijering method) (phenotypic.enhance.FocusEdgePhase method) (phenotypic.enhance.FocusEdgeSato method) (phenotypic.enhance.FocusEdgeSobel method) (phenotypic.enhance.GaussianBlur method) (phenotypic.enhance.GrayOpening method) (phenotypic.enhance.ImageInverter method) (phenotypic.enhance.LocalEdgeDenoise method) (phenotypic.enhance.MedianFilter method) (phenotypic.enhance.NonLocalMeansDenoiser method) (phenotypic.enhance.RankMedianEnhancer method) (phenotypic.enhance.SetDetectMode method) (phenotypic.enhance.SharpenEdgeGauss method) (phenotypic.enhance.StructureSmoothing method) (phenotypic.enhance.SubtractGaussian method) (phenotypic.enhance.SubtractOpening method) (phenotypic.enhance.SubtractRollingBall method) (phenotypic.enhance.SubtractWhiteTophat method) (phenotypic.enhance.VisuShrinkEnhancer method) (phenotypic.enhance.WhiteTophatEnhance method) (phenotypic.grid.GridApply method) (phenotypic.ImagePipeline method) (phenotypic.prefab.FilamentousFungiPipeline method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.prefab.RoundPeaksPipeline method) (phenotypic.prefab.SpImagerPipeline method) (phenotypic.refine.ExtractColonyCore method) (phenotypic.refine.GridAlignmentRefiner method) (phenotypic.refine.GridOversizedObjectRemover method) (phenotypic.refine.KeepNearestCenter method) (phenotypic.refine.KeepSectionLargest method) (phenotypic.refine.ManualRefine method) (phenotypic.refine.MaskClosing method) (phenotypic.refine.MaskDilation method) (phenotypic.refine.MaskErosion method) (phenotypic.refine.MaskFill method) (phenotypic.refine.MaskGradient method) (phenotypic.refine.MaskOpening method) (phenotypic.refine.MaskWhiteTophat method) (phenotypic.refine.MergeFragmentChains method) (phenotypic.refine.NearestNeighborMerger method) (phenotypic.refine.ReduceSectionsByLine method) (phenotypic.refine.RefineBySineFit method) (phenotypic.refine.RemoveBorderObjects method) (phenotypic.refine.RemoveByFeature method) (phenotypic.refine.RemoveGridOutliers method) (phenotypic.refine.RemoveLowCircularity method) (phenotypic.refine.SeparateObjects method) (phenotypic.refine.Skeletonize method) (phenotypic.refine.SmallObjectRemover method) (phenotypic.refine.SmallToLargeMerger method) (phenotypic.refine.Thinning method) (phenotypic.refine.TrimAsymmetry method) apply_and_measure() (phenotypic.abc_.PrefabPipeline method) (phenotypic.ImagePipeline method) (phenotypic.prefab.FilamentousFungiPipeline method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.prefab.RoundPeaksPipeline method) (phenotypic.prefab.SpImagerPipeline method) apply_napari() (phenotypic.abc_.PrefabPipeline method) (phenotypic.prefab.FilamentousFungiPipeline method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.prefab.RoundPeaksPipeline method) (phenotypic.prefab.SpImagerPipeline method) apply_with_intermediates() (phenotypic.abc_.PrefabPipeline method) (phenotypic.prefab.FilamentousFungiPipeline method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.prefab.RoundPeaksPipeline method) (phenotypic.prefab.SpImagerPipeline method) args (phenotypic.grid.CenteredAutoGridFinderFallbackWarning attribute) (phenotypic.sdk_.exceptions_.ArrayKeyValueShapeMismatchError attribute) (phenotypic.sdk_.exceptions_.DataIntegrityError attribute) (phenotypic.sdk_.exceptions_.EmptyImageError attribute) (phenotypic.sdk_.exceptions_.GrayscaleOutOfRangeError attribute) (phenotypic.sdk_.exceptions_.GridImageInputError attribute) (phenotypic.sdk_.exceptions_.IllegalAssignmentError attribute) (phenotypic.sdk_.exceptions_.IllegalElementAssignmentError attribute) (phenotypic.sdk_.exceptions_.ImageOperationError attribute) (phenotypic.sdk_.exceptions_.ImmutableComponentError attribute) (phenotypic.sdk_.exceptions_.InputShapeMismatchError attribute) (phenotypic.sdk_.exceptions_.InterfaceError attribute) (phenotypic.sdk_.exceptions_.InvalidHsvSchemaError attribute) (phenotypic.sdk_.exceptions_.InvalidMapValueError attribute) (phenotypic.sdk_.exceptions_.InvalidMaskScalarValueError attribute) (phenotypic.sdk_.exceptions_.InvalidMaskValueError attribute) (phenotypic.sdk_.exceptions_.InvalidShapeError attribute) (phenotypic.sdk_.exceptions_.MetadataKeySpacesError attribute) (phenotypic.sdk_.exceptions_.MetadataKeyValueError attribute) (phenotypic.sdk_.exceptions_.MetadataValueNonScalarError attribute) (phenotypic.sdk_.exceptions_.NoArrayError attribute) (phenotypic.sdk_.exceptions_.NoComponentError attribute) (phenotypic.sdk_.exceptions_.NoImageDataError attribute) (phenotypic.sdk_.exceptions_.NoObjectsError attribute) (phenotypic.sdk_.exceptions_.NoOutputError attribute) (phenotypic.sdk_.exceptions_.ObjectNotFoundError attribute) (phenotypic.sdk_.exceptions_.OperationFailedError attribute) (phenotypic.sdk_.exceptions_.OperationIntegrityError attribute) (phenotypic.sdk_.exceptions_.OutputValueError attribute) (phenotypic.sdk_.exceptions_.PhenoTypicError attribute) (phenotypic.sdk_.exceptions_.UnknownError attribute) (phenotypic.sdk_.exceptions_.UnsupportedFileTypeError attribute) (phenotypic.sdk_.exceptions_.UnsupportedImageFormat attribute) (phenotypic.sdk_.exceptions_.UuidAssignmentError attribute) (phenotypic.sdk_.exceptions_.UUIDReassignmentError attribute) ArrayKeyValueShapeMismatchError as_coo() (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap method) as_csc() (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap method) assert_swmr_on() (phenotypic.sdk_.HDF static method) atomic_write_bytes() (in module phenotypic.sdk_) atomic_write_text() (in module phenotypic.sdk_) AutoGridFinder (class in phenotypic.grid) availability() (phenotypic.tune.score.CompositeScorer method) (phenotypic.tune.score.QCScorer method) (phenotypic.tune.score.ReferenceFreeScorer method) (phenotypic.tune.score.Scorer method) (phenotypic.tune.score.SupervisedScorer method) available() (phenotypic.sdk_.register.AnalysisPluginRegistry class method) (phenotypic.sdk_.register.BaseRegistry class method) (phenotypic.sdk_.register.PlotterRegistry class method) available_analysis_plugins() (in module phenotypic.sdk_.register) available_names() (phenotypic.tune.score.GroundTruthMasks method) available_plotters() (in module phenotypic.sdk_.register) axis (phenotypic.correction.GridAligner attribute) (phenotypic.refine.RemoveGridOutliers attribute) B background_estimate (phenotypic.util.BackgroundMetrics attribute) BackgroundMetrics (class in phenotypic.util) BackgroundSubtraction (class in phenotypic.abc_) BASE (phenotypic.sdk_.constants_.IMAGE_TYPES attribute) BaseOperation (class in phenotypic.abc_) BaseRegistry (class in phenotypic.sdk_.register) BayesShrinkCorrector (class in phenotypic.correction) BayesShrinkEnhancer (class in phenotypic.enhance) beehive_threshold (phenotypic.refine.TrimAsymmetry attribute) benchmark (phenotypic.abc_.PrefabPipeline attribute) (phenotypic.prefab.FilamentousFungiPipeline attribute) (phenotypic.prefab.GridSectionPipeline attribute) (phenotypic.prefab.HeavyOtsuPipeline attribute) (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] (phenotypic.prefab.HeavyWatershedPipeline attribute) (phenotypic.prefab.RoundPeaksPipeline attribute) (phenotypic.prefab.SpImagerPipeline attribute) benchmark_results() (phenotypic.abc_.PrefabPipeline method) (phenotypic.ImagePipeline method) (phenotypic.prefab.FilamentousFungiPipeline method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.prefab.RoundPeaksPipeline method) (phenotypic.prefab.SpImagerPipeline method) best() (phenotypic.tune.JournalStudyStore method) best_params_path() (in module phenotypic.sdk_) best_pipeline() (phenotypic.tune.TuningEngine method) best_pipeline_path() (in module phenotypic.sdk_) beta (phenotypic.analysis.LinearCapAndLagModel attribute) (phenotypic.analysis.LogGrowthModel attribute) (phenotypic.detect.FilamentousFungiDetector attribute) (phenotypic.enhance.FocusEdgeFrangi attribute) (phenotypic.enhance.FocusEdgeHessian attribute) BGR (phenotypic.sdk_.constants_.IMAGE_MODE attribute) BGRA (phenotypic.sdk_.constants_.IMAGE_MODE attribute) bio_desc (phenotypic.abc_.MeasurementInfo attribute), [1] (phenotypic.sdk_.constants_.ConstantLabels attribute) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS attribute) (phenotypic.sdk_.constants_.PIPE_STATUS attribute) bit_depth (phenotypic.util.ImageMetricsCalculator attribute) (phenotypic.util.ImageMetricsCalculator property) black_ridges (phenotypic.enhance.FocusEdgeFrangi attribute) (phenotypic.enhance.FocusEdgeHessian attribute) (phenotypic.enhance.FocusEdgeMeijering attribute) (phenotypic.enhance.FocusEdgeSato attribute) blend (phenotypic.tune.score.CompositeScorer attribute) block_id (phenotypic.gui.builder._state.BlockNode attribute), [1] (phenotypic.gui.builder._validation.Issue attribute), [1] block_size (phenotypic.correction.ColorDenoise attribute) (phenotypic.correction.DenoiseBlockMatch attribute) (phenotypic.enhance.EnhanceBlockMatch attribute) BlockNode (class in phenotypic.gui.builder._state) blocks (phenotypic.gui.builder._state._DagBuilderScope attribute), [1] bm3d_block_size (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) bm3d_clip (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) bm3d_sigma (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) bm3d_stage_arg (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) border_margin_px (phenotypic.detect.FilamentousFungiDetector attribute) border_remover_size (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) border_size (phenotypic.refine.RemoveBorderObjects attribute) bottom (phenotypic.correction.ImageCropper attribute) (phenotypic.correction.ImagePadder attribute) boundary_displacement() (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) BoundFigures (class in phenotypic.abc_) bounds (phenotypic.abc_.Control attribute) breadcrumb (phenotypic.gui.builder._state._DagBuilderState attribute), [1] Budget (class in phenotypic.tune) budget (phenotypic.tune.TuningSpec attribute) build() (phenotypic.tune.strategy.GridConfig method) (phenotypic.tune.strategy.OptunaConfig method) (phenotypic.tune.strategy.RandomConfig method) (phenotypic.tune.strategy.StrategyConfig method) build_pipeline() (in module phenotypic.tune) build_reduced_space() (in module phenotypic.tune) BundleLayout (class in phenotypic.sdk_) by_module() (phenotypic._core._image_parts.accessors._metadata_accessor.MetadataAccessor method) C C (phenotypic.enhance.StructureSmoothing attribute) calculate_optimal_array_chunks() (in module phenotypic.sdk_.slurm) calibration_score (phenotypic.tune.GeneralizationReport attribute) calibration_stability (phenotypic.tune.GeneralizationReport attribute) camera_make (phenotypic.correction.CaptureMetadata attribute), [1] camera_model (phenotypic.correction.CaptureMetadata attribute), [1] CannyDetector (class in phenotypic.detect) canonical_metadata_order() (in module phenotypic.sdk_) capitalize() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) capture_metadata (phenotypic.correction.ColorCheckerProfile attribute), [1] CaptureMetadata (class in phenotypic.correction) casefold() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) Categorical (class in phenotypic.tune) categories (phenotypic.tune.TuneSpec attribute) CATEGORY (phenotypic.abc_.MeasurementInfo attribute) (phenotypic.abc_.MeasurementInfo property) (phenotypic.sdk_.constants_.ConstantLabels property) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS property) (phenotypic.sdk_.constants_.PIPE_STATUS property) category() (phenotypic.abc_.MeasurementInfo class method) (phenotypic.sdk_.constants_.ConstantLabels class method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS class method) (phenotypic.sdk_.constants_.PIPE_STATUS class method) cell_label (phenotypic.analysis.GridOccupancy attribute) center() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) CenteredAutoGridFinder (class in phenotypic.grid) CenteredAutoGridFinderFallbackWarning centers (phenotypic.detect.ManualPointDetector attribute) (phenotypic.refine.ManualRefine attribute) CHANNELS_DEFAULT (phenotypic.sdk_.constants_.IMAGE_MODE attribute) ChanVeseDetector (class in phenotypic.detect) check (phenotypic.tune.score.QCScorer attribute) checker_type (phenotypic.correction.ColorCheckerProfile attribute) checkpoint_lock_filename() (in module phenotypic.sdk_) checkpoint_lock_path() (in module phenotypic.sdk_) choices (phenotypic.tune.Categorical attribute) CHUNK_JOB_IDS (phenotypic.sdk_.DashboardManifestSlurmInfoKey attribute) (phenotypic.sdk_.JobMetadataKey attribute) chunk_lock_path() (in module phenotypic.sdk_) chunk_manifest_path() (in module phenotypic.sdk_) chunk_parquet_filename() (in module phenotypic.sdk_) chunk_parquet_path() (in module phenotypic.sdk_) CHUNK_SCRIPTS (phenotypic.sdk_.DashboardManifestSlurmInfoKey attribute) (phenotypic.sdk_.JobMetadataKey attribute) chunk_state_path() (in module phenotypic.sdk_) CHUNKED_FILES (phenotypic.sdk_.ChunkStateKey attribute) ChunkManifestKey (class in phenotypic.sdk_) CHUNKS (phenotypic.sdk_.ChunkManifestKey attribute) chunks_dir() (in module phenotypic.sdk_) ChunkStateKey (class in phenotypic.sdk_) clahe_clip_limit (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) clahe_kernel_size (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) class_name (phenotypic.gui.builder._state.BlockNode attribute), [1] clear() (phenotypic.util.BackgroundMetrics method) (phenotypic.util.ContrastMetrics method) (phenotypic.util.NoiseMetrics method) (phenotypic.util.QualityScores method) (phenotypic.util.StructureMetrics method) clear_machine_state() (in module phenotypic.sdk_) clip (phenotypic.correction.BayesShrinkCorrector attribute) (phenotypic.correction.ColorDenoise attribute) (phenotypic.correction.VisuShrinkCorrector attribute) (phenotypic.enhance.BayesShrinkEnhancer attribute) (phenotypic.enhance.CompositeEnhance attribute) (phenotypic.enhance.EnhanceBlockMatch attribute) (phenotypic.enhance.LocalEdgeDenoise attribute) (phenotypic.enhance.VisuShrinkEnhancer attribute) clip_limit (phenotypic.enhance.EnhanceLocalContrast attribute) ClipControlMixin (class in phenotypic.sdk_) close_handle() (phenotypic.sdk_.HDF static method) Coherence (phenotypic.util.QualityScores attribute) coherence_map (phenotypic.util.StructureMetrics attribute) coherence_window_radius (phenotypic.detect.FilamentousFungiDetector attribute) col_edges (phenotypic.grid.ManualGridFinder attribute), [1] COL_LINREG_B (phenotypic.sdk_.constants_.GRID_LINREG_STATS_EXTRACTOR attribute) COL_LINREG_M (phenotypic.sdk_.constants_.GRID_LINREG_STATS_EXTRACTOR attribute) collapsed (phenotypic.gui.builder._state.BlockNode attribute), [1] colony color_chroma_min (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) color_include_XYZ (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) color_white_chroma_max (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) ColorAccessor (class in phenotypic._core._image_parts.accessors._color_accessor) ColorCheckerProfile (class in phenotypic.correction) ColorCorrector (class in phenotypic.correction) ColorDenoise (class in phenotypic.correction) compactness (phenotypic.detect.WatershedDetector attribute) compare() (phenotypic.correction.CaptureMetadata method) COMPLETED (phenotypic.sdk_.DashboardManifestKey attribute) (phenotypic.sdk_.ProcessingStateKey attribute) COMPLETED_CHUNKS (phenotypic.sdk_.DashboardManifestSlurmInfoKey attribute) completed_count() (phenotypic.tune.JournalStudyStore method) CompositeDetector (class in phenotypic.detect) CompositeEnhance (class in phenotypic.enhance) CompositeScorer (class in phenotypic.tune.score) compute() (phenotypic.abc_.DetectionMode method) compute_all() (phenotypic.util.ImageMetricsCalculator method) compute_background_metrics() (phenotypic.util.ImageMetricsCalculator method) compute_contrast_metrics() (phenotypic.util.ImageMetricsCalculator method) compute_generalization_gap() (in module phenotypic.tune) compute_local_contrast() (phenotypic.util.ImageMetricsCalculator method) compute_local_variance() (phenotypic.util.ImageMetricsCalculator method) compute_noise_metrics() (phenotypic.util.ImageMetricsCalculator method) compute_param_importance() (in module phenotypic.tune) compute_param_importance_report() (in module phenotypic.tune) compute_psd() (phenotypic.util.ImageMetricsCalculator method) compute_quality_scores() (phenotypic.util.ImageMetricsCalculator method) compute_structure_metrics() (phenotypic.util.ImageMetricsCalculator method) conditional_on (phenotypic.tune.Knob attribute) cone_to_hsv() (in module phenotypic.util) CONFIG (phenotypic.sdk_.ProcessingStateKey attribute) connectivity (phenotypic.abc_.GpuDetector attribute) (phenotypic.analysis.EdgeCorrector attribute) (phenotypic.detect.CannyDetector attribute) (phenotypic.detect.ChanVeseDetector attribute) (phenotypic.detect.MadHysteresisDetector attribute) (phenotypic.detect.WatershedDetector attribute) constant_value (phenotypic.correction.ImagePadder attribute) ConstantLabels (class in phenotypic.sdk_.constants_) construct() (phenotypic.abc_.BackgroundSubtraction class method) (phenotypic.abc_.BaseOperation class method) (phenotypic.abc_.ContrastAdjustment class method) (phenotypic.abc_.FocusBlob class method) (phenotypic.abc_.FocusEdge class method) (phenotypic.abc_.GpuDetector class method) (phenotypic.abc_.GridCorrector class method) (phenotypic.abc_.GridFinder class method) (phenotypic.abc_.GridMeasureFeatures class method) (phenotypic.abc_.GridObjectDetector class method) (phenotypic.abc_.GridObjectRefiner class method) (phenotypic.abc_.GridOperation class method) (phenotypic.abc_.ImageCorrector class method) (phenotypic.abc_.ImageDenoiser class method) (phenotypic.abc_.ImageEnhancer class method) (phenotypic.abc_.ImageOperation class method) (phenotypic.abc_.MeasureFeatures class method) (phenotypic.abc_.MorphologicalFiltering class method) (phenotypic.abc_.ObjectDetector class method) (phenotypic.abc_.ObjectRefiner class method) (phenotypic.abc_.PostMeasurement class method) (phenotypic.abc_.PrefabPipeline class method) (phenotypic.abc_.Smoothing class method) (phenotypic.abc_.ThresholdDetector class method) (phenotypic.analysis.EdgeCorrector class method) (phenotypic.analysis.ErrorCutoffFinder class method) (phenotypic.analysis.ExpectedVsDetectedCount class method) (phenotypic.analysis.GridOccupancy class method) (phenotypic.analysis.ICC class method) (phenotypic.analysis.LinearCapAndLagModel class method) (phenotypic.analysis.LinearLagModel class method) (phenotypic.analysis.LogGrowthModel class method) (phenotypic.analysis.MADOutlierRemover class method) (phenotypic.analysis.MaxModifiedZScore class method) (phenotypic.analysis.RelativeMAD class method) (phenotypic.analysis.ReplicateAgreement class method) (phenotypic.analysis.TukeyOutlierFraction class method) (phenotypic.analysis.TukeyOutlierRemover class method) (phenotypic.correction.BayesShrinkCorrector class method) (phenotypic.correction.CaptureMetadata class method) (phenotypic.correction.ColorCheckerProfile class method) (phenotypic.correction.ColorCorrector class method) (phenotypic.correction.ColorDenoise class method) (phenotypic.correction.DenoiseBlockMatch class method) (phenotypic.correction.GridAligner class method) (phenotypic.correction.ImageCropper class method) (phenotypic.correction.ImagePadder class method) (phenotypic.correction.VisuShrinkCorrector class method) (phenotypic.detect.CannyDetector class method) (phenotypic.detect.ChanVeseDetector class method) (phenotypic.detect.CompositeDetector class method) (phenotypic.detect.FilamentousFungiDetector class method) (phenotypic.detect.HysteresisDetector class method) (phenotypic.detect.InoculumDetector class method) (phenotypic.detect.IsodataDetector class method) (phenotypic.detect.LiDetector class method) (phenotypic.detect.MadHysteresisDetector class method) (phenotypic.detect.ManualGridPointDetector class method) (phenotypic.detect.ManualPointDetector class method) (phenotypic.detect.MeanDetector class method) (phenotypic.detect.MinimumDetector class method) (phenotypic.detect.OtsuDetector class method) (phenotypic.detect.RankOtsuDetector class method) (phenotypic.detect.RoundPeaksDetector class method) (phenotypic.detect.SecondaryOtsuDetector class method) (phenotypic.detect.SinePeakDetector class method) (phenotypic.detect.TriangleDetector class method) (phenotypic.detect.UserThreshold class method) (phenotypic.detect.WatershedDetector class method) (phenotypic.detect.YenDetector class method) (phenotypic.enhance.BayesShrinkEnhancer class method) (phenotypic.enhance.CompositeEnhance class method) (phenotypic.enhance.ContrastStretching class method) (phenotypic.enhance.EnhanceBlockMatch class method) (phenotypic.enhance.EnhanceLocalContrast class method) (phenotypic.enhance.FlattenIllumination class method) (phenotypic.enhance.FocusBlobLoG class method) (phenotypic.enhance.FocusEdgeFrangi class method) (phenotypic.enhance.FocusEdgeHessian class method) (phenotypic.enhance.FocusEdgeLaplace class method) (phenotypic.enhance.FocusEdgeMeijering class method) (phenotypic.enhance.FocusEdgePhase class method) (phenotypic.enhance.FocusEdgeSato class method) (phenotypic.enhance.FocusEdgeSobel class method) (phenotypic.enhance.GaussianBlur class method) (phenotypic.enhance.GrayOpening class method) (phenotypic.enhance.ImageInverter class method) (phenotypic.enhance.LocalEdgeDenoise class method) (phenotypic.enhance.MedianFilter class method) (phenotypic.enhance.NonLocalMeansDenoiser class method) (phenotypic.enhance.RankMedianEnhancer class method) (phenotypic.enhance.SetDetectMode class method) (phenotypic.enhance.SharpenEdgeGauss class method) (phenotypic.enhance.StructureSmoothing class method) (phenotypic.enhance.SubtractGaussian class method) (phenotypic.enhance.SubtractOpening class method) (phenotypic.enhance.SubtractRollingBall class method) (phenotypic.enhance.SubtractWhiteTophat class method) (phenotypic.enhance.VisuShrinkEnhancer class method) (phenotypic.enhance.WhiteTophatEnhance class method) (phenotypic.grid.AutoGridFinder class method) (phenotypic.grid.CenteredAutoGridFinder class method) (phenotypic.grid.GridApply class method) (phenotypic.grid.ManualGridFinder class method) (phenotypic.measure.MeasureBounds class method) (phenotypic.measure.MeasureColor class method) (phenotypic.measure.MeasureGridLinRegStats class method) (phenotypic.measure.MeasureGridSpread class method) (phenotypic.measure.MeasureIntensity class method) (phenotypic.measure.MeasureNeighborDist class method) (phenotypic.measure.MeasureOrientationZones class method) (phenotypic.measure.MeasureShape class method) (phenotypic.measure.MeasureSize class method) (phenotypic.measure.MeasureSymmetricZones class method) (phenotypic.measure.MeasureTexture class method) (phenotypic.prefab.FilamentousFungiPipeline class method) (phenotypic.prefab.GridSectionPipeline class method) (phenotypic.prefab.HeavyOtsuPipeline class method) (phenotypic.prefab.HeavyRoundPeaksPipeline class method) (phenotypic.prefab.HeavyWatershedPipeline class method) (phenotypic.prefab.RoundPeaksPipeline class method) (phenotypic.prefab.SpImagerPipeline class method) (phenotypic.refine.ExtractColonyCore class method) (phenotypic.refine.GridAlignmentRefiner class method) (phenotypic.refine.GridOversizedObjectRemover class method) (phenotypic.refine.KeepNearestCenter class method) (phenotypic.refine.KeepSectionLargest class method) (phenotypic.refine.ManualRefine class method) (phenotypic.refine.MaskClosing class method) (phenotypic.refine.MaskDilation class method) (phenotypic.refine.MaskErosion class method) (phenotypic.refine.MaskFill class method) (phenotypic.refine.MaskGradient class method) (phenotypic.refine.MaskOpening class method) (phenotypic.refine.MaskWhiteTophat class method) (phenotypic.refine.MergeFragmentChains class method) (phenotypic.refine.NearestNeighborMerger class method) (phenotypic.refine.ReduceSectionsByLine class method) (phenotypic.refine.RefineBySineFit class method) (phenotypic.refine.RemoveBorderObjects class method) (phenotypic.refine.RemoveByFeature class method) (phenotypic.refine.RemoveGridOutliers class method) (phenotypic.refine.RemoveLowCircularity class method) (phenotypic.refine.SeparateObjects class method) (phenotypic.refine.Skeletonize class method) (phenotypic.refine.SmallObjectRemover class method) (phenotypic.refine.SmallToLargeMerger class method) (phenotypic.refine.Thinning class method) (phenotypic.refine.TrimAsymmetry class method) (phenotypic.tune.Budget class method) (phenotypic.tune.Categorical class method) (phenotypic.tune.EvaluationResult class method) (phenotypic.tune.Evaluator class method) (phenotypic.tune.Excluded class method) (phenotypic.tune.Fixed class method) (phenotypic.tune.FloatRange class method) (phenotypic.tune.HeldOutConfig class method) (phenotypic.tune.ImportanceReport class method) (phenotypic.tune.InferredSearchSpace class method) (phenotypic.tune.IntRange class method) (phenotypic.tune.Knob class method) (phenotypic.tune.score.CompositeScorer class method) (phenotypic.tune.score.GroundTruthMasks class method) (phenotypic.tune.score.QCScorer class method) (phenotypic.tune.score.ReferenceFreeScorer class method) (phenotypic.tune.score.Scorer class method) (phenotypic.tune.score.SupervisedScorer class method) (phenotypic.tune.SearchSpace class method) (phenotypic.tune.strategy.GridConfig class method) (phenotypic.tune.strategy.OptunaConfig class method) (phenotypic.tune.strategy.RandomConfig class method) (phenotypic.tune.strategy.StrategyConfig class method) (phenotypic.tune.Trial class method) (phenotypic.tune.TuningSpec class method) Contrast (phenotypic.util.QualityScores attribute) ContrastAdjustment (class in phenotypic.abc_) ContrastMetrics (class in phenotypic.util) ContrastStretching (class in phenotypic.enhance) Control (class in phenotypic.abc_) controls (phenotypic.abc_.FigureSpec attribute), [1] convert2ycbcr (phenotypic.correction.BayesShrinkCorrector attribute) (phenotypic.correction.VisuShrinkCorrector attribute) coord1 (phenotypic.detect.ManualGridPointDetector attribute) coord2 (phenotypic.detect.ManualGridPointDetector attribute) 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) (phenotypic.abc_.BaseOperation method) (phenotypic.abc_.ContrastAdjustment method) (phenotypic.abc_.FocusBlob method) (phenotypic.abc_.FocusEdge method) (phenotypic.abc_.GpuDetector method) (phenotypic.abc_.GridCorrector method) (phenotypic.abc_.GridFinder method) (phenotypic.abc_.GridMeasureFeatures method) (phenotypic.abc_.GridObjectDetector method) (phenotypic.abc_.GridObjectRefiner method) (phenotypic.abc_.GridOperation method) (phenotypic.abc_.ImageCorrector method) (phenotypic.abc_.ImageDenoiser method) (phenotypic.abc_.ImageEnhancer method) (phenotypic.abc_.ImageOperation method) (phenotypic.abc_.MeasureFeatures method) (phenotypic.abc_.MorphologicalFiltering method) (phenotypic.abc_.ObjectDetector method) (phenotypic.abc_.ObjectRefiner method) (phenotypic.abc_.PostMeasurement method) (phenotypic.abc_.PrefabPipeline method) (phenotypic.abc_.Smoothing method) (phenotypic.abc_.ThresholdDetector method) (phenotypic.analysis.EdgeCorrector method) (phenotypic.analysis.ErrorCutoffFinder method) (phenotypic.analysis.ExpectedVsDetectedCount method) (phenotypic.analysis.GridOccupancy method) (phenotypic.analysis.ICC method) (phenotypic.analysis.LinearCapAndLagModel method) (phenotypic.analysis.LinearLagModel method) (phenotypic.analysis.LogGrowthModel method) (phenotypic.analysis.MADOutlierRemover method) (phenotypic.analysis.MaxModifiedZScore method) (phenotypic.analysis.RelativeMAD method) (phenotypic.analysis.ReplicateAgreement method) (phenotypic.analysis.TukeyOutlierFraction method) (phenotypic.analysis.TukeyOutlierRemover method) (phenotypic.correction.BayesShrinkCorrector method) (phenotypic.correction.CaptureMetadata method) (phenotypic.correction.ColorCheckerProfile method) (phenotypic.correction.ColorCorrector method) (phenotypic.correction.ColorDenoise method) (phenotypic.correction.DenoiseBlockMatch method) (phenotypic.correction.GridAligner method) (phenotypic.correction.ImageCropper method) (phenotypic.correction.ImagePadder method) (phenotypic.correction.VisuShrinkCorrector method) (phenotypic.detect.CannyDetector method) (phenotypic.detect.ChanVeseDetector method) (phenotypic.detect.CompositeDetector method) (phenotypic.detect.FilamentousFungiDetector method) (phenotypic.detect.HysteresisDetector method) (phenotypic.detect.InoculumDetector method) (phenotypic.detect.IsodataDetector method) (phenotypic.detect.LiDetector method) (phenotypic.detect.MadHysteresisDetector method) (phenotypic.detect.ManualGridPointDetector method) (phenotypic.detect.ManualPointDetector method) (phenotypic.detect.MeanDetector method) (phenotypic.detect.MinimumDetector method) (phenotypic.detect.OtsuDetector method) (phenotypic.detect.RankOtsuDetector method) (phenotypic.detect.RoundPeaksDetector method) (phenotypic.detect.SecondaryOtsuDetector method) (phenotypic.detect.SinePeakDetector method) (phenotypic.detect.TriangleDetector method) (phenotypic.detect.UserThreshold method) (phenotypic.detect.WatershedDetector method) (phenotypic.detect.YenDetector method) (phenotypic.enhance.BayesShrinkEnhancer method) (phenotypic.enhance.CompositeEnhance method) (phenotypic.enhance.ContrastStretching method) (phenotypic.enhance.EnhanceBlockMatch method) (phenotypic.enhance.EnhanceLocalContrast method) (phenotypic.enhance.FlattenIllumination method) (phenotypic.enhance.FocusBlobLoG method) (phenotypic.enhance.FocusEdgeFrangi method) (phenotypic.enhance.FocusEdgeHessian method) (phenotypic.enhance.FocusEdgeLaplace method) (phenotypic.enhance.FocusEdgeMeijering method) (phenotypic.enhance.FocusEdgePhase method) (phenotypic.enhance.FocusEdgeSato method) (phenotypic.enhance.FocusEdgeSobel method) (phenotypic.enhance.GaussianBlur method) (phenotypic.enhance.GrayOpening method) (phenotypic.enhance.ImageInverter method) (phenotypic.enhance.LocalEdgeDenoise method) (phenotypic.enhance.MedianFilter method) (phenotypic.enhance.NonLocalMeansDenoiser method) (phenotypic.enhance.RankMedianEnhancer method) (phenotypic.enhance.SetDetectMode method) (phenotypic.enhance.SharpenEdgeGauss method) (phenotypic.enhance.StructureSmoothing method) (phenotypic.enhance.SubtractGaussian method) (phenotypic.enhance.SubtractOpening method) (phenotypic.enhance.SubtractRollingBall method) (phenotypic.enhance.SubtractWhiteTophat method) (phenotypic.enhance.VisuShrinkEnhancer method) (phenotypic.enhance.WhiteTophatEnhance method) (phenotypic.grid.AutoGridFinder method) (phenotypic.grid.CenteredAutoGridFinder method) (phenotypic.grid.GridApply method) (phenotypic.grid.ManualGridFinder method) (phenotypic.GridImage method) (phenotypic.Image method) (phenotypic.measure.MeasureBounds method) (phenotypic.measure.MeasureColor method) (phenotypic.measure.MeasureGridLinRegStats method) (phenotypic.measure.MeasureGridSpread method) (phenotypic.measure.MeasureIntensity method) (phenotypic.measure.MeasureNeighborDist method) (phenotypic.measure.MeasureOrientationZones method) (phenotypic.measure.MeasureShape method) (phenotypic.measure.MeasureSize method) (phenotypic.measure.MeasureSymmetricZones method) (phenotypic.measure.MeasureTexture method) (phenotypic.prefab.FilamentousFungiPipeline method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.prefab.RoundPeaksPipeline method) (phenotypic.prefab.SpImagerPipeline method) (phenotypic.refine.ExtractColonyCore method) (phenotypic.refine.GridAlignmentRefiner method) (phenotypic.refine.GridOversizedObjectRemover method) (phenotypic.refine.KeepNearestCenter method) (phenotypic.refine.KeepSectionLargest method) (phenotypic.refine.ManualRefine method) (phenotypic.refine.MaskClosing method) (phenotypic.refine.MaskDilation method) (phenotypic.refine.MaskErosion method) (phenotypic.refine.MaskFill method) (phenotypic.refine.MaskGradient method) (phenotypic.refine.MaskOpening method) (phenotypic.refine.MaskWhiteTophat method) (phenotypic.refine.MergeFragmentChains method) (phenotypic.refine.NearestNeighborMerger method) (phenotypic.refine.ReduceSectionsByLine method) (phenotypic.refine.RefineBySineFit method) (phenotypic.refine.RemoveBorderObjects method) (phenotypic.refine.RemoveByFeature method) (phenotypic.refine.RemoveGridOutliers method) (phenotypic.refine.RemoveLowCircularity method) (phenotypic.refine.SeparateObjects method) (phenotypic.refine.Skeletonize method) (phenotypic.refine.SmallObjectRemover method) (phenotypic.refine.SmallToLargeMerger method) (phenotypic.refine.Thinning method) (phenotypic.refine.TrimAsymmetry method) (phenotypic.tune.Budget method) (phenotypic.tune.Categorical method) (phenotypic.tune.EvaluationResult method) (phenotypic.tune.Evaluator method) (phenotypic.tune.Excluded method) (phenotypic.tune.Fixed method) (phenotypic.tune.FloatRange method) (phenotypic.tune.HeldOutConfig method) (phenotypic.tune.ImportanceReport method) (phenotypic.tune.InferredSearchSpace method) (phenotypic.tune.IntRange method) (phenotypic.tune.Knob method) (phenotypic.tune.score.CompositeScorer method) (phenotypic.tune.score.GroundTruthMasks method) (phenotypic.tune.score.QCScorer method) (phenotypic.tune.score.ReferenceFreeScorer method) (phenotypic.tune.score.Scorer method) (phenotypic.tune.score.SupervisedScorer method) (phenotypic.tune.SearchSpace method) (phenotypic.tune.strategy.GridConfig method) (phenotypic.tune.strategy.OptunaConfig method) (phenotypic.tune.strategy.RandomConfig method) (phenotypic.tune.strategy.StrategyConfig method) (phenotypic.tune.Trial method) (phenotypic.tune.TuningSpec method) (phenotypic.util.BackgroundMetrics method) (phenotypic.util.ContrastMetrics method) (phenotypic.util.NoiseMetrics method) (phenotypic.util.QualityScores method) (phenotypic.util.StructureMetrics method) core_fraction (phenotypic.correction.ColorCheckerProfile attribute) correction_matrix (phenotypic.correction.ColorCheckerProfile attribute), [1] (phenotypic.correction.ColorCorrector property) correlation_length (phenotypic.util.NoiseMetrics attribute) correlation_threshold (phenotypic.detect.SinePeakDetector attribute) (phenotypic.refine.RefineBySineFit attribute) count() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) count_check (phenotypic.tune.score.ReferenceFreeScorer attribute) (phenotypic.tune.score.SupervisedScorer attribute) count_free_params() (in module phenotypic.tune) count_term_name (phenotypic.tune.score.ReferenceFreeScorer attribute) (phenotypic.tune.score.SupervisedScorer attribute) CROP (phenotypic.sdk_.constants_.IMAGE_TYPES attribute) curation_labels_parquet (phenotypic.sdk_.BundleLayout property) curation_labels_parquet_path() (in module phenotypic.sdk_) custom_categories_json (phenotypic.sdk_.BundleLayout property) custom_categories_json_path() (in module phenotypic.sdk_) cutoff (phenotypic.enhance.FocusEdgePhase attribute) (phenotypic.refine.RemoveLowCircularity attribute) cutoff_multiplier (phenotypic.refine.RemoveGridOutliers attribute) cv_deferred (phenotypic.tune.GeneralizationReport attribute) cval (phenotypic.enhance.FocusEdgeHessian attribute) (phenotypic.enhance.FocusEdgeMeijering attribute) (phenotypic.enhance.FocusEdgeSato attribute) (phenotypic.enhance.GaussianBlur attribute) (phenotypic.enhance.LocalEdgeDenoise attribute) (phenotypic.enhance.MedianFilter attribute) (phenotypic.enhance.SubtractGaussian 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) (phenotypic.analysis.EdgeCorrector method) (phenotypic.analysis.ExpectedVsDetectedCount method) (phenotypic.analysis.GridOccupancy method) (phenotypic.analysis.ICC method) (phenotypic.analysis.LinearCapAndLagModel method) (phenotypic.analysis.LinearLagModel method) (phenotypic.analysis.LogGrowthModel method) (phenotypic.analysis.MADOutlierRemover method) (phenotypic.analysis.MaxModifiedZScore method) (phenotypic.analysis.RelativeMAD method) (phenotypic.analysis.ReplicateAgreement method) (phenotypic.analysis.TukeyOutlierFraction method) (phenotypic.analysis.TukeyOutlierRemover method) (phenotypic.measure.MeasureOrientationZones method) (phenotypic.measure.MeasureSymmetricZones method) dashboard() (phenotypic.correction.ColorCheckerProfile method) (phenotypic.correction.ColorCorrector method) (phenotypic.grid.AutoGridFinder method) (phenotypic.measure.MeasureOrientationZones method) dashboard_html_path() (in module phenotypic.sdk_) DashboardManifestKey (class in phenotypic.sdk_) DashboardManifestSlurmInfoKey (class in phenotypic.sdk_) DataIntegrityError dataset_changed (phenotypic.tune.GeneralizationReport attribute) dataset_hdf_dir() (in module phenotypic.sdk_) dataset_measurements_dir() (in module phenotypic.sdk_) dataset_overlays_dir() (in module phenotypic.sdk_) dataset_results_dir() (in module phenotypic.sdk_) DATASETS (phenotypic.sdk_.ChunkManifestKey attribute) (phenotypic.sdk_.DashboardManifestKey attribute) (phenotypic.sdk_.JobMetadataKey attribute) (phenotypic.sdk_.ProcessingStateKey attribute) decode_srgb() (in module phenotypic.sdk_.colourspace) decode_well_position() (in module phenotypic.util) default (phenotypic.abc_.Control attribute) default_output_dir_name() (in module phenotypic.sdk_) DEFAULT_SCHEMA (phenotypic.sdk_.constants_.IMAGE_MODE attribute) degree (phenotypic.correction.ColorCheckerProfile attribute) (phenotypic.correction.ColorCorrector property) deliverables_base (phenotypic.sdk_.BundleLayout attribute), [1] deliverables_dir() (in module phenotypic.sdk_) delta (phenotypic.detect.FilamentousFungiDetector attribute) delta_e2000_spread() (in module phenotypic.util) DenoiseBlockMatch (class in phenotypic.correction) derivation_type (phenotypic.abc_.MeasurementInfo attribute) (phenotypic.sdk_.constants_.ConstantLabels attribute) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS attribute) (phenotypic.sdk_.constants_.PIPE_STATUS attribute) derives_from (phenotypic.abc_.MeasurementInfo attribute) (phenotypic.sdk_.constants_.ConstantLabels attribute) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS attribute) (phenotypic.sdk_.constants_.PIPE_STATUS attribute) desc (phenotypic.abc_.MeasurementInfo attribute), [1] (phenotypic.abc_.PrefabPipeline property) (phenotypic.gui.builder._state._DagBuilderScope attribute), [1] (phenotypic.prefab.FilamentousFungiPipeline property) (phenotypic.prefab.GridSectionPipeline property) (phenotypic.prefab.HeavyOtsuPipeline property) (phenotypic.prefab.HeavyRoundPeaksPipeline property) (phenotypic.prefab.HeavyWatershedPipeline property) (phenotypic.prefab.RoundPeaksPipeline property) (phenotypic.prefab.SpImagerPipeline property) (phenotypic.sdk_.constants_.ConstantLabels attribute) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS attribute) (phenotypic.sdk_.constants_.PIPE_STATUS attribute) desc_value (phenotypic.abc_.PrefabPipeline attribute) (phenotypic.prefab.FilamentousFungiPipeline attribute) (phenotypic.prefab.GridSectionPipeline attribute) (phenotypic.prefab.HeavyOtsuPipeline attribute) (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) (phenotypic.prefab.HeavyWatershedPipeline attribute) (phenotypic.prefab.RoundPeaksPipeline attribute) (phenotypic.prefab.SpImagerPipeline attribute) description (phenotypic.abc_.FigureSpec attribute), [1] (phenotypic.tune.Knob attribute) DET_EPS (phenotypic.grid.CenteredAutoGridFinder attribute) detail (phenotypic.gui.builder._validation.Issue attribute), [1] detect() (phenotypic.sdk_.BundleLayout class method) detect_mat (phenotypic.Image property) detect_modes() (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) DetectionMode (class in phenotypic.abc_) DetectMatAccessor (class in phenotypic._core._image_parts.accessors._detect_mat_accessor) detector_edge_refinement (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) detector_footprint_width (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) detector_min_peak_distance (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) detector_noise_radius (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) detector_peak_prominence (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) detector_remove_noise (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) detector_selection_mode (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) detector_smoothing_sigma (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) detector_split_merged (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) detector_subtract_background (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) detector_thresh_method (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) diagnostics (phenotypic.correction.ColorCheckerProfile attribute), [1] diagnostics() (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) dict() (phenotypic.abc_.BackgroundSubtraction method) (phenotypic.abc_.BaseOperation method) (phenotypic.abc_.ContrastAdjustment method) (phenotypic.abc_.FocusBlob method) (phenotypic.abc_.FocusEdge method) (phenotypic.abc_.GpuDetector method) (phenotypic.abc_.GridCorrector method) (phenotypic.abc_.GridFinder method) (phenotypic.abc_.GridMeasureFeatures method) (phenotypic.abc_.GridObjectDetector method) (phenotypic.abc_.GridObjectRefiner method) (phenotypic.abc_.GridOperation method) (phenotypic.abc_.ImageCorrector method) (phenotypic.abc_.ImageDenoiser method) (phenotypic.abc_.ImageEnhancer method) (phenotypic.abc_.ImageOperation method) (phenotypic.abc_.MeasureFeatures method) (phenotypic.abc_.MorphologicalFiltering method) (phenotypic.abc_.ObjectDetector method) (phenotypic.abc_.ObjectRefiner method) (phenotypic.abc_.PostMeasurement method) (phenotypic.abc_.PrefabPipeline method) (phenotypic.abc_.Smoothing method) (phenotypic.abc_.ThresholdDetector method) (phenotypic.analysis.EdgeCorrector method) (phenotypic.analysis.ErrorCutoffFinder method) (phenotypic.analysis.ExpectedVsDetectedCount method) (phenotypic.analysis.GridOccupancy method) (phenotypic.analysis.ICC method) (phenotypic.analysis.LinearCapAndLagModel method) (phenotypic.analysis.LinearLagModel method) (phenotypic.analysis.LogGrowthModel method) (phenotypic.analysis.MADOutlierRemover method) (phenotypic.analysis.MaxModifiedZScore method) (phenotypic.analysis.RelativeMAD method) (phenotypic.analysis.ReplicateAgreement method) (phenotypic.analysis.TukeyOutlierFraction method) (phenotypic.analysis.TukeyOutlierRemover method) (phenotypic.correction.BayesShrinkCorrector method) (phenotypic.correction.CaptureMetadata method) (phenotypic.correction.ColorCheckerProfile method) (phenotypic.correction.ColorCorrector method) (phenotypic.correction.ColorDenoise method) (phenotypic.correction.DenoiseBlockMatch method) (phenotypic.correction.GridAligner method) (phenotypic.correction.ImageCropper method) (phenotypic.correction.ImagePadder method) (phenotypic.correction.VisuShrinkCorrector method) (phenotypic.detect.CannyDetector method) (phenotypic.detect.ChanVeseDetector method) (phenotypic.detect.CompositeDetector method) (phenotypic.detect.FilamentousFungiDetector method) (phenotypic.detect.HysteresisDetector method) (phenotypic.detect.InoculumDetector method) (phenotypic.detect.IsodataDetector method) (phenotypic.detect.LiDetector method) (phenotypic.detect.MadHysteresisDetector method) (phenotypic.detect.ManualGridPointDetector method) (phenotypic.detect.ManualPointDetector method) (phenotypic.detect.MeanDetector method) (phenotypic.detect.MinimumDetector method) (phenotypic.detect.OtsuDetector method) (phenotypic.detect.RankOtsuDetector method) (phenotypic.detect.RoundPeaksDetector method) (phenotypic.detect.SecondaryOtsuDetector method) (phenotypic.detect.SinePeakDetector method) (phenotypic.detect.TriangleDetector method) (phenotypic.detect.UserThreshold method) (phenotypic.detect.WatershedDetector method) (phenotypic.detect.YenDetector method) (phenotypic.enhance.BayesShrinkEnhancer method) (phenotypic.enhance.CompositeEnhance method) (phenotypic.enhance.ContrastStretching method) (phenotypic.enhance.EnhanceBlockMatch method) (phenotypic.enhance.EnhanceLocalContrast method) (phenotypic.enhance.FlattenIllumination method) (phenotypic.enhance.FocusBlobLoG method) (phenotypic.enhance.FocusEdgeFrangi method) (phenotypic.enhance.FocusEdgeHessian method) (phenotypic.enhance.FocusEdgeLaplace method) (phenotypic.enhance.FocusEdgeMeijering method) (phenotypic.enhance.FocusEdgePhase method) (phenotypic.enhance.FocusEdgeSato method) (phenotypic.enhance.FocusEdgeSobel method) (phenotypic.enhance.GaussianBlur method) (phenotypic.enhance.GrayOpening method) (phenotypic.enhance.ImageInverter method) (phenotypic.enhance.LocalEdgeDenoise method) (phenotypic.enhance.MedianFilter method) (phenotypic.enhance.NonLocalMeansDenoiser method) (phenotypic.enhance.RankMedianEnhancer method) (phenotypic.enhance.SetDetectMode method) (phenotypic.enhance.SharpenEdgeGauss method) (phenotypic.enhance.StructureSmoothing method) (phenotypic.enhance.SubtractGaussian method) (phenotypic.enhance.SubtractOpening method) (phenotypic.enhance.SubtractRollingBall method) (phenotypic.enhance.SubtractWhiteTophat method) (phenotypic.enhance.VisuShrinkEnhancer method) (phenotypic.enhance.WhiteTophatEnhance method) (phenotypic.grid.AutoGridFinder method) (phenotypic.grid.CenteredAutoGridFinder method) (phenotypic.grid.GridApply method) (phenotypic.grid.ManualGridFinder method) (phenotypic.measure.MeasureBounds method) (phenotypic.measure.MeasureColor method) (phenotypic.measure.MeasureGridLinRegStats method) (phenotypic.measure.MeasureGridSpread method) (phenotypic.measure.MeasureIntensity method) (phenotypic.measure.MeasureNeighborDist method) (phenotypic.measure.MeasureOrientationZones method) (phenotypic.measure.MeasureShape method) (phenotypic.measure.MeasureSize method) (phenotypic.measure.MeasureSymmetricZones method) (phenotypic.measure.MeasureTexture method) (phenotypic.prefab.FilamentousFungiPipeline method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.prefab.RoundPeaksPipeline method) (phenotypic.prefab.SpImagerPipeline method) (phenotypic.refine.ExtractColonyCore method) (phenotypic.refine.GridAlignmentRefiner method) (phenotypic.refine.GridOversizedObjectRemover method) (phenotypic.refine.KeepNearestCenter method) (phenotypic.refine.KeepSectionLargest method) (phenotypic.refine.ManualRefine method) (phenotypic.refine.MaskClosing method) (phenotypic.refine.MaskDilation method) (phenotypic.refine.MaskErosion method) (phenotypic.refine.MaskFill method) (phenotypic.refine.MaskGradient method) (phenotypic.refine.MaskOpening method) (phenotypic.refine.MaskWhiteTophat method) (phenotypic.refine.MergeFragmentChains method) (phenotypic.refine.NearestNeighborMerger method) (phenotypic.refine.ReduceSectionsByLine method) (phenotypic.refine.RefineBySineFit method) (phenotypic.refine.RemoveBorderObjects method) (phenotypic.refine.RemoveByFeature method) (phenotypic.refine.RemoveGridOutliers method) (phenotypic.refine.RemoveLowCircularity method) (phenotypic.refine.SeparateObjects method) (phenotypic.refine.Skeletonize method) (phenotypic.refine.SmallObjectRemover method) (phenotypic.refine.SmallToLargeMerger method) (phenotypic.refine.Thinning method) (phenotypic.refine.TrimAsymmetry method) (phenotypic.tune.Budget method) (phenotypic.tune.Categorical method) (phenotypic.tune.EvaluationResult method) (phenotypic.tune.Evaluator method) (phenotypic.tune.Excluded method) (phenotypic.tune.Fixed method) (phenotypic.tune.FloatRange method) (phenotypic.tune.HeldOutConfig method) (phenotypic.tune.ImportanceReport method) (phenotypic.tune.InferredSearchSpace method) (phenotypic.tune.IntRange method) (phenotypic.tune.Knob method) (phenotypic.tune.score.CompositeScorer method) (phenotypic.tune.score.GroundTruthMasks method) (phenotypic.tune.score.QCScorer method) (phenotypic.tune.score.ReferenceFreeScorer method) (phenotypic.tune.score.Scorer method) (phenotypic.tune.score.SupervisedScorer method) (phenotypic.tune.SearchSpace method) (phenotypic.tune.strategy.GridConfig method) (phenotypic.tune.strategy.OptunaConfig method) (phenotypic.tune.strategy.RandomConfig method) (phenotypic.tune.strategy.StrategyConfig method) (phenotypic.tune.Trial method) (phenotypic.tune.TuningSpec method) distance_threshold (phenotypic.refine.MergeFragmentChains attribute) (phenotypic.refine.NearestNeighborMerger attribute) (phenotypic.refine.SmallToLargeMerger attribute) domain (phenotypic.tune.Knob attribute) domain() (phenotypic.tune.SearchSpace method) draw() (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap method) (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask method) dt (phenotypic.detect.ChanVeseDetector attribute) (phenotypic.enhance.StructureSmoothing attribute) 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) E Edge (class in phenotypic.gui.builder._state) edge_id (phenotypic.gui.builder._state.Edge attribute), [1] edge_noise_threshold (phenotypic.detect.FilamentousFungiDetector attribute) edge_refinement (phenotypic.detect.RoundPeaksDetector attribute) (phenotypic.detect.SinePeakDetector attribute) (phenotypic.refine.GridAlignmentRefiner attribute) (phenotypic.refine.RefineBySineFit attribute) EdgeCorrector (class in phenotypic.analysis) edges (phenotypic.gui.builder._state._DagBuilderScope attribute), [1] EmptyImageError enable_gmm (phenotypic.detect.InoculumDetector attribute) encode() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) encode_srgb() (in module phenotypic.sdk_.colourspace) endswith() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) enhance (phenotypic.measure.MeasureTexture attribute) EnhanceBlockMatch (class in phenotypic.enhance) EnhanceLocalContrast (class in phenotypic.enhance) enough_data() (phenotypic.analysis.ErrorCutoffFinder method) ensure_metadata_prefix() (in module phenotypic.sdk_) ensure_typed_json_suffix() (in module phenotypic.sdk_) EnvVar (class in phenotypic.sdk_) eps (phenotypic.analysis.RelativeMAD attribute) (phenotypic.analysis.ReplicateAgreement attribute) (phenotypic.enhance.FlattenIllumination attribute) error_analysis_csv (phenotypic.sdk_.BundleLayout property) error_analysis_csv_path() (in module phenotypic.sdk_) error_analysis_html (phenotypic.sdk_.BundleLayout property) error_analysis_html_path() (in module phenotypic.sdk_) error_analysis_parquet (phenotypic.sdk_.BundleLayout property) error_analysis_parquet_path() (in module phenotypic.sdk_) error_category_parquet() (phenotypic.sdk_.BundleLayout method) error_category_parquet_path() (in module phenotypic.sdk_) ErrorCutoffFinder (class in phenotypic.analysis) ERRORS (phenotypic.sdk_.ProcessingStateKey attribute) errors_dir (phenotypic.sdk_.BundleLayout property) errors_dir() (in module phenotypic.sdk_) estimate (phenotypic.tune.GeneralizationReport attribute) estimate_concurrent_capacity() (in module phenotypic.sdk_.slurm) evaluate() (phenotypic.tune.Evaluator method) EvaluationResult (class in phenotypic.tune) Evaluator (class in phenotypic.tune) evaluator (phenotypic.tune.TuningSpec attribute) event_log_path() (in module phenotypic.sdk_) Excluded (class in phenotypic.tune) excluded (phenotypic.tune.InferredSearchSpace attribute) EXECUTION_MODE (phenotypic.sdk_.DashboardManifestKey attribute) (phenotypic.sdk_.JobMetadataKey attribute) (phenotypic.sdk_.ProcessingStateKey attribute) expandtabs() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) ExpectedVsDetectedCount (class in phenotypic.analysis) exposure_time (phenotypic.correction.CaptureMetadata attribute), [1] EXT (phenotypic.sdk_.HDF attribute), [1] extent_margin (phenotypic.measure.MeasureOrientationZones attribute) (phenotypic.measure.MeasureSymmetricZones attribute) ExtractColonyCore (class in phenotypic.refine) F f_number (phenotypic.correction.CaptureMetadata attribute), [1] f_scale (phenotypic.analysis.LinearCapAndLagModel attribute) (phenotypic.analysis.LinearLagModel attribute) (phenotypic.analysis.LogGrowthModel attribute) fail_threshold (phenotypic.analysis.ExpectedVsDetectedCount attribute) (phenotypic.analysis.GridOccupancy attribute) (phenotypic.analysis.ICC attribute) (phenotypic.analysis.MaxModifiedZScore attribute) (phenotypic.analysis.RelativeMAD attribute) (phenotypic.analysis.ReplicateAgreement attribute) (phenotypic.analysis.TukeyOutlierFraction attribute) FAILED (phenotypic.sdk_.DashboardManifestKey attribute) (phenotypic.sdk_.ProcessingStateKey attribute) failed (phenotypic.tune.EvaluationResult attribute) (phenotypic.tune.Trial attribute) FAILURE_CATEGORIES (phenotypic.sdk_.DashboardManifestKey attribute) failure_score (phenotypic.tune.Evaluator attribute) failures_jsonl_path() (in module phenotypic.sdk_) fast_mode (phenotypic.enhance.NonLocalMeansDenoiser attribute) feature (phenotypic.refine.RemoveByFeature attribute) field_type (phenotypic.tune.Excluded attribute) figure() (in module phenotypic.abc_) FigureProvider (class in phenotypic.abc_) figures() (phenotypic.abc_.FigureProvider method) (phenotypic.measure.MeasureOrientationZones method) (phenotypic.measure.MeasureSymmetricZones method) FigureSpec (class in phenotypic.abc_) FilamentousFungiDetector (class in phenotypic.detect) FilamentousFungiPipeline (class in phenotypic.prefab) filepath (phenotypic.sdk_.HDF attribute), [1] filter_spec_json() (in module phenotypic.analysis) filter_spec_query() (in module phenotypic.analysis) filters (phenotypic.abc_.PrefabPipeline attribute) (phenotypic.prefab.FilamentousFungiPipeline attribute) (phenotypic.prefab.GridSectionPipeline attribute) (phenotypic.prefab.HeavyOtsuPipeline attribute) (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) (phenotypic.prefab.HeavyWatershedPipeline attribute) (phenotypic.prefab.RoundPeaksPipeline attribute) (phenotypic.prefab.SpImagerPipeline attribute) finalize() (phenotypic.tune.score.CompositeScorer method) (phenotypic.tune.score.QCScorer method) (phenotypic.tune.score.ReferenceFreeScorer method) (phenotypic.tune.score.Scorer method) (phenotypic.tune.score.SupervisedScorer method) find() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) fit() (phenotypic.correction.ColorCheckerProfile method) Fixed (class in phenotypic.tune) flag_col() (phenotypic.analysis.ExpectedVsDetectedCount class method) (phenotypic.analysis.GridOccupancy class method) (phenotypic.analysis.ICC class method) (phenotypic.analysis.MaxModifiedZScore class method) (phenotypic.analysis.RelativeMAD class method) (phenotypic.analysis.ReplicateAgreement class method) (phenotypic.analysis.TukeyOutlierFraction class method) flagged (phenotypic.tune.GeneralizationReport attribute) flagged_keys() (phenotypic.analysis.ExpectedVsDetectedCount method) (phenotypic.analysis.GridOccupancy method) (phenotypic.analysis.ICC method) (phenotypic.analysis.MaxModifiedZScore method) (phenotypic.analysis.RelativeMAD method) (phenotypic.analysis.ReplicateAgreement method) (phenotypic.analysis.TukeyOutlierFraction method) FlattenIllumination (class in phenotypic.enhance) FloatRange (class in phenotypic.tune) focal_length (phenotypic.correction.CaptureMetadata attribute), [1] FocusBlob (class in phenotypic.abc_) FocusBlobLoG (class in phenotypic.enhance) FocusEdge (class in phenotypic.abc_) FocusEdgeFrangi (class in phenotypic.enhance) FocusEdgeHessian (class in phenotypic.enhance) FocusEdgeLaplace (class in phenotypic.enhance) FocusEdgeMeijering (class in phenotypic.enhance) FocusEdgePhase (class in phenotypic.enhance) FocusEdgeSato (class in phenotypic.enhance) FocusEdgeSobel (class in phenotypic.enhance) footprint (phenotypic.detect.WatershedDetector attribute) footprint_width (phenotypic.detect.RoundPeaksDetector attribute) (phenotypic.detect.SinePeakDetector attribute) FootprintMixin (class in phenotypic.abc_) (class in phenotypic.sdk_) 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) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) format_map() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) format_sbatch_directives() (in module phenotypic.sdk_.slurm) frag_reach_px (phenotypic.detect.FilamentousFungiDetector attribute) free_param_floor (phenotypic.tune.ScreeningConfig attribute) freeze_epsilon (phenotypic.tune.ScreeningConfig attribute) freeze_flagged (phenotypic.tune.ScreeningResult attribute) freeze_value() (in module phenotypic.tune) from_image() (phenotypic.correction.CaptureMetadata class method) from_json() (phenotypic.abc_.BackgroundSubtraction class method) (phenotypic.abc_.BaseOperation class method) (phenotypic.abc_.ContrastAdjustment class method) (phenotypic.abc_.FocusBlob class method) (phenotypic.abc_.FocusEdge class method) (phenotypic.abc_.GpuDetector class method) (phenotypic.abc_.GridCorrector class method) (phenotypic.abc_.GridFinder class method) (phenotypic.abc_.GridMeasureFeatures class method) (phenotypic.abc_.GridObjectDetector class method) (phenotypic.abc_.GridObjectRefiner class method) (phenotypic.abc_.GridOperation class method) (phenotypic.abc_.ImageCorrector class method) (phenotypic.abc_.ImageDenoiser class method) (phenotypic.abc_.ImageEnhancer class method) (phenotypic.abc_.ImageOperation class method) (phenotypic.abc_.MeasureFeatures class method) (phenotypic.abc_.MorphologicalFiltering class method) (phenotypic.abc_.ObjectDetector class method) (phenotypic.abc_.ObjectRefiner class method) (phenotypic.abc_.PostMeasurement class method) (phenotypic.abc_.PrefabPipeline class method) (phenotypic.abc_.Smoothing class method) (phenotypic.abc_.ThresholdDetector class method) (phenotypic.correction.BayesShrinkCorrector class method) (phenotypic.correction.ColorCheckerProfile class method) (phenotypic.correction.ColorCorrector class method) (phenotypic.correction.ColorDenoise class method) (phenotypic.correction.DenoiseBlockMatch class method) (phenotypic.correction.GridAligner class method) (phenotypic.correction.ImageCropper class method) (phenotypic.correction.ImagePadder class method) (phenotypic.correction.VisuShrinkCorrector class method) (phenotypic.detect.CannyDetector class method) (phenotypic.detect.ChanVeseDetector class method) (phenotypic.detect.CompositeDetector class method) (phenotypic.detect.FilamentousFungiDetector class method) (phenotypic.detect.HysteresisDetector class method) (phenotypic.detect.InoculumDetector class method) (phenotypic.detect.IsodataDetector class method) (phenotypic.detect.LiDetector class method) (phenotypic.detect.MadHysteresisDetector class method) (phenotypic.detect.ManualGridPointDetector class method) (phenotypic.detect.ManualPointDetector class method) (phenotypic.detect.MeanDetector class method) (phenotypic.detect.MinimumDetector class method) (phenotypic.detect.OtsuDetector class method) (phenotypic.detect.RankOtsuDetector class method) (phenotypic.detect.RoundPeaksDetector class method) (phenotypic.detect.SecondaryOtsuDetector class method) (phenotypic.detect.SinePeakDetector class method) (phenotypic.detect.TriangleDetector class method) (phenotypic.detect.UserThreshold class method) (phenotypic.detect.WatershedDetector class method) (phenotypic.detect.YenDetector class method) (phenotypic.enhance.BayesShrinkEnhancer class method) (phenotypic.enhance.CompositeEnhance class method) (phenotypic.enhance.ContrastStretching class method) (phenotypic.enhance.EnhanceBlockMatch class method) (phenotypic.enhance.EnhanceLocalContrast class method) (phenotypic.enhance.FlattenIllumination class method) (phenotypic.enhance.FocusBlobLoG class method) (phenotypic.enhance.FocusEdgeFrangi class method) (phenotypic.enhance.FocusEdgeHessian class method) (phenotypic.enhance.FocusEdgeLaplace class method) (phenotypic.enhance.FocusEdgeMeijering class method) (phenotypic.enhance.FocusEdgePhase class method) (phenotypic.enhance.FocusEdgeSato class method) (phenotypic.enhance.FocusEdgeSobel class method) (phenotypic.enhance.GaussianBlur class method) (phenotypic.enhance.GrayOpening class method) (phenotypic.enhance.ImageInverter class method) (phenotypic.enhance.LocalEdgeDenoise class method) (phenotypic.enhance.MedianFilter class method) (phenotypic.enhance.NonLocalMeansDenoiser class method) (phenotypic.enhance.RankMedianEnhancer class method) (phenotypic.enhance.SetDetectMode class method) (phenotypic.enhance.SharpenEdgeGauss class method) (phenotypic.enhance.StructureSmoothing class method) (phenotypic.enhance.SubtractGaussian class method) (phenotypic.enhance.SubtractOpening class method) (phenotypic.enhance.SubtractRollingBall class method) (phenotypic.enhance.SubtractWhiteTophat class method) (phenotypic.enhance.VisuShrinkEnhancer class method) (phenotypic.enhance.WhiteTophatEnhance class method) (phenotypic.grid.AutoGridFinder class method) (phenotypic.grid.CenteredAutoGridFinder class method) (phenotypic.grid.GridApply class method) (phenotypic.grid.ManualGridFinder class method) (phenotypic.ImagePipeline class method) (phenotypic.measure.MeasureBounds class method) (phenotypic.measure.MeasureColor class method) (phenotypic.measure.MeasureGridLinRegStats class method) (phenotypic.measure.MeasureGridSpread class method) (phenotypic.measure.MeasureIntensity class method) (phenotypic.measure.MeasureNeighborDist class method) (phenotypic.measure.MeasureOrientationZones class method) (phenotypic.measure.MeasureShape class method) (phenotypic.measure.MeasureSize class method) (phenotypic.measure.MeasureSymmetricZones class method) (phenotypic.measure.MeasureTexture class method) (phenotypic.prefab.FilamentousFungiPipeline class method) (phenotypic.prefab.GridSectionPipeline class method) (phenotypic.prefab.HeavyOtsuPipeline class method) (phenotypic.prefab.HeavyRoundPeaksPipeline class method) (phenotypic.prefab.HeavyWatershedPipeline class method) (phenotypic.prefab.RoundPeaksPipeline class method) (phenotypic.prefab.SpImagerPipeline class method) (phenotypic.refine.ExtractColonyCore class method) (phenotypic.refine.GridAlignmentRefiner class method) (phenotypic.refine.GridOversizedObjectRemover class method) (phenotypic.refine.KeepNearestCenter class method) (phenotypic.refine.KeepSectionLargest class method) (phenotypic.refine.ManualRefine class method) (phenotypic.refine.MaskClosing class method) (phenotypic.refine.MaskDilation class method) (phenotypic.refine.MaskErosion class method) (phenotypic.refine.MaskFill class method) (phenotypic.refine.MaskGradient class method) (phenotypic.refine.MaskOpening class method) (phenotypic.refine.MaskWhiteTophat class method) (phenotypic.refine.MergeFragmentChains class method) (phenotypic.refine.NearestNeighborMerger class method) (phenotypic.refine.ReduceSectionsByLine class method) (phenotypic.refine.RefineBySineFit class method) (phenotypic.refine.RemoveBorderObjects class method) (phenotypic.refine.RemoveByFeature class method) (phenotypic.refine.RemoveGridOutliers class method) (phenotypic.refine.RemoveLowCircularity class method) (phenotypic.refine.SeparateObjects class method) (phenotypic.refine.Skeletonize class method) (phenotypic.refine.SmallObjectRemover class method) (phenotypic.refine.SmallToLargeMerger class method) (phenotypic.refine.Thinning class method) (phenotypic.refine.TrimAsymmetry class method) from_orm() (phenotypic.abc_.BackgroundSubtraction class method) (phenotypic.abc_.BaseOperation class method) (phenotypic.abc_.ContrastAdjustment class method) (phenotypic.abc_.FocusBlob class method) (phenotypic.abc_.FocusEdge class method) (phenotypic.abc_.GpuDetector class method) (phenotypic.abc_.GridCorrector class method) (phenotypic.abc_.GridFinder class method) (phenotypic.abc_.GridMeasureFeatures class method) (phenotypic.abc_.GridObjectDetector class method) (phenotypic.abc_.GridObjectRefiner class method) (phenotypic.abc_.GridOperation class method) (phenotypic.abc_.ImageCorrector class method) (phenotypic.abc_.ImageDenoiser class method) (phenotypic.abc_.ImageEnhancer class method) (phenotypic.abc_.ImageOperation class method) (phenotypic.abc_.MeasureFeatures class method) (phenotypic.abc_.MorphologicalFiltering class method) (phenotypic.abc_.ObjectDetector class method) (phenotypic.abc_.ObjectRefiner class method) (phenotypic.abc_.PostMeasurement class method) (phenotypic.abc_.PrefabPipeline class method) (phenotypic.abc_.Smoothing class method) (phenotypic.abc_.ThresholdDetector class method) (phenotypic.analysis.EdgeCorrector class method) (phenotypic.analysis.ErrorCutoffFinder class method) (phenotypic.analysis.ExpectedVsDetectedCount class method) (phenotypic.analysis.GridOccupancy class method) (phenotypic.analysis.ICC class method) (phenotypic.analysis.LinearCapAndLagModel class method) (phenotypic.analysis.LinearLagModel class method) (phenotypic.analysis.LogGrowthModel class method) (phenotypic.analysis.MADOutlierRemover class method) (phenotypic.analysis.MaxModifiedZScore class method) (phenotypic.analysis.RelativeMAD class method) (phenotypic.analysis.ReplicateAgreement class method) (phenotypic.analysis.TukeyOutlierFraction class method) (phenotypic.analysis.TukeyOutlierRemover class method) (phenotypic.correction.BayesShrinkCorrector class method) (phenotypic.correction.CaptureMetadata class method) (phenotypic.correction.ColorCheckerProfile class method) (phenotypic.correction.ColorCorrector class method) (phenotypic.correction.ColorDenoise class method) (phenotypic.correction.DenoiseBlockMatch class method) (phenotypic.correction.GridAligner class method) (phenotypic.correction.ImageCropper class method) (phenotypic.correction.ImagePadder class method) (phenotypic.correction.VisuShrinkCorrector class method) (phenotypic.detect.CannyDetector class method) (phenotypic.detect.ChanVeseDetector class method) (phenotypic.detect.CompositeDetector class method) (phenotypic.detect.FilamentousFungiDetector class method) (phenotypic.detect.HysteresisDetector class method) (phenotypic.detect.InoculumDetector class method) (phenotypic.detect.IsodataDetector class method) (phenotypic.detect.LiDetector class method) (phenotypic.detect.MadHysteresisDetector class method) (phenotypic.detect.ManualGridPointDetector class method) (phenotypic.detect.ManualPointDetector class method) (phenotypic.detect.MeanDetector class method) (phenotypic.detect.MinimumDetector class method) (phenotypic.detect.OtsuDetector class method) (phenotypic.detect.RankOtsuDetector class method) (phenotypic.detect.RoundPeaksDetector class method) (phenotypic.detect.SecondaryOtsuDetector class method) (phenotypic.detect.SinePeakDetector class method) (phenotypic.detect.TriangleDetector class method) (phenotypic.detect.UserThreshold class method) (phenotypic.detect.WatershedDetector class method) (phenotypic.detect.YenDetector class method) (phenotypic.enhance.BayesShrinkEnhancer class method) (phenotypic.enhance.CompositeEnhance class method) (phenotypic.enhance.ContrastStretching class method) (phenotypic.enhance.EnhanceBlockMatch class method) (phenotypic.enhance.EnhanceLocalContrast class method) (phenotypic.enhance.FlattenIllumination class method) (phenotypic.enhance.FocusBlobLoG class method) (phenotypic.enhance.FocusEdgeFrangi class method) (phenotypic.enhance.FocusEdgeHessian class method) (phenotypic.enhance.FocusEdgeLaplace class method) (phenotypic.enhance.FocusEdgeMeijering class method) (phenotypic.enhance.FocusEdgePhase class method) (phenotypic.enhance.FocusEdgeSato class method) (phenotypic.enhance.FocusEdgeSobel class method) (phenotypic.enhance.GaussianBlur class method) (phenotypic.enhance.GrayOpening class method) (phenotypic.enhance.ImageInverter class method) (phenotypic.enhance.LocalEdgeDenoise class method) (phenotypic.enhance.MedianFilter class method) (phenotypic.enhance.NonLocalMeansDenoiser class method) (phenotypic.enhance.RankMedianEnhancer class method) (phenotypic.enhance.SetDetectMode class method) (phenotypic.enhance.SharpenEdgeGauss class method) (phenotypic.enhance.StructureSmoothing class method) (phenotypic.enhance.SubtractGaussian class method) (phenotypic.enhance.SubtractOpening class method) (phenotypic.enhance.SubtractRollingBall class method) (phenotypic.enhance.SubtractWhiteTophat class method) (phenotypic.enhance.VisuShrinkEnhancer class method) (phenotypic.enhance.WhiteTophatEnhance class method) (phenotypic.grid.AutoGridFinder class method) (phenotypic.grid.CenteredAutoGridFinder class method) (phenotypic.grid.GridApply class method) (phenotypic.grid.ManualGridFinder class method) (phenotypic.measure.MeasureBounds class method) (phenotypic.measure.MeasureColor class method) (phenotypic.measure.MeasureGridLinRegStats class method) (phenotypic.measure.MeasureGridSpread class method) (phenotypic.measure.MeasureIntensity class method) (phenotypic.measure.MeasureNeighborDist class method) (phenotypic.measure.MeasureOrientationZones class method) (phenotypic.measure.MeasureShape class method) (phenotypic.measure.MeasureSize class method) (phenotypic.measure.MeasureSymmetricZones class method) (phenotypic.measure.MeasureTexture class method) (phenotypic.prefab.FilamentousFungiPipeline class method) (phenotypic.prefab.GridSectionPipeline class method) (phenotypic.prefab.HeavyOtsuPipeline class method) (phenotypic.prefab.HeavyRoundPeaksPipeline class method) (phenotypic.prefab.HeavyWatershedPipeline class method) (phenotypic.prefab.RoundPeaksPipeline class method) (phenotypic.prefab.SpImagerPipeline class method) (phenotypic.refine.ExtractColonyCore class method) (phenotypic.refine.GridAlignmentRefiner class method) (phenotypic.refine.GridOversizedObjectRemover class method) (phenotypic.refine.KeepNearestCenter class method) (phenotypic.refine.KeepSectionLargest class method) (phenotypic.refine.ManualRefine class method) (phenotypic.refine.MaskClosing class method) (phenotypic.refine.MaskDilation class method) (phenotypic.refine.MaskErosion class method) (phenotypic.refine.MaskFill class method) (phenotypic.refine.MaskGradient class method) (phenotypic.refine.MaskOpening class method) (phenotypic.refine.MaskWhiteTophat class method) (phenotypic.refine.MergeFragmentChains class method) (phenotypic.refine.NearestNeighborMerger class method) (phenotypic.refine.ReduceSectionsByLine class method) (phenotypic.refine.RefineBySineFit class method) (phenotypic.refine.RemoveBorderObjects class method) (phenotypic.refine.RemoveByFeature class method) (phenotypic.refine.RemoveGridOutliers class method) (phenotypic.refine.RemoveLowCircularity class method) (phenotypic.refine.SeparateObjects class method) (phenotypic.refine.Skeletonize class method) (phenotypic.refine.SmallObjectRemover class method) (phenotypic.refine.SmallToLargeMerger class method) (phenotypic.refine.Thinning class method) (phenotypic.refine.TrimAsymmetry class method) (phenotypic.tune.Budget class method) (phenotypic.tune.Categorical class method) (phenotypic.tune.EvaluationResult class method) (phenotypic.tune.Evaluator class method) (phenotypic.tune.Excluded class method) (phenotypic.tune.Fixed class method) (phenotypic.tune.FloatRange class method) (phenotypic.tune.HeldOutConfig class method) (phenotypic.tune.ImportanceReport class method) (phenotypic.tune.InferredSearchSpace class method) (phenotypic.tune.IntRange class method) (phenotypic.tune.Knob class method) (phenotypic.tune.score.CompositeScorer class method) (phenotypic.tune.score.GroundTruthMasks class method) (phenotypic.tune.score.QCScorer class method) (phenotypic.tune.score.ReferenceFreeScorer class method) (phenotypic.tune.score.Scorer class method) (phenotypic.tune.score.SupervisedScorer class method) (phenotypic.tune.SearchSpace class method) (phenotypic.tune.strategy.GridConfig class method) (phenotypic.tune.strategy.OptunaConfig class method) (phenotypic.tune.strategy.RandomConfig class method) (phenotypic.tune.strategy.StrategyConfig class method) (phenotypic.tune.Trial class method) (phenotypic.tune.TuningSpec class method) from_parquet() (phenotypic.tune.JournalStudyStore class method) from_pipeline_dag() (in module phenotypic.gui.builder._conversion_dag) fromkeys() (phenotypic.util.BackgroundMetrics class method) (phenotypic.util.ContrastMetrics class method) (phenotypic.util.NoiseMetrics class method) (phenotypic.util.QualityScores class method) (phenotypic.util.StructureMetrics class method) frozen (phenotypic.tune.ScreeningResult attribute) G g (phenotypic.enhance.FocusEdgePhase attribute) gain (phenotypic.correction.DenoiseBlockMatch attribute) gamma (phenotypic.detect.FilamentousFungiDetector attribute) (phenotypic.enhance.FocusEdgeFrangi attribute) (phenotypic.enhance.FocusEdgeHessian attribute) GAMMA_ENCODINGS (class in phenotypic.sdk_.constants_) gamma_high (phenotypic.enhance.FlattenIllumination attribute) gamma_low (phenotypic.enhance.FlattenIllumination attribute) gap (phenotypic.tune.EvaluationResult attribute) (phenotypic.tune.GeneralizationReport attribute) (phenotypic.tune.Trial attribute) gap_crossing_penalty (phenotypic.detect.FilamentousFungiDetector attribute) gap_margin_absolute (phenotypic.tune.GeneralizationReport attribute) (phenotypic.tune.HeldOutConfig attribute) gap_margin_relative (phenotypic.tune.GeneralizationReport attribute) (phenotypic.tune.HeldOutConfig attribute) gat_gain (phenotypic.correction.BayesShrinkCorrector attribute) (phenotypic.correction.ColorDenoise attribute) (phenotypic.correction.VisuShrinkCorrector attribute) (phenotypic.enhance.BayesShrinkEnhancer attribute) (phenotypic.enhance.EnhanceBlockMatch attribute) (phenotypic.enhance.LocalEdgeDenoise attribute) (phenotypic.enhance.NonLocalMeansDenoiser attribute) (phenotypic.enhance.VisuShrinkEnhancer attribute) gat_mu (phenotypic.correction.BayesShrinkCorrector attribute) (phenotypic.correction.ColorDenoise attribute) (phenotypic.correction.VisuShrinkCorrector attribute) (phenotypic.enhance.BayesShrinkEnhancer attribute) (phenotypic.enhance.EnhanceBlockMatch attribute) (phenotypic.enhance.LocalEdgeDenoise attribute) (phenotypic.enhance.NonLocalMeansDenoiser attribute) (phenotypic.enhance.VisuShrinkEnhancer attribute) gat_read_sigma (phenotypic.correction.BayesShrinkCorrector attribute) (phenotypic.correction.ColorDenoise attribute) (phenotypic.correction.VisuShrinkCorrector attribute) (phenotypic.enhance.BayesShrinkEnhancer attribute) (phenotypic.enhance.EnhanceBlockMatch attribute) (phenotypic.enhance.LocalEdgeDenoise attribute) (phenotypic.enhance.NonLocalMeansDenoiser attribute) (phenotypic.enhance.VisuShrinkEnhancer attribute) gat_scale_factor (phenotypic.correction.BayesShrinkCorrector attribute) (phenotypic.correction.ColorDenoise attribute) (phenotypic.correction.VisuShrinkCorrector attribute) (phenotypic.enhance.BayesShrinkEnhancer attribute) (phenotypic.enhance.EnhanceBlockMatch attribute) (phenotypic.enhance.LocalEdgeDenoise attribute) (phenotypic.enhance.NonLocalMeansDenoiser attribute) (phenotypic.enhance.VisuShrinkEnhancer attribute) gauss_n_iter (phenotypic.detect.FilamentousFungiDetector attribute) gauss_sigma (phenotypic.detect.FilamentousFungiDetector attribute) GaussianBlur (class in phenotypic.enhance) generalization_path() (in module phenotypic.sdk_) GeneralizationReport (class in phenotypic.tune) generate_dispatcher_chain() (in module phenotypic.sdk_.slurm) generate_dispatcher_script() (in module phenotypic.sdk_.slurm) generate_interpretation() (phenotypic.util.ImageMetricsCalculator static method) generate_output_key() (in module phenotypic.util) generate_recommendations() (phenotypic.util.ImageMetricsCalculator static method) geomedian_max_iter (phenotypic.measure.MeasureColor attribute) geomedian_tol (phenotypic.measure.MeasureColor attribute) geometric_median() (in module phenotypic.util) get() (phenotypic._core._image_parts.accessors._metadata_accessor.MetadataAccessor method) (phenotypic.sdk_.register.AnalysisPluginRegistry class method) (phenotypic.sdk_.register.BaseRegistry class method) (phenotypic.sdk_.register.PlotterRegistry class method) (phenotypic.util.BackgroundMetrics method) (phenotypic.util.ContrastMetrics method) (phenotypic.util.NoiseMetrics method) (phenotypic.util.QualityScores method) (phenotypic.util.StructureMetrics method) get_analysis_plugin() (in module phenotypic.sdk_.register) get_col_edges() (phenotypic.abc_.GridFinder method) (phenotypic.grid.AutoGridFinder method) (phenotypic.grid.CenteredAutoGridFinder method) (phenotypic.grid.ManualGridFinder method) get_data_group() (phenotypic.sdk_.HDF method) get_filters() (phenotypic.abc_.PrefabPipeline method) (phenotypic.prefab.FilamentousFungiPipeline method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.prefab.RoundPeaksPipeline method) (phenotypic.prefab.SpImagerPipeline method) get_group() (phenotypic.sdk_.HDF static method) get_headers() (phenotypic.abc_.MeasurementInfo class method) (phenotypic.sdk_.constants_.ConstantLabels class method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS class method) (phenotypic.sdk_.constants_.PIPE_STATUS class method) get_home() (phenotypic.sdk_.HDF method) get_image_group() (phenotypic.sdk_.HDF method) get_image_measurement_subgroup() (phenotypic.sdk_.HDF method) get_label_idx() (phenotypic._core._image_parts.accessors._objects_accessor.ObjectsAccessor method) get_labels() (phenotypic.abc_.MeasurementInfo class method) (phenotypic.sdk_.constants_.ConstantLabels class method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS class method) (phenotypic.sdk_.constants_.PIPE_STATUS class method) get_meas() (phenotypic.abc_.PrefabPipeline method) (phenotypic.prefab.FilamentousFungiPipeline method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.prefab.RoundPeaksPipeline method) (phenotypic.prefab.SpImagerPipeline method) get_model() (phenotypic.abc_.PrefabPipeline method) (phenotypic.prefab.FilamentousFungiPipeline method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.prefab.RoundPeaksPipeline method) (phenotypic.prefab.SpImagerPipeline method) get_ops() (phenotypic.abc_.PrefabPipeline method) (phenotypic.prefab.FilamentousFungiPipeline method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.prefab.RoundPeaksPipeline method) (phenotypic.prefab.SpImagerPipeline method) get_plotter() (in module phenotypic.sdk_.register) get_post() (phenotypic.abc_.PrefabPipeline method) (phenotypic.prefab.FilamentousFungiPipeline method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.prefab.RoundPeaksPipeline method) (phenotypic.prefab.SpImagerPipeline method) get_protected_metadata_subgroup() (phenotypic.sdk_.HDF method) get_public_metadata_subgroup() (phenotypic.sdk_.HDF method) get_qc() (phenotypic.abc_.PrefabPipeline method) (phenotypic.prefab.FilamentousFungiPipeline method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.prefab.RoundPeaksPipeline method) (phenotypic.prefab.SpImagerPipeline method) get_root_group() (phenotypic.sdk_.HDF method) get_row_edges() (phenotypic.abc_.GridFinder method) (phenotypic.grid.AutoGridFinder method) (phenotypic.grid.CenteredAutoGridFinder method) (phenotypic.grid.ManualGridFinder method) get_slurm_array_limit() (in module phenotypic.sdk_.slurm) get_slurm_max_submit_jobs() (in module phenotypic.sdk_.slurm) get_status_subgroup() (phenotypic.sdk_.HDF method) get_uncompressed_sizes_for_group() (phenotypic.sdk_.HDF static method) gmm_n_components (phenotypic.detect.InoculumDetector attribute) gmm_separation_threshold (phenotypic.detect.InoculumDetector attribute) GpuDetector (class in phenotypic.abc_) gray (phenotypic.Image property) GrayOpening (class in phenotypic.enhance) Grayscale (class in phenotypic._core._image_parts.accessors._grayscale_accessor) GRAYSCALE (phenotypic.sdk_.constants_.IMAGE_MODE attribute) GRAYSCALE_SINGLE_CHANNEL (phenotypic.sdk_.constants_.IMAGE_MODE attribute) GrayscaleOutOfRangeError grid (phenotypic.GridImage property) GRID (phenotypic.sdk_.constants_.IMAGE_TYPES attribute) grid section grid_aligner_axis (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) grid_aligner_mode (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) GRID_LINREG_STATS_EXTRACTOR (class in phenotypic.sdk_.constants_) GRID_SECTION (phenotypic.sdk_.constants_.IMAGE_TYPES attribute) GridAligner (class in phenotypic.correction) GridAlignmentRefiner (class in phenotypic.refine) GridApply (class in phenotypic.grid) GridConfig (class in phenotypic.tune.strategy) GridCorrector (class in phenotypic.abc_) GridFinder (class in phenotypic.abc_) GridImage GridImageInputError GridInferenceMixin (class in phenotypic.sdk_) GridMeasureFeatures (class in phenotypic.abc_) GridObjectDetector (class in phenotypic.abc_) GridObjectRefiner (class in phenotypic.abc_) GridOccupancy (class in phenotypic.analysis) GridOperation (class in phenotypic.abc_) GridOversizedObjectRemover (class in phenotypic.refine) GridSectionPipeline (class in phenotypic.prefab) GridStrategy (class in phenotypic.tune.strategy) GroundTruthMasks (class in phenotypic.tune.score) group_key (phenotypic.tune.HeldOutConfig attribute) group_members() (phenotypic.analysis.ExpectedVsDetectedCount method) (phenotypic.analysis.GridOccupancy method) (phenotypic.analysis.ICC method) (phenotypic.analysis.MaxModifiedZScore method) (phenotypic.analysis.RelativeMAD method) (phenotypic.analysis.ReplicateAgreement method) (phenotypic.analysis.TukeyOutlierFraction method) groupby (phenotypic.analysis.EdgeCorrector attribute) (phenotypic.analysis.ExpectedVsDetectedCount attribute) (phenotypic.analysis.GridOccupancy attribute) (phenotypic.analysis.ICC attribute) (phenotypic.analysis.LinearCapAndLagModel attribute) (phenotypic.analysis.LinearLagModel attribute) (phenotypic.analysis.LogGrowthModel attribute) (phenotypic.analysis.MADOutlierRemover attribute), [1] (phenotypic.analysis.MaxModifiedZScore attribute) (phenotypic.analysis.RelativeMAD attribute) (phenotypic.analysis.ReplicateAgreement attribute) (phenotypic.analysis.TukeyOutlierFraction attribute) (phenotypic.analysis.TukeyOutlierRemover attribute), [1] gt (phenotypic.tune.score.SupervisedScorer attribute) gt_format (phenotypic.tune.score.GroundTruthMasks attribute) gt_masks_source (phenotypic.tune.score.GroundTruthMasks attribute) (phenotypic.tune.score.ReferenceFreeScorer attribute) H h (phenotypic.enhance.NonLocalMeansDenoiser attribute) has_config_suffix() (in module phenotypic.sdk_) has_results (phenotypic.sdk_.BundleLayout property) HDF (class in phenotypic.sdk_) hdf_path() (phenotypic.sdk_.BundleLayout method) HdfAttr (class in phenotypic.sdk_) header_scheme() (phenotypic.abc_.MeasurementInfo class method) (phenotypic.sdk_.constants_.ConstantLabels class method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS class method) (phenotypic.sdk_.constants_.PIPE_STATUS class method) HeavyOtsuPipeline (class in phenotypic.prefab) HeavyRoundPeaksPipeline (class in phenotypic.prefab) HeavyWatershedPipeline (class in phenotypic.prefab) held_out (phenotypic.tune.TuningSpec attribute) held_out_fraction (phenotypic.tune.HeldOutConfig attribute) heldout_score (phenotypic.tune.GeneralizationReport attribute) HeldOutConfig (class in phenotypic.tune) help (phenotypic.abc_.Control attribute) high (phenotypic.detect.HysteresisDetector attribute) (phenotypic.tune.FloatRange attribute) (phenotypic.tune.IntRange attribute) (phenotypic.tune.TuneSpec attribute) high_threshold (phenotypic.detect.CannyDetector attribute) 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] hsv (phenotypic._core._image_parts.accessors._color_accessor.ColorAccessor property) HSV (phenotypic.sdk_.constants_.IMAGE_MODE attribute) hsv_to_cone() (in module phenotypic.util) hyphae HysteresisDetector (class in phenotypic.detect) I ICC (class in phenotypic.analysis) ignore_borders (phenotypic.detect.FilamentousFungiDetector attribute) (phenotypic.detect.HysteresisDetector attribute) (phenotypic.detect.IsodataDetector attribute) (phenotypic.detect.LiDetector attribute) (phenotypic.detect.MadHysteresisDetector attribute) (phenotypic.detect.MeanDetector attribute) (phenotypic.detect.MinimumDetector attribute) (phenotypic.detect.OtsuDetector attribute) (phenotypic.detect.UserThreshold attribute) (phenotypic.detect.YenDetector attribute) ignore_zeros (phenotypic.detect.HysteresisDetector attribute) (phenotypic.detect.IsodataDetector attribute) (phenotypic.detect.LiDetector attribute) (phenotypic.detect.MadHysteresisDetector attribute) (phenotypic.detect.MeanDetector attribute) (phenotypic.detect.MinimumDetector attribute) (phenotypic.detect.OtsuDetector attribute) (phenotypic.detect.RankOtsuDetector attribute) (phenotypic.detect.UserThreshold attribute) (phenotypic.detect.WatershedDetector attribute) (phenotypic.detect.YenDetector attribute) IllegalAssignmentError IllegalElementAssignmentError iloc() (phenotypic._core._image_parts.accessors._objects_accessor.ObjectsAccessor method) Image image (phenotypic.abc_.MeasurementInfo attribute), [1] (phenotypic.sdk_.constants_.ConstantLabels attribute) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS attribute) (phenotypic.sdk_.constants_.PIPE_STATUS attribute) IMAGE_MEASUREMENT_IMAGE_SUBGROUP_KEY (phenotypic.sdk_.constants_.IO attribute) IMAGE_MEASUREMENT_SUBGROUP_KEY (phenotypic.sdk_.HDF attribute), [1] IMAGE_MODE (class in phenotypic.sdk_.constants_) image_op (phenotypic.grid.GridApply attribute) IMAGE_SET_DATA_POSIX (phenotypic.sdk_.HDF attribute), [1] IMAGE_SET_HDF5_PARENT_GROUP (phenotypic.sdk_.constants_.IO attribute) IMAGE_SET_ROOT_POSIX (phenotypic.sdk_.HDF attribute), [1] IMAGE_STATUS_SUBGROUP_KEY (phenotypic.sdk_.constants_.IO attribute) (phenotypic.sdk_.HDF attribute), [1] IMAGE_TASK_MAPPING (phenotypic.sdk_.JobMetadataKey attribute) IMAGE_TYPES (class in phenotypic.sdk_.constants_) ImageCorrector (class in phenotypic.abc_) ImageCropper (class in phenotypic.correction) ImageDenoiser (class in phenotypic.abc_) ImageEnhancer (class in phenotypic.abc_) ImageInverter (class in phenotypic.enhance) ImageMetricsCalculator (class in phenotypic.util) ImageOperation (class in phenotypic.abc_) ImageOperationError ImagePadder (class in phenotypic.correction) ImagePipeline ImageRGB (class in phenotypic._core._image_parts.accessors._rgb_accessor) ImmutableComponentError ImportanceReport (class in phenotypic.tune) importances (phenotypic.tune.ImportanceReport attribute) 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) include_xy (phenotypic.measure.MeasureColor attribute) include_XYZ (phenotypic.measure.MeasureColor attribute) index() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) infer_group_key() (in module phenotypic.tune) infer_search_space() (in module phenotypic.tune) InferredSearchSpace (class in phenotypic.tune) info() (phenotypic._core._image_parts.accessors._objects_accessor.ObjectsAccessor method) init_level_set (phenotypic.detect.ChanVeseDetector attribute) INITIAL_IMAGES (phenotypic.sdk_.ProcessingStateKey attribute) inoculum inoculum_detector (phenotypic.detect.FilamentousFungiDetector attribute) InoculumDetector (class in phenotypic.detect) INPUT_IMAGE_CLASS_NAME (in module phenotypic.gui.builder._state) input_layer (phenotypic.abc_.GpuDetector attribute) INPUT_PATH (phenotypic.sdk_.DashboardManifestKey attribute) (phenotypic.sdk_.JobMetadataKey attribute) (phenotypic.sdk_.ProcessingStateKey attribute) InputShapeMismatchError insert_metadata() (phenotypic._core._image_parts.accessors._metadata_accessor.MetadataAccessor method) inspect() (phenotypic.abc_.FigureProvider method) (phenotypic.measure.MeasureOrientationZones method) (phenotypic.measure.MeasureSymmetricZones method) intensity_source (phenotypic.measure.MeasureOrientationZones attribute) (phenotypic.measure.MeasureSymmetricZones attribute) interactions_estimated (phenotypic.tune.ImportanceReport attribute) (phenotypic.tune.ScreeningResult attribute) InterfaceError IntRange (class in phenotypic.tune) InvalidHsvSchemaError InvalidMapValueError InvalidMaskScalarValueError InvalidMaskValueError InvalidShapeError invert_edges (phenotypic.detect.CannyDetector attribute) IO (class in phenotypic.sdk_.constants_) iou_tau (phenotypic.tune.score.SupervisedScorer attribute) is_active() (phenotypic.tune.Knob method) is_ambiguous() (phenotypic.sdk_.constants_.IMAGE_MODE method) is_array() (phenotypic.sdk_.constants_.IMAGE_MODE method) is_binary_mask() (in module phenotypic.sdk_) IS_COMPLETE (phenotypic.sdk_.DashboardManifestKey attribute) is_exhausted() (phenotypic.tune.strategy.GridStrategy method) (phenotypic.tune.strategy.RandomStrategy method) (phenotypic.tune.strategy.SearchStrategy method) is_fitted (phenotypic.correction.ColorCheckerProfile attribute), [1] is_matrix() (phenotypic.sdk_.constants_.IMAGE_MODE method) is_metadata_header() (in module phenotypic.sdk_) is_none() (phenotypic.sdk_.constants_.IMAGE_MODE method) is_resumable_in_place() (phenotypic.tune.JournalStudyStore method) is_unattended_safe() (phenotypic.tune.score.ReferenceFreeScorer method) isalnum() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) isalpha() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) isascii() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) isdecimal() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) isdigit() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) 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) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) islower() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) isnumeric() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) iso (phenotypic.correction.CaptureMetadata attribute), [1] IsodataDetector (class in phenotypic.detect) isprintable() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) isspace() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) Issue (class in phenotypic.gui.builder._validation) istitle() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) isupper() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) items() (phenotypic._core._image_parts.accessors._metadata_accessor.MetadataAccessor method) (phenotypic.util.BackgroundMetrics method) (phenotypic.util.ContrastMetrics method) (phenotypic.util.NoiseMetrics method) (phenotypic.util.QualityScores method) (phenotypic.util.StructureMetrics method) iter_figures() (phenotypic.abc_.FigureProvider method) (phenotypic.measure.MeasureOrientationZones method) (phenotypic.measure.MeasureSymmetricZones method) J job_metadata_path() (in module phenotypic.sdk_) JobMetadataKey (class in phenotypic.sdk_) join() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) JournalStudyStore (class in phenotypic.tune) JPEG_FILE_EXTENSIONS (phenotypic.sdk_.constants_.IO attribute) json() (phenotypic.abc_.BackgroundSubtraction method) (phenotypic.abc_.BaseOperation method) (phenotypic.abc_.ContrastAdjustment method) (phenotypic.abc_.FocusBlob method) (phenotypic.abc_.FocusEdge method) (phenotypic.abc_.GpuDetector method) (phenotypic.abc_.GridCorrector method) (phenotypic.abc_.GridFinder method) (phenotypic.abc_.GridMeasureFeatures method) (phenotypic.abc_.GridObjectDetector method) (phenotypic.abc_.GridObjectRefiner method) (phenotypic.abc_.GridOperation method) (phenotypic.abc_.ImageCorrector method) (phenotypic.abc_.ImageDenoiser method) (phenotypic.abc_.ImageEnhancer method) (phenotypic.abc_.ImageOperation method) (phenotypic.abc_.MeasureFeatures method) (phenotypic.abc_.MorphologicalFiltering method) (phenotypic.abc_.ObjectDetector method) (phenotypic.abc_.ObjectRefiner method) (phenotypic.abc_.PostMeasurement method) (phenotypic.abc_.PrefabPipeline method) (phenotypic.abc_.Smoothing method) (phenotypic.abc_.ThresholdDetector method) (phenotypic.analysis.EdgeCorrector method) (phenotypic.analysis.ErrorCutoffFinder method) (phenotypic.analysis.ExpectedVsDetectedCount method) (phenotypic.analysis.GridOccupancy method) (phenotypic.analysis.ICC method) (phenotypic.analysis.LinearCapAndLagModel method) (phenotypic.analysis.LinearLagModel method) (phenotypic.analysis.LogGrowthModel method) (phenotypic.analysis.MADOutlierRemover method) (phenotypic.analysis.MaxModifiedZScore method) (phenotypic.analysis.RelativeMAD method) (phenotypic.analysis.ReplicateAgreement method) (phenotypic.analysis.TukeyOutlierFraction method) (phenotypic.analysis.TukeyOutlierRemover method) (phenotypic.correction.BayesShrinkCorrector method) (phenotypic.correction.CaptureMetadata method) (phenotypic.correction.ColorCheckerProfile method) (phenotypic.correction.ColorCorrector method) (phenotypic.correction.ColorDenoise method) (phenotypic.correction.DenoiseBlockMatch method) (phenotypic.correction.GridAligner method) (phenotypic.correction.ImageCropper method) (phenotypic.correction.ImagePadder method) (phenotypic.correction.VisuShrinkCorrector method) (phenotypic.detect.CannyDetector method) (phenotypic.detect.ChanVeseDetector method) (phenotypic.detect.CompositeDetector method) (phenotypic.detect.FilamentousFungiDetector method) (phenotypic.detect.HysteresisDetector method) (phenotypic.detect.InoculumDetector method) (phenotypic.detect.IsodataDetector method) (phenotypic.detect.LiDetector method) (phenotypic.detect.MadHysteresisDetector method) (phenotypic.detect.ManualGridPointDetector method) (phenotypic.detect.ManualPointDetector method) (phenotypic.detect.MeanDetector method) (phenotypic.detect.MinimumDetector method) (phenotypic.detect.OtsuDetector method) (phenotypic.detect.RankOtsuDetector method) (phenotypic.detect.RoundPeaksDetector method) (phenotypic.detect.SecondaryOtsuDetector method) (phenotypic.detect.SinePeakDetector method) (phenotypic.detect.TriangleDetector method) (phenotypic.detect.UserThreshold method) (phenotypic.detect.WatershedDetector method) (phenotypic.detect.YenDetector method) (phenotypic.enhance.BayesShrinkEnhancer method) (phenotypic.enhance.CompositeEnhance method) (phenotypic.enhance.ContrastStretching method) (phenotypic.enhance.EnhanceBlockMatch method) (phenotypic.enhance.EnhanceLocalContrast method) (phenotypic.enhance.FlattenIllumination method) (phenotypic.enhance.FocusBlobLoG method) (phenotypic.enhance.FocusEdgeFrangi method) (phenotypic.enhance.FocusEdgeHessian method) (phenotypic.enhance.FocusEdgeLaplace method) (phenotypic.enhance.FocusEdgeMeijering method) (phenotypic.enhance.FocusEdgePhase method) (phenotypic.enhance.FocusEdgeSato method) (phenotypic.enhance.FocusEdgeSobel method) (phenotypic.enhance.GaussianBlur method) (phenotypic.enhance.GrayOpening method) (phenotypic.enhance.ImageInverter method) (phenotypic.enhance.LocalEdgeDenoise method) (phenotypic.enhance.MedianFilter method) (phenotypic.enhance.NonLocalMeansDenoiser method) (phenotypic.enhance.RankMedianEnhancer method) (phenotypic.enhance.SetDetectMode method) (phenotypic.enhance.SharpenEdgeGauss method) (phenotypic.enhance.StructureSmoothing method) (phenotypic.enhance.SubtractGaussian method) (phenotypic.enhance.SubtractOpening method) (phenotypic.enhance.SubtractRollingBall method) (phenotypic.enhance.SubtractWhiteTophat method) (phenotypic.enhance.VisuShrinkEnhancer method) (phenotypic.enhance.WhiteTophatEnhance method) (phenotypic.grid.AutoGridFinder method) (phenotypic.grid.CenteredAutoGridFinder method) (phenotypic.grid.GridApply method) (phenotypic.grid.ManualGridFinder method) (phenotypic.measure.MeasureBounds method) (phenotypic.measure.MeasureColor method) (phenotypic.measure.MeasureGridLinRegStats method) (phenotypic.measure.MeasureGridSpread method) (phenotypic.measure.MeasureIntensity method) (phenotypic.measure.MeasureNeighborDist method) (phenotypic.measure.MeasureOrientationZones method) (phenotypic.measure.MeasureShape method) (phenotypic.measure.MeasureSize method) (phenotypic.measure.MeasureSymmetricZones method) (phenotypic.measure.MeasureTexture method) (phenotypic.prefab.FilamentousFungiPipeline method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.prefab.RoundPeaksPipeline method) (phenotypic.prefab.SpImagerPipeline method) (phenotypic.refine.ExtractColonyCore method) (phenotypic.refine.GridAlignmentRefiner method) (phenotypic.refine.GridOversizedObjectRemover method) (phenotypic.refine.KeepNearestCenter method) (phenotypic.refine.KeepSectionLargest method) (phenotypic.refine.ManualRefine method) (phenotypic.refine.MaskClosing method) (phenotypic.refine.MaskDilation method) (phenotypic.refine.MaskErosion method) (phenotypic.refine.MaskFill method) (phenotypic.refine.MaskGradient method) (phenotypic.refine.MaskOpening method) (phenotypic.refine.MaskWhiteTophat method) (phenotypic.refine.MergeFragmentChains method) (phenotypic.refine.NearestNeighborMerger method) (phenotypic.refine.ReduceSectionsByLine method) (phenotypic.refine.RefineBySineFit method) (phenotypic.refine.RemoveBorderObjects method) (phenotypic.refine.RemoveByFeature method) (phenotypic.refine.RemoveGridOutliers method) (phenotypic.refine.RemoveLowCircularity method) (phenotypic.refine.SeparateObjects method) (phenotypic.refine.Skeletonize method) (phenotypic.refine.SmallObjectRemover method) (phenotypic.refine.SmallToLargeMerger method) (phenotypic.refine.Thinning method) (phenotypic.refine.TrimAsymmetry method) (phenotypic.tune.Budget method) (phenotypic.tune.Categorical method) (phenotypic.tune.EvaluationResult method) (phenotypic.tune.Evaluator method) (phenotypic.tune.Excluded method) (phenotypic.tune.Fixed method) (phenotypic.tune.FloatRange method) (phenotypic.tune.HeldOutConfig method) (phenotypic.tune.ImportanceReport method) (phenotypic.tune.InferredSearchSpace method) (phenotypic.tune.IntRange method) (phenotypic.tune.Knob method) (phenotypic.tune.score.CompositeScorer method) (phenotypic.tune.score.GroundTruthMasks method) (phenotypic.tune.score.QCScorer method) (phenotypic.tune.score.ReferenceFreeScorer method) (phenotypic.tune.score.Scorer method) (phenotypic.tune.score.SupervisedScorer method) (phenotypic.tune.SearchSpace method) (phenotypic.tune.strategy.GridConfig method) (phenotypic.tune.strategy.OptunaConfig method) (phenotypic.tune.strategy.RandomConfig method) (phenotypic.tune.strategy.StrategyConfig method) (phenotypic.tune.Trial method) (phenotypic.tune.TuningSpec method) K k (phenotypic.analysis.TukeyOutlierFraction attribute) (phenotypic.analysis.TukeyOutlierRemover attribute), [1] (phenotypic.enhance.FocusEdgePhase attribute) k_high (phenotypic.detect.MadHysteresisDetector attribute) k_low (phenotypic.detect.MadHysteresisDetector attribute) KeepNearestCenter (class in phenotypic.refine) KeepSectionLargest (class in phenotypic.refine) kernel (phenotypic.enhance.SubtractRollingBall attribute) kernel_size (phenotypic.enhance.EnhanceLocalContrast attribute) (phenotypic.enhance.FocusEdgeLaplace attribute) key (phenotypic.tune.Excluded attribute) (phenotypic.tune.Knob property) keys() (phenotypic._core._image_parts.accessors._metadata_accessor.MetadataAccessor method) (phenotypic.tune.SearchSpace method) (phenotypic.util.BackgroundMetrics method) (phenotypic.util.ContrastMetrics method) (phenotypic.util.NoiseMetrics method) (phenotypic.util.QualityScores method) (phenotypic.util.StructureMetrics method) kind (phenotypic.abc_.Control attribute) (phenotypic.gui.builder._state.Edge attribute), [1] (phenotypic.gui.builder._validation.Issue attribute), [1] (phenotypic.tune.Categorical attribute) (phenotypic.tune.Fixed attribute) (phenotypic.tune.FloatRange attribute) (phenotypic.tune.GeneralizationReport attribute) (phenotypic.tune.IntRange attribute) (phenotypic.tune.strategy.GridConfig attribute) (phenotypic.tune.strategy.OptunaConfig attribute) (phenotypic.tune.strategy.RandomConfig attribute) kind() (phenotypic.abc_.MeasurementInfo class method) (phenotypic.sdk_.constants_.ConstantLabels class method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS class method) (phenotypic.sdk_.constants_.PIPE_STATUS class method) Kmax_label (phenotypic.analysis.LogGrowthModel attribute) knee_point() (phenotypic.tune.JournalStudyStore method) Knob (class in phenotypic.tune) knobs (phenotypic.tune.InferredSearchSpace attribute) (phenotypic.tune.SearchSpace attribute) L Lab (phenotypic._core._image_parts.accessors._color_accessor.ColorAccessor property) lab_to_srgb_hex() (in module phenotypic.util) label (phenotypic.abc_.Control attribute) (phenotypic.abc_.MeasurementInfo attribute), [1] (phenotypic.gui.builder._state.BlockNode attribute), [1] (phenotypic.sdk_.constants_.ConstantLabels attribute) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS attribute) (phenotypic.sdk_.constants_.PIPE_STATUS attribute) LabelEditorWidget (class in phenotypic.sdk_.napari_) labels (phenotypic._core._image_parts.accessors._objects_accessor.ObjectsAccessor property) labels2series() (phenotypic._core._image_parts.accessors._objects_accessor.ObjectsAccessor method) lam (phenotypic.analysis.LogGrowthModel attribute) lambda1 (phenotypic.detect.ChanVeseDetector attribute) lambda2 (phenotypic.detect.ChanVeseDetector attribute) LAST_UPDATED (phenotypic.sdk_.DashboardManifestKey attribute) (phenotypic.sdk_.ProcessingStateKey attribute) LazyWidgetMixin (class in phenotypic.sdk_) left (phenotypic.correction.ImageCropper attribute) (phenotypic.correction.ImagePadder attribute) lens_model (phenotypic.correction.CaptureMetadata attribute), [1] LiDetector (class in phenotypic.detect) LINEAR (phenotypic.sdk_.constants_.GAMMA_ENCODINGS attribute) LINEAR_RGB (phenotypic.sdk_.constants_.IMAGE_MODE attribute) LinearCapAndLagModel (class in phenotypic.analysis) LinearLagModel (class in phenotypic.analysis) list_slot_counts (phenotypic.gui.builder._state.BlockNode attribute), [1] ljust() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) 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) load_early_colony() (in module phenotypic.data) load_faint_early_colony() (in module phenotypic.data) load_frame() (phenotypic.sdk_.HDF static method) load_fungi_plate() (in module phenotypic.data) load_fungi_plate_full() (in module phenotypic.data) load_hdf5() (phenotypic.Image class method) load_image_from_hdf() (in module phenotypic.sdk_) load_master_measurements() (in module phenotypic.sdk_) load_plate_12hr() (in module phenotypic.data) load_plate_72hr() (in module phenotypic.data) load_series() (phenotypic.sdk_.HDF static method) load_synth_yeast_plate() (in module phenotypic.data) load_yeast_plate() (in module phenotypic.data) load_yeast_plate_full() (in module phenotypic.data) loc() (phenotypic._core._image_parts.accessors._objects_accessor.ObjectsAccessor method) LocalEdgeDenoise (class in phenotypic.enhance) log (phenotypic.tune.FloatRange attribute) (phenotypic.tune.IntRange attribute) (phenotypic.tune.TuneSpec attribute) LogGrowthModel (class in phenotypic.analysis) logs_dir() (in module phenotypic.sdk_) loss (phenotypic.analysis.LinearCapAndLagModel attribute) (phenotypic.analysis.LinearLagModel attribute) (phenotypic.analysis.LogGrowthModel attribute) low (phenotypic.detect.HysteresisDetector attribute) (phenotypic.tune.FloatRange attribute) (phenotypic.tune.IntRange attribute) (phenotypic.tune.TuneSpec attribute) low_threshold (phenotypic.detect.CannyDetector attribute) lower() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) lower_percentile (phenotypic.enhance.ContrastStretching attribute) lstrip() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) M mad_window (phenotypic.detect.FilamentousFungiDetector attribute) MadHysteresisDetector (class in phenotypic.detect) MADOutlierRemover (class in phenotypic.analysis) make_synthetic_colony() (in module phenotypic.data) make_synthetic_filamentous_plate() (in module phenotypic.data) make_synthetic_plate() (in module phenotypic.data) maketrans() (phenotypic.abc_.MeasurementInfo static method) (phenotypic.sdk_.constants_.ConstantLabels static method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS static method) (phenotypic.sdk_.constants_.PIPE_STATUS static method) manifest_json_path() (in module phenotypic.sdk_) ManualGridFinder (class in phenotypic.grid) ManualGridPointDetector (class in phenotypic.detect) ManualPointDetector (class in phenotypic.detect) ManualRefine (class in phenotypic.refine) mask (phenotypic.enhance.FocusEdgeLaplace attribute) mask_fill_origin (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) mask_fill_structure (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) mask_opener_footprint (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) mask_opener_n_iter (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) mask_opener_width (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) MaskClosing (class in phenotypic.refine) MaskDilation (class in phenotypic.refine) MaskErosion (class in phenotypic.refine) MaskFill (class in phenotypic.refine) MaskGradient (class in phenotypic.refine) MaskOpening (class in phenotypic.refine) masks_for() (phenotypic.tune.score.GroundTruthMasks method) MaskWhiteTophat (class in phenotypic.refine) master_csv (phenotypic.sdk_.BundleLayout property) master_measurements_csv_path() (in module phenotypic.sdk_) master_measurements_parquet_path() (in module phenotypic.sdk_) master_parquet (phenotypic.sdk_.BundleLayout property) match_strategy (phenotypic.tune.score.SupervisedScorer attribute) matches_any_suffix() (in module phenotypic.sdk_) MATRIX_FORMATS (phenotypic.sdk_.constants_.IMAGE_MODE attribute) max_coeff_variance (phenotypic.refine.RemoveGridOutliers attribute) max_colony_radius_px (phenotypic.detect.FilamentousFungiDetector attribute) max_diameter (phenotypic.detect.InoculumDetector attribute) max_failures (phenotypic.tune.Budget attribute) max_gap_length (phenotypic.detect.FilamentousFungiDetector attribute) max_intensity (phenotypic.util.ImageMetricsCalculator property) max_iter (phenotypic.grid.AutoGridFinder attribute) (phenotypic.grid.CenteredAutoGridFinder attribute) max_num_iter (phenotypic.detect.ChanVeseDetector attribute) (phenotypic.refine.Thinning attribute) max_radius (phenotypic.enhance.FocusBlobLoG attribute) max_value (phenotypic.refine.RemoveByFeature attribute) MaxModifiedZScore (class in phenotypic.analysis) mean_coherence (phenotypic.util.StructureMetrics attribute) mean_gradient (phenotypic.util.BackgroundMetrics attribute) MeanDetector (class in phenotypic.detect) meas (phenotypic.abc_.PrefabPipeline attribute) (phenotypic.prefab.FilamentousFungiPipeline attribute) (phenotypic.prefab.GridSectionPipeline attribute) (phenotypic.prefab.HeavyOtsuPipeline attribute) (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) (phenotypic.prefab.HeavyWatershedPipeline attribute) (phenotypic.prefab.RoundPeaksPipeline attribute) (phenotypic.prefab.SpImagerPipeline attribute) measure() (phenotypic.abc_.GridFinder method) (phenotypic.abc_.GridMeasureFeatures method) (phenotypic.abc_.MeasureFeatures method) (phenotypic.abc_.PrefabPipeline method) (phenotypic.grid.AutoGridFinder method) (phenotypic.grid.CenteredAutoGridFinder method) (phenotypic.grid.ManualGridFinder method) (phenotypic.ImagePipeline method) (phenotypic.measure.MeasureBounds method) (phenotypic.measure.MeasureColor method) (phenotypic.measure.MeasureGridLinRegStats method) (phenotypic.measure.MeasureGridSpread method) (phenotypic.measure.MeasureIntensity method) (phenotypic.measure.MeasureNeighborDist method) (phenotypic.measure.MeasureOrientationZones method) (phenotypic.measure.MeasureShape method) (phenotypic.measure.MeasureSize method) (phenotypic.measure.MeasureSymmetricZones method) (phenotypic.measure.MeasureTexture method) (phenotypic.prefab.FilamentousFungiPipeline method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.prefab.RoundPeaksPipeline method) (phenotypic.prefab.SpImagerPipeline method) measure_kwargs (phenotypic.refine.RemoveByFeature attribute) MeasureBounds (class in phenotypic.measure) MeasureColor (class in phenotypic.measure) MEASURED (phenotypic.sdk_.constants_.PIPE_STATUS attribute) MeasureFeatures (class in phenotypic.abc_) MeasureGridLinRegStats (class in phenotypic.measure) MeasureGridSpread (class in phenotypic.measure) MeasureIntensity (class in phenotypic.measure) measurement_columns() (phenotypic.analysis.ErrorCutoffFinder method) measurement_prefixes (phenotypic.analysis.ErrorCutoffFinder attribute) MeasurementInfo (class in phenotypic.abc_) measurements_by_feature_dir() (in module phenotypic.sdk_) measurements_csv_path() (in module phenotypic.sdk_) measurements_parquet_path() (in module phenotypic.sdk_) MeasureNeighborDist (class in phenotypic.measure) MeasureOrientationZones (class in phenotypic.measure) MeasureShape (class in phenotypic.measure) MeasureSize (class in phenotypic.measure) MeasureSymmetricZones (class in phenotypic.measure) MeasureTexture (class in phenotypic.measure) median_cval (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) median_filter_size (phenotypic.correction.ColorCheckerProfile attribute) median_mode (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) median_radius (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) median_shape (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) MedianFilter (class in phenotypic.enhance) medoid_ciede2000() (in module phenotypic.util) medoid_max_pixels (phenotypic.measure.MeasureColor attribute) member_for_header() (phenotypic.abc_.MeasurementInfo class method) (phenotypic.sdk_.constants_.ConstantLabels class method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS class method) (phenotypic.sdk_.constants_.PIPE_STATUS class method) member_key_cols (phenotypic.analysis.ExpectedVsDetectedCount attribute) (phenotypic.analysis.GridOccupancy attribute) (phenotypic.analysis.ICC attribute) (phenotypic.analysis.MaxModifiedZScore attribute) (phenotypic.analysis.RelativeMAD attribute) (phenotypic.analysis.ReplicateAgreement attribute) (phenotypic.analysis.TukeyOutlierFraction attribute) MergeFragmentChains (class in phenotypic.refine) meta_validate() (phenotypic.tune.score.ReferenceFreeScorer method) metadata (phenotypic.analysis.ExpectedVsDetectedCount attribute) (phenotypic.analysis.GridOccupancy attribute) (phenotypic.Image property) metadata_category_for_label() (in module phenotypic.sdk_) metadata_category_prefixes() (in module phenotypic.sdk_) METADATA_CSV (phenotypic.sdk_.JobMetadataKey attribute) metadata_csv_deliverable_path() (in module phenotypic.sdk_) MetadataAccessor (class in phenotypic._core._image_parts.accessors._metadata_accessor) MetadataKeySpacesError MetadataKeyValueError MetadataValueNonScalarError method (phenotypic.abc_.FigureSpec attribute), [1] (phenotypic.measure.MeasureOrientationZones attribute) (phenotypic.measure.MeasureSymmetricZones attribute) (phenotypic.refine.Skeletonize attribute) (phenotypic.refine.TrimAsymmetry attribute) (phenotypic.tune.ImportanceReport attribute) (phenotypic.tune.ScreeningResult attribute) metric_col() (phenotypic.analysis.ExpectedVsDetectedCount class method) (phenotypic.analysis.GridOccupancy class method) (phenotypic.analysis.ICC class method) (phenotypic.analysis.MaxModifiedZScore class method) (phenotypic.analysis.RelativeMAD class method) (phenotypic.analysis.ReplicateAgreement class method) (phenotypic.analysis.TukeyOutlierFraction class method) michelson (phenotypic.util.ContrastMetrics attribute) migrate_legacy_machine_state() (in module phenotypic.sdk_) migrate_legacy_qc() (in module phenotypic.sdk_) min_area (phenotypic.tune.score.ReferenceFreeScorer attribute) min_branch_width_px (phenotypic.detect.FilamentousFungiDetector attribute) min_cc_area (phenotypic.refine.TrimAsymmetry attribute) min_core_area (phenotypic.refine.ExtractColonyCore attribute) min_diameter (phenotypic.detect.InoculumDetector attribute) min_distance (phenotypic.refine.SeparateObjects attribute) min_error_n (phenotypic.analysis.ErrorCutoffFinder attribute) min_fit_objects (phenotypic.grid.CenteredAutoGridFinder attribute) min_good_n (phenotypic.analysis.ErrorCutoffFinder attribute) min_heldout_plates (phenotypic.tune.HeldOutConfig attribute) min_object_area (phenotypic.refine.TrimAsymmetry attribute) min_overlap_ratio (phenotypic.detect.CompositeDetector attribute) min_peak_distance (phenotypic.detect.RoundPeaksDetector attribute) (phenotypic.detect.SinePeakDetector attribute) (phenotypic.refine.GridAlignmentRefiner attribute) (phenotypic.refine.RefineBySineFit attribute) min_radius (phenotypic.enhance.FocusBlobLoG attribute) min_replicates (phenotypic.analysis.MaxModifiedZScore attribute) (phenotypic.analysis.RelativeMAD attribute) (phenotypic.analysis.ReplicateAgreement attribute) (phenotypic.analysis.TukeyOutlierFraction attribute) min_rungs (phenotypic.tune.Evaluator attribute) min_samples_per_ring (phenotypic.measure.MeasureOrientationZones attribute) (phenotypic.measure.MeasureSymmetricZones attribute) min_size (phenotypic.detect.CannyDetector attribute) (phenotypic.detect.ChanVeseDetector attribute) (phenotypic.detect.MadHysteresisDetector attribute) (phenotypic.detect.WatershedDetector attribute) (phenotypic.refine.NearestNeighborMerger attribute) (phenotypic.refine.SmallObjectRemover attribute) min_stability_n (phenotypic.tune.Evaluator attribute) min_swatch_area_frac (phenotypic.correction.ColorCheckerProfile attribute) min_value (phenotypic.refine.RemoveByFeature attribute) min_wavelength (phenotypic.enhance.FocusEdgePhase attribute) MinimumDetector (class in phenotypic.detect) mirror_csv (phenotypic.sdk_.BundleLayout property) mirror_parquet (phenotypic.sdk_.BundleLayout property) modality() (phenotypic.tune.score.GroundTruthMasks method) mode (phenotypic.correction.BayesShrinkCorrector attribute) (phenotypic.correction.GridAligner attribute) (phenotypic.correction.ImagePadder attribute) (phenotypic.correction.VisuShrinkCorrector attribute) (phenotypic.detect.CompositeDetector attribute) (phenotypic.enhance.BayesShrinkEnhancer attribute) (phenotypic.enhance.CompositeEnhance attribute) (phenotypic.enhance.FocusEdgeHessian attribute) (phenotypic.enhance.FocusEdgeMeijering attribute) (phenotypic.enhance.FocusEdgeSato attribute) (phenotypic.enhance.GaussianBlur attribute) (phenotypic.enhance.LocalEdgeDenoise attribute) (phenotypic.enhance.MedianFilter attribute) (phenotypic.enhance.SetDetectMode attribute) (phenotypic.enhance.SubtractGaussian attribute) (phenotypic.enhance.VisuShrinkEnhancer attribute) (phenotypic.sdk_.HDF attribute), [1] model (phenotypic.abc_.PrefabPipeline attribute) (phenotypic.prefab.FilamentousFungiPipeline attribute) (phenotypic.prefab.GridSectionPipeline attribute) (phenotypic.prefab.HeavyOtsuPipeline attribute) (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) (phenotypic.prefab.HeavyWatershedPipeline attribute) (phenotypic.prefab.RoundPeaksPipeline attribute) (phenotypic.prefab.SpImagerPipeline attribute) model_computed_fields (phenotypic.abc_.BackgroundSubtraction attribute) (phenotypic.abc_.BaseOperation attribute) (phenotypic.abc_.ContrastAdjustment attribute) (phenotypic.abc_.FocusBlob attribute) (phenotypic.abc_.FocusEdge attribute) (phenotypic.abc_.GpuDetector attribute) (phenotypic.abc_.GridCorrector attribute) (phenotypic.abc_.GridFinder attribute) (phenotypic.abc_.GridMeasureFeatures attribute) (phenotypic.abc_.GridObjectDetector attribute) (phenotypic.abc_.GridObjectRefiner attribute) (phenotypic.abc_.GridOperation attribute) (phenotypic.abc_.ImageCorrector attribute) (phenotypic.abc_.ImageDenoiser attribute) (phenotypic.abc_.ImageEnhancer attribute) (phenotypic.abc_.ImageOperation attribute) (phenotypic.abc_.MeasureFeatures attribute) (phenotypic.abc_.MorphologicalFiltering attribute) (phenotypic.abc_.ObjectDetector attribute) (phenotypic.abc_.ObjectRefiner attribute) (phenotypic.abc_.PostMeasurement attribute) (phenotypic.abc_.PrefabPipeline attribute) (phenotypic.abc_.Smoothing attribute) (phenotypic.abc_.ThresholdDetector attribute) (phenotypic.analysis.EdgeCorrector attribute) (phenotypic.analysis.ErrorCutoffFinder attribute) (phenotypic.analysis.ExpectedVsDetectedCount attribute) (phenotypic.analysis.GridOccupancy attribute) (phenotypic.analysis.ICC attribute) (phenotypic.analysis.LinearCapAndLagModel attribute) (phenotypic.analysis.LinearLagModel attribute) (phenotypic.analysis.LogGrowthModel attribute) (phenotypic.analysis.MADOutlierRemover attribute) (phenotypic.analysis.MaxModifiedZScore attribute) (phenotypic.analysis.RelativeMAD attribute) (phenotypic.analysis.ReplicateAgreement attribute) (phenotypic.analysis.TukeyOutlierFraction attribute) (phenotypic.analysis.TukeyOutlierRemover attribute) (phenotypic.correction.BayesShrinkCorrector attribute) (phenotypic.correction.CaptureMetadata attribute) (phenotypic.correction.ColorCheckerProfile attribute) (phenotypic.correction.ColorCorrector attribute) (phenotypic.correction.ColorDenoise attribute) (phenotypic.correction.DenoiseBlockMatch attribute) (phenotypic.correction.GridAligner attribute) (phenotypic.correction.ImageCropper attribute) (phenotypic.correction.ImagePadder attribute) (phenotypic.correction.VisuShrinkCorrector attribute) (phenotypic.detect.CannyDetector attribute) (phenotypic.detect.ChanVeseDetector attribute) (phenotypic.detect.CompositeDetector attribute) (phenotypic.detect.FilamentousFungiDetector attribute) (phenotypic.detect.HysteresisDetector attribute) (phenotypic.detect.InoculumDetector attribute) (phenotypic.detect.IsodataDetector attribute) (phenotypic.detect.LiDetector attribute) (phenotypic.detect.MadHysteresisDetector attribute) (phenotypic.detect.ManualGridPointDetector attribute) (phenotypic.detect.ManualPointDetector attribute) (phenotypic.detect.MeanDetector attribute) (phenotypic.detect.MinimumDetector attribute) (phenotypic.detect.OtsuDetector attribute) (phenotypic.detect.RankOtsuDetector attribute) (phenotypic.detect.RoundPeaksDetector attribute) (phenotypic.detect.SecondaryOtsuDetector attribute) (phenotypic.detect.SinePeakDetector attribute) (phenotypic.detect.TriangleDetector attribute) (phenotypic.detect.UserThreshold attribute) (phenotypic.detect.WatershedDetector attribute) (phenotypic.detect.YenDetector attribute) (phenotypic.enhance.BayesShrinkEnhancer attribute) (phenotypic.enhance.CompositeEnhance attribute) (phenotypic.enhance.ContrastStretching attribute) (phenotypic.enhance.EnhanceBlockMatch attribute) (phenotypic.enhance.EnhanceLocalContrast attribute) (phenotypic.enhance.FlattenIllumination attribute) (phenotypic.enhance.FocusBlobLoG attribute) (phenotypic.enhance.FocusEdgeFrangi attribute) (phenotypic.enhance.FocusEdgeHessian attribute) (phenotypic.enhance.FocusEdgeLaplace attribute) (phenotypic.enhance.FocusEdgeMeijering attribute) (phenotypic.enhance.FocusEdgePhase attribute) (phenotypic.enhance.FocusEdgeSato attribute) (phenotypic.enhance.FocusEdgeSobel attribute) (phenotypic.enhance.GaussianBlur attribute) (phenotypic.enhance.GrayOpening attribute) (phenotypic.enhance.ImageInverter attribute) (phenotypic.enhance.LocalEdgeDenoise attribute) (phenotypic.enhance.MedianFilter attribute) (phenotypic.enhance.NonLocalMeansDenoiser attribute) (phenotypic.enhance.RankMedianEnhancer attribute) (phenotypic.enhance.SetDetectMode attribute) (phenotypic.enhance.SharpenEdgeGauss attribute) (phenotypic.enhance.StructureSmoothing attribute) (phenotypic.enhance.SubtractGaussian attribute) (phenotypic.enhance.SubtractOpening attribute) (phenotypic.enhance.SubtractRollingBall attribute) (phenotypic.enhance.SubtractWhiteTophat attribute) (phenotypic.enhance.VisuShrinkEnhancer attribute) (phenotypic.enhance.WhiteTophatEnhance attribute) (phenotypic.grid.AutoGridFinder attribute) (phenotypic.grid.CenteredAutoGridFinder attribute) (phenotypic.grid.GridApply attribute) (phenotypic.grid.ManualGridFinder attribute) (phenotypic.measure.MeasureBounds attribute) (phenotypic.measure.MeasureColor attribute) (phenotypic.measure.MeasureGridLinRegStats attribute) (phenotypic.measure.MeasureGridSpread attribute) (phenotypic.measure.MeasureIntensity attribute) (phenotypic.measure.MeasureNeighborDist attribute) (phenotypic.measure.MeasureOrientationZones attribute) (phenotypic.measure.MeasureShape attribute) (phenotypic.measure.MeasureSize attribute) (phenotypic.measure.MeasureSymmetricZones attribute) (phenotypic.measure.MeasureTexture attribute) (phenotypic.prefab.FilamentousFungiPipeline attribute) (phenotypic.prefab.GridSectionPipeline attribute) (phenotypic.prefab.HeavyOtsuPipeline attribute) (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) (phenotypic.prefab.HeavyWatershedPipeline attribute) (phenotypic.prefab.RoundPeaksPipeline attribute) (phenotypic.prefab.SpImagerPipeline attribute) (phenotypic.refine.ExtractColonyCore attribute) (phenotypic.refine.GridAlignmentRefiner attribute) (phenotypic.refine.GridOversizedObjectRemover attribute) (phenotypic.refine.KeepNearestCenter attribute) (phenotypic.refine.KeepSectionLargest attribute) (phenotypic.refine.ManualRefine attribute) (phenotypic.refine.MaskClosing attribute) (phenotypic.refine.MaskDilation attribute) (phenotypic.refine.MaskErosion attribute) (phenotypic.refine.MaskFill attribute) (phenotypic.refine.MaskGradient attribute) (phenotypic.refine.MaskOpening attribute) (phenotypic.refine.MaskWhiteTophat attribute) (phenotypic.refine.MergeFragmentChains attribute) (phenotypic.refine.NearestNeighborMerger attribute) (phenotypic.refine.ReduceSectionsByLine attribute) (phenotypic.refine.RefineBySineFit attribute) (phenotypic.refine.RemoveBorderObjects attribute) (phenotypic.refine.RemoveByFeature attribute) (phenotypic.refine.RemoveGridOutliers attribute) (phenotypic.refine.RemoveLowCircularity attribute) (phenotypic.refine.SeparateObjects attribute) (phenotypic.refine.Skeletonize attribute) (phenotypic.refine.SmallObjectRemover attribute) (phenotypic.refine.SmallToLargeMerger attribute) (phenotypic.refine.Thinning attribute) (phenotypic.refine.TrimAsymmetry attribute) (phenotypic.tune.Budget attribute) (phenotypic.tune.Categorical attribute) (phenotypic.tune.EvaluationResult attribute) (phenotypic.tune.Evaluator attribute) (phenotypic.tune.Excluded attribute) (phenotypic.tune.Fixed attribute) (phenotypic.tune.FloatRange attribute) (phenotypic.tune.HeldOutConfig attribute) (phenotypic.tune.ImportanceReport attribute) (phenotypic.tune.InferredSearchSpace attribute) (phenotypic.tune.IntRange attribute) (phenotypic.tune.Knob attribute) (phenotypic.tune.score.CompositeScorer attribute) (phenotypic.tune.score.GroundTruthMasks attribute) (phenotypic.tune.score.QCScorer attribute) (phenotypic.tune.score.ReferenceFreeScorer attribute) (phenotypic.tune.score.Scorer attribute) (phenotypic.tune.score.SupervisedScorer attribute) (phenotypic.tune.SearchSpace attribute) (phenotypic.tune.strategy.GridConfig attribute) (phenotypic.tune.strategy.OptunaConfig attribute) (phenotypic.tune.strategy.RandomConfig attribute) (phenotypic.tune.strategy.StrategyConfig attribute) (phenotypic.tune.Trial attribute) (phenotypic.tune.TuningSpec attribute) model_config (phenotypic.abc_.BackgroundSubtraction attribute) (phenotypic.abc_.BaseOperation attribute) (phenotypic.abc_.ContrastAdjustment attribute) (phenotypic.abc_.FocusBlob attribute) (phenotypic.abc_.FocusEdge attribute) (phenotypic.abc_.GpuDetector attribute) (phenotypic.abc_.GridCorrector attribute) (phenotypic.abc_.GridFinder attribute) (phenotypic.abc_.GridMeasureFeatures attribute) (phenotypic.abc_.GridObjectDetector attribute) (phenotypic.abc_.GridObjectRefiner attribute) (phenotypic.abc_.GridOperation attribute) (phenotypic.abc_.ImageCorrector attribute) (phenotypic.abc_.ImageDenoiser attribute) (phenotypic.abc_.ImageEnhancer attribute) (phenotypic.abc_.ImageOperation attribute) (phenotypic.abc_.MeasureFeatures attribute) (phenotypic.abc_.MorphologicalFiltering attribute) (phenotypic.abc_.ObjectDetector attribute) (phenotypic.abc_.ObjectRefiner attribute) (phenotypic.abc_.PostMeasurement attribute) (phenotypic.abc_.PrefabPipeline attribute) (phenotypic.abc_.Smoothing attribute) (phenotypic.abc_.ThresholdDetector attribute) (phenotypic.analysis.EdgeCorrector attribute) (phenotypic.analysis.ErrorCutoffFinder attribute) (phenotypic.analysis.ExpectedVsDetectedCount attribute) (phenotypic.analysis.GridOccupancy attribute) (phenotypic.analysis.ICC attribute) (phenotypic.analysis.LinearCapAndLagModel attribute) (phenotypic.analysis.LinearLagModel attribute) (phenotypic.analysis.LogGrowthModel attribute) (phenotypic.analysis.MADOutlierRemover attribute) (phenotypic.analysis.MaxModifiedZScore attribute) (phenotypic.analysis.RelativeMAD attribute) (phenotypic.analysis.ReplicateAgreement attribute) (phenotypic.analysis.TukeyOutlierFraction attribute) (phenotypic.analysis.TukeyOutlierRemover attribute) (phenotypic.correction.BayesShrinkCorrector attribute) (phenotypic.correction.CaptureMetadata attribute) (phenotypic.correction.ColorCheckerProfile attribute) (phenotypic.correction.ColorCorrector attribute) (phenotypic.correction.ColorDenoise attribute) (phenotypic.correction.DenoiseBlockMatch attribute) (phenotypic.correction.GridAligner attribute) (phenotypic.correction.ImageCropper attribute) (phenotypic.correction.ImagePadder attribute) (phenotypic.correction.VisuShrinkCorrector attribute) (phenotypic.detect.CannyDetector attribute) (phenotypic.detect.ChanVeseDetector attribute) (phenotypic.detect.CompositeDetector attribute) (phenotypic.detect.FilamentousFungiDetector attribute) (phenotypic.detect.HysteresisDetector attribute) (phenotypic.detect.InoculumDetector attribute) (phenotypic.detect.IsodataDetector attribute) (phenotypic.detect.LiDetector attribute) (phenotypic.detect.MadHysteresisDetector attribute) (phenotypic.detect.ManualGridPointDetector attribute) (phenotypic.detect.ManualPointDetector attribute) (phenotypic.detect.MeanDetector attribute) (phenotypic.detect.MinimumDetector attribute) (phenotypic.detect.OtsuDetector attribute) (phenotypic.detect.RankOtsuDetector attribute) (phenotypic.detect.RoundPeaksDetector attribute) (phenotypic.detect.SecondaryOtsuDetector attribute) (phenotypic.detect.SinePeakDetector attribute) (phenotypic.detect.TriangleDetector attribute) (phenotypic.detect.UserThreshold attribute) (phenotypic.detect.WatershedDetector attribute) (phenotypic.detect.YenDetector attribute) (phenotypic.enhance.BayesShrinkEnhancer attribute) (phenotypic.enhance.CompositeEnhance attribute) (phenotypic.enhance.ContrastStretching attribute) (phenotypic.enhance.EnhanceBlockMatch attribute) (phenotypic.enhance.EnhanceLocalContrast attribute) (phenotypic.enhance.FlattenIllumination attribute) (phenotypic.enhance.FocusBlobLoG attribute) (phenotypic.enhance.FocusEdgeFrangi attribute) (phenotypic.enhance.FocusEdgeHessian attribute) (phenotypic.enhance.FocusEdgeLaplace attribute) (phenotypic.enhance.FocusEdgeMeijering attribute) (phenotypic.enhance.FocusEdgePhase attribute) (phenotypic.enhance.FocusEdgeSato attribute) (phenotypic.enhance.FocusEdgeSobel attribute) (phenotypic.enhance.GaussianBlur attribute) (phenotypic.enhance.GrayOpening attribute) (phenotypic.enhance.ImageInverter attribute) (phenotypic.enhance.LocalEdgeDenoise attribute) (phenotypic.enhance.MedianFilter attribute) (phenotypic.enhance.NonLocalMeansDenoiser attribute) (phenotypic.enhance.RankMedianEnhancer attribute) (phenotypic.enhance.SetDetectMode attribute) (phenotypic.enhance.SharpenEdgeGauss attribute) (phenotypic.enhance.StructureSmoothing attribute) (phenotypic.enhance.SubtractGaussian attribute) (phenotypic.enhance.SubtractOpening attribute) (phenotypic.enhance.SubtractRollingBall attribute) (phenotypic.enhance.SubtractWhiteTophat attribute) (phenotypic.enhance.VisuShrinkEnhancer attribute) (phenotypic.enhance.WhiteTophatEnhance attribute) (phenotypic.grid.AutoGridFinder attribute) (phenotypic.grid.CenteredAutoGridFinder attribute) (phenotypic.grid.GridApply attribute) (phenotypic.grid.ManualGridFinder attribute) (phenotypic.measure.MeasureBounds attribute) (phenotypic.measure.MeasureColor attribute) (phenotypic.measure.MeasureGridLinRegStats attribute) (phenotypic.measure.MeasureGridSpread attribute) (phenotypic.measure.MeasureIntensity attribute) (phenotypic.measure.MeasureNeighborDist attribute) (phenotypic.measure.MeasureOrientationZones attribute) (phenotypic.measure.MeasureShape attribute) (phenotypic.measure.MeasureSize attribute) (phenotypic.measure.MeasureSymmetricZones attribute) (phenotypic.measure.MeasureTexture attribute) (phenotypic.prefab.FilamentousFungiPipeline attribute) (phenotypic.prefab.GridSectionPipeline attribute) (phenotypic.prefab.HeavyOtsuPipeline attribute) (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) (phenotypic.prefab.HeavyWatershedPipeline attribute) (phenotypic.prefab.RoundPeaksPipeline attribute) (phenotypic.prefab.SpImagerPipeline attribute) (phenotypic.refine.ExtractColonyCore attribute) (phenotypic.refine.GridAlignmentRefiner attribute) (phenotypic.refine.GridOversizedObjectRemover attribute) (phenotypic.refine.KeepNearestCenter attribute) (phenotypic.refine.KeepSectionLargest attribute) (phenotypic.refine.ManualRefine attribute) (phenotypic.refine.MaskClosing attribute) (phenotypic.refine.MaskDilation attribute) (phenotypic.refine.MaskErosion attribute) (phenotypic.refine.MaskFill attribute) (phenotypic.refine.MaskGradient attribute) (phenotypic.refine.MaskOpening attribute) (phenotypic.refine.MaskWhiteTophat attribute) (phenotypic.refine.MergeFragmentChains attribute) (phenotypic.refine.NearestNeighborMerger attribute) (phenotypic.refine.ReduceSectionsByLine attribute) (phenotypic.refine.RefineBySineFit attribute) (phenotypic.refine.RemoveBorderObjects attribute) (phenotypic.refine.RemoveByFeature attribute) (phenotypic.refine.RemoveGridOutliers attribute) (phenotypic.refine.RemoveLowCircularity attribute) (phenotypic.refine.SeparateObjects attribute) (phenotypic.refine.Skeletonize attribute) (phenotypic.refine.SmallObjectRemover attribute) (phenotypic.refine.SmallToLargeMerger attribute) (phenotypic.refine.Thinning attribute) (phenotypic.refine.TrimAsymmetry attribute) (phenotypic.tune.Budget attribute) (phenotypic.tune.Categorical attribute) (phenotypic.tune.EvaluationResult attribute) (phenotypic.tune.Evaluator attribute) (phenotypic.tune.Excluded attribute) (phenotypic.tune.Fixed attribute) (phenotypic.tune.FloatRange attribute) (phenotypic.tune.HeldOutConfig attribute) (phenotypic.tune.ImportanceReport attribute) (phenotypic.tune.InferredSearchSpace attribute) (phenotypic.tune.IntRange attribute) (phenotypic.tune.Knob attribute) (phenotypic.tune.score.CompositeScorer attribute) (phenotypic.tune.score.GroundTruthMasks attribute) (phenotypic.tune.score.QCScorer attribute) (phenotypic.tune.score.ReferenceFreeScorer attribute) (phenotypic.tune.score.Scorer attribute) (phenotypic.tune.score.SupervisedScorer attribute) (phenotypic.tune.SearchSpace attribute) (phenotypic.tune.strategy.GridConfig attribute) (phenotypic.tune.strategy.OptunaConfig attribute) (phenotypic.tune.strategy.RandomConfig attribute) (phenotypic.tune.strategy.StrategyConfig attribute) (phenotypic.tune.Trial attribute) (phenotypic.tune.TuningSpec attribute) model_construct() (phenotypic.abc_.BackgroundSubtraction class method) (phenotypic.abc_.BaseOperation class method) (phenotypic.abc_.ContrastAdjustment class method) (phenotypic.abc_.FocusBlob class method) (phenotypic.abc_.FocusEdge class method) (phenotypic.abc_.GpuDetector class method) (phenotypic.abc_.GridCorrector class method) (phenotypic.abc_.GridFinder class method) (phenotypic.abc_.GridMeasureFeatures class method) (phenotypic.abc_.GridObjectDetector class method) (phenotypic.abc_.GridObjectRefiner class method) (phenotypic.abc_.GridOperation class method) (phenotypic.abc_.ImageCorrector class method) (phenotypic.abc_.ImageDenoiser class method) (phenotypic.abc_.ImageEnhancer class method) (phenotypic.abc_.ImageOperation class method) (phenotypic.abc_.MeasureFeatures class method) (phenotypic.abc_.MorphologicalFiltering class method) (phenotypic.abc_.ObjectDetector class method) (phenotypic.abc_.ObjectRefiner class method) (phenotypic.abc_.PostMeasurement class method) (phenotypic.abc_.PrefabPipeline class method) (phenotypic.abc_.Smoothing class method) (phenotypic.abc_.ThresholdDetector class method) (phenotypic.analysis.EdgeCorrector class method) (phenotypic.analysis.ErrorCutoffFinder class method) (phenotypic.analysis.ExpectedVsDetectedCount class method) (phenotypic.analysis.GridOccupancy class method) (phenotypic.analysis.ICC class method) (phenotypic.analysis.LinearCapAndLagModel class method) (phenotypic.analysis.LinearLagModel class method) (phenotypic.analysis.LogGrowthModel class method) (phenotypic.analysis.MADOutlierRemover class method) (phenotypic.analysis.MaxModifiedZScore class method) (phenotypic.analysis.RelativeMAD class method) (phenotypic.analysis.ReplicateAgreement class method) (phenotypic.analysis.TukeyOutlierFraction class method) (phenotypic.analysis.TukeyOutlierRemover class method) (phenotypic.correction.BayesShrinkCorrector class method) (phenotypic.correction.CaptureMetadata class method) (phenotypic.correction.ColorCheckerProfile class method) (phenotypic.correction.ColorCorrector class method) (phenotypic.correction.ColorDenoise class method) (phenotypic.correction.DenoiseBlockMatch class method) (phenotypic.correction.GridAligner class method) (phenotypic.correction.ImageCropper class method) (phenotypic.correction.ImagePadder class method) (phenotypic.correction.VisuShrinkCorrector class method) (phenotypic.detect.CannyDetector class method) (phenotypic.detect.ChanVeseDetector class method) (phenotypic.detect.CompositeDetector class method) (phenotypic.detect.FilamentousFungiDetector class method) (phenotypic.detect.HysteresisDetector class method) (phenotypic.detect.InoculumDetector class method) (phenotypic.detect.IsodataDetector class method) (phenotypic.detect.LiDetector class method) (phenotypic.detect.MadHysteresisDetector class method) (phenotypic.detect.ManualGridPointDetector class method) (phenotypic.detect.ManualPointDetector class method) (phenotypic.detect.MeanDetector class method) (phenotypic.detect.MinimumDetector class method) (phenotypic.detect.OtsuDetector class method) (phenotypic.detect.RankOtsuDetector class method) (phenotypic.detect.RoundPeaksDetector class method) (phenotypic.detect.SecondaryOtsuDetector class method) (phenotypic.detect.SinePeakDetector class method) (phenotypic.detect.TriangleDetector class method) (phenotypic.detect.UserThreshold class method) (phenotypic.detect.WatershedDetector class method) (phenotypic.detect.YenDetector class method) (phenotypic.enhance.BayesShrinkEnhancer class method) (phenotypic.enhance.CompositeEnhance class method) (phenotypic.enhance.ContrastStretching class method) (phenotypic.enhance.EnhanceBlockMatch class method) (phenotypic.enhance.EnhanceLocalContrast class method) (phenotypic.enhance.FlattenIllumination class method) (phenotypic.enhance.FocusBlobLoG class method) (phenotypic.enhance.FocusEdgeFrangi class method) (phenotypic.enhance.FocusEdgeHessian class method) (phenotypic.enhance.FocusEdgeLaplace class method) (phenotypic.enhance.FocusEdgeMeijering class method) (phenotypic.enhance.FocusEdgePhase class method) (phenotypic.enhance.FocusEdgeSato class method) (phenotypic.enhance.FocusEdgeSobel class method) (phenotypic.enhance.GaussianBlur class method) (phenotypic.enhance.GrayOpening class method) (phenotypic.enhance.ImageInverter class method) (phenotypic.enhance.LocalEdgeDenoise class method) (phenotypic.enhance.MedianFilter class method) (phenotypic.enhance.NonLocalMeansDenoiser class method) (phenotypic.enhance.RankMedianEnhancer class method) (phenotypic.enhance.SetDetectMode class method) (phenotypic.enhance.SharpenEdgeGauss class method) (phenotypic.enhance.StructureSmoothing class method) (phenotypic.enhance.SubtractGaussian class method) (phenotypic.enhance.SubtractOpening class method) (phenotypic.enhance.SubtractRollingBall class method) (phenotypic.enhance.SubtractWhiteTophat class method) (phenotypic.enhance.VisuShrinkEnhancer class method) (phenotypic.enhance.WhiteTophatEnhance class method) (phenotypic.grid.AutoGridFinder class method) (phenotypic.grid.CenteredAutoGridFinder class method) (phenotypic.grid.GridApply class method) (phenotypic.grid.ManualGridFinder class method) (phenotypic.measure.MeasureBounds class method) (phenotypic.measure.MeasureColor class method) (phenotypic.measure.MeasureGridLinRegStats class method) (phenotypic.measure.MeasureGridSpread class method) (phenotypic.measure.MeasureIntensity class method) (phenotypic.measure.MeasureNeighborDist class method) (phenotypic.measure.MeasureOrientationZones class method) (phenotypic.measure.MeasureShape class method) (phenotypic.measure.MeasureSize class method) (phenotypic.measure.MeasureSymmetricZones class method) (phenotypic.measure.MeasureTexture class method) (phenotypic.prefab.FilamentousFungiPipeline class method) (phenotypic.prefab.GridSectionPipeline class method) (phenotypic.prefab.HeavyOtsuPipeline class method) (phenotypic.prefab.HeavyRoundPeaksPipeline class method) (phenotypic.prefab.HeavyWatershedPipeline class method) (phenotypic.prefab.RoundPeaksPipeline class method) (phenotypic.prefab.SpImagerPipeline class method) (phenotypic.refine.ExtractColonyCore class method) (phenotypic.refine.GridAlignmentRefiner class method) (phenotypic.refine.GridOversizedObjectRemover class method) (phenotypic.refine.KeepNearestCenter class method) (phenotypic.refine.KeepSectionLargest class method) (phenotypic.refine.ManualRefine class method) (phenotypic.refine.MaskClosing class method) (phenotypic.refine.MaskDilation class method) (phenotypic.refine.MaskErosion class method) (phenotypic.refine.MaskFill class method) (phenotypic.refine.MaskGradient class method) (phenotypic.refine.MaskOpening class method) (phenotypic.refine.MaskWhiteTophat class method) (phenotypic.refine.MergeFragmentChains class method) (phenotypic.refine.NearestNeighborMerger class method) (phenotypic.refine.ReduceSectionsByLine class method) (phenotypic.refine.RefineBySineFit class method) (phenotypic.refine.RemoveBorderObjects class method) (phenotypic.refine.RemoveByFeature class method) (phenotypic.refine.RemoveGridOutliers class method) (phenotypic.refine.RemoveLowCircularity class method) (phenotypic.refine.SeparateObjects class method) (phenotypic.refine.Skeletonize class method) (phenotypic.refine.SmallObjectRemover class method) (phenotypic.refine.SmallToLargeMerger class method) (phenotypic.refine.Thinning class method) (phenotypic.refine.TrimAsymmetry class method) (phenotypic.tune.Budget class method) (phenotypic.tune.Categorical class method) (phenotypic.tune.EvaluationResult class method) (phenotypic.tune.Evaluator class method) (phenotypic.tune.Excluded class method) (phenotypic.tune.Fixed class method) (phenotypic.tune.FloatRange class method) (phenotypic.tune.HeldOutConfig class method) (phenotypic.tune.ImportanceReport class method) (phenotypic.tune.InferredSearchSpace class method) (phenotypic.tune.IntRange class method) (phenotypic.tune.Knob class method) (phenotypic.tune.score.CompositeScorer class method) (phenotypic.tune.score.GroundTruthMasks class method) (phenotypic.tune.score.QCScorer class method) (phenotypic.tune.score.ReferenceFreeScorer class method) (phenotypic.tune.score.Scorer class method) (phenotypic.tune.score.SupervisedScorer class method) (phenotypic.tune.SearchSpace class method) (phenotypic.tune.strategy.GridConfig class method) (phenotypic.tune.strategy.OptunaConfig class method) (phenotypic.tune.strategy.RandomConfig class method) (phenotypic.tune.strategy.StrategyConfig class method) (phenotypic.tune.Trial class method) (phenotypic.tune.TuningSpec class method) model_copy() (phenotypic.abc_.BackgroundSubtraction method) (phenotypic.abc_.BaseOperation method) (phenotypic.abc_.ContrastAdjustment method) (phenotypic.abc_.FocusBlob method) (phenotypic.abc_.FocusEdge method) (phenotypic.abc_.GpuDetector method) (phenotypic.abc_.GridCorrector method) (phenotypic.abc_.GridFinder method) (phenotypic.abc_.GridMeasureFeatures method) (phenotypic.abc_.GridObjectDetector method) (phenotypic.abc_.GridObjectRefiner method) (phenotypic.abc_.GridOperation method) (phenotypic.abc_.ImageCorrector method) (phenotypic.abc_.ImageDenoiser method) (phenotypic.abc_.ImageEnhancer method) (phenotypic.abc_.ImageOperation method) (phenotypic.abc_.MeasureFeatures method) (phenotypic.abc_.MorphologicalFiltering method) (phenotypic.abc_.ObjectDetector method) (phenotypic.abc_.ObjectRefiner method) (phenotypic.abc_.PostMeasurement method) (phenotypic.abc_.PrefabPipeline method) (phenotypic.abc_.Smoothing method) (phenotypic.abc_.ThresholdDetector method) (phenotypic.analysis.EdgeCorrector method) (phenotypic.analysis.ErrorCutoffFinder method) (phenotypic.analysis.ExpectedVsDetectedCount method) (phenotypic.analysis.GridOccupancy method) (phenotypic.analysis.ICC method) (phenotypic.analysis.LinearCapAndLagModel method) (phenotypic.analysis.LinearLagModel method) (phenotypic.analysis.LogGrowthModel method) (phenotypic.analysis.MADOutlierRemover method) (phenotypic.analysis.MaxModifiedZScore method) (phenotypic.analysis.RelativeMAD method) (phenotypic.analysis.ReplicateAgreement method) (phenotypic.analysis.TukeyOutlierFraction method) (phenotypic.analysis.TukeyOutlierRemover method) (phenotypic.correction.BayesShrinkCorrector method) (phenotypic.correction.CaptureMetadata method) (phenotypic.correction.ColorCheckerProfile method) (phenotypic.correction.ColorCorrector method) (phenotypic.correction.ColorDenoise method) (phenotypic.correction.DenoiseBlockMatch method) (phenotypic.correction.GridAligner method) (phenotypic.correction.ImageCropper method) (phenotypic.correction.ImagePadder method) (phenotypic.correction.VisuShrinkCorrector method) (phenotypic.detect.CannyDetector method) (phenotypic.detect.ChanVeseDetector method) (phenotypic.detect.CompositeDetector method) (phenotypic.detect.FilamentousFungiDetector method) (phenotypic.detect.HysteresisDetector method) (phenotypic.detect.InoculumDetector method) (phenotypic.detect.IsodataDetector method) (phenotypic.detect.LiDetector method) (phenotypic.detect.MadHysteresisDetector method) (phenotypic.detect.ManualGridPointDetector method) (phenotypic.detect.ManualPointDetector method) (phenotypic.detect.MeanDetector method) (phenotypic.detect.MinimumDetector method) (phenotypic.detect.OtsuDetector method) (phenotypic.detect.RankOtsuDetector method) (phenotypic.detect.RoundPeaksDetector method) (phenotypic.detect.SecondaryOtsuDetector method) (phenotypic.detect.SinePeakDetector method) (phenotypic.detect.TriangleDetector method) (phenotypic.detect.UserThreshold method) (phenotypic.detect.WatershedDetector method) (phenotypic.detect.YenDetector method) (phenotypic.enhance.BayesShrinkEnhancer method) (phenotypic.enhance.CompositeEnhance method) (phenotypic.enhance.ContrastStretching method) (phenotypic.enhance.EnhanceBlockMatch method) (phenotypic.enhance.EnhanceLocalContrast method) (phenotypic.enhance.FlattenIllumination method) (phenotypic.enhance.FocusBlobLoG method) (phenotypic.enhance.FocusEdgeFrangi method) (phenotypic.enhance.FocusEdgeHessian method) (phenotypic.enhance.FocusEdgeLaplace method) (phenotypic.enhance.FocusEdgeMeijering method) (phenotypic.enhance.FocusEdgePhase method) (phenotypic.enhance.FocusEdgeSato method) (phenotypic.enhance.FocusEdgeSobel method) (phenotypic.enhance.GaussianBlur method) (phenotypic.enhance.GrayOpening method) (phenotypic.enhance.ImageInverter method) (phenotypic.enhance.LocalEdgeDenoise method) (phenotypic.enhance.MedianFilter method) (phenotypic.enhance.NonLocalMeansDenoiser method) (phenotypic.enhance.RankMedianEnhancer method) (phenotypic.enhance.SetDetectMode method) (phenotypic.enhance.SharpenEdgeGauss method) (phenotypic.enhance.StructureSmoothing method) (phenotypic.enhance.SubtractGaussian method) (phenotypic.enhance.SubtractOpening method) (phenotypic.enhance.SubtractRollingBall method) (phenotypic.enhance.SubtractWhiteTophat method) (phenotypic.enhance.VisuShrinkEnhancer method) (phenotypic.enhance.WhiteTophatEnhance method) (phenotypic.grid.AutoGridFinder method) (phenotypic.grid.CenteredAutoGridFinder method) (phenotypic.grid.GridApply method) (phenotypic.grid.ManualGridFinder method) (phenotypic.measure.MeasureBounds method) (phenotypic.measure.MeasureColor method) (phenotypic.measure.MeasureGridLinRegStats method) (phenotypic.measure.MeasureGridSpread method) (phenotypic.measure.MeasureIntensity method) (phenotypic.measure.MeasureNeighborDist method) (phenotypic.measure.MeasureOrientationZones method) (phenotypic.measure.MeasureShape method) (phenotypic.measure.MeasureSize method) (phenotypic.measure.MeasureSymmetricZones method) (phenotypic.measure.MeasureTexture method) (phenotypic.prefab.FilamentousFungiPipeline method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.prefab.RoundPeaksPipeline method) (phenotypic.prefab.SpImagerPipeline method) (phenotypic.refine.ExtractColonyCore method) (phenotypic.refine.GridAlignmentRefiner method) (phenotypic.refine.GridOversizedObjectRemover method) (phenotypic.refine.KeepNearestCenter method) (phenotypic.refine.KeepSectionLargest method) (phenotypic.refine.ManualRefine method) (phenotypic.refine.MaskClosing method) (phenotypic.refine.MaskDilation method) (phenotypic.refine.MaskErosion method) (phenotypic.refine.MaskFill method) (phenotypic.refine.MaskGradient method) (phenotypic.refine.MaskOpening method) (phenotypic.refine.MaskWhiteTophat method) (phenotypic.refine.MergeFragmentChains method) (phenotypic.refine.NearestNeighborMerger method) (phenotypic.refine.ReduceSectionsByLine method) (phenotypic.refine.RefineBySineFit method) (phenotypic.refine.RemoveBorderObjects method) (phenotypic.refine.RemoveByFeature method) (phenotypic.refine.RemoveGridOutliers method) (phenotypic.refine.RemoveLowCircularity method) (phenotypic.refine.SeparateObjects method) (phenotypic.refine.Skeletonize method) (phenotypic.refine.SmallObjectRemover method) (phenotypic.refine.SmallToLargeMerger method) (phenotypic.refine.Thinning method) (phenotypic.refine.TrimAsymmetry method) (phenotypic.tune.Budget method) (phenotypic.tune.Categorical method) (phenotypic.tune.EvaluationResult method) (phenotypic.tune.Evaluator method) (phenotypic.tune.Excluded method) (phenotypic.tune.Fixed method) (phenotypic.tune.FloatRange method) (phenotypic.tune.HeldOutConfig method) (phenotypic.tune.ImportanceReport method) (phenotypic.tune.InferredSearchSpace method) (phenotypic.tune.IntRange method) (phenotypic.tune.Knob method) (phenotypic.tune.score.CompositeScorer method) (phenotypic.tune.score.GroundTruthMasks method) (phenotypic.tune.score.QCScorer method) (phenotypic.tune.score.ReferenceFreeScorer method) (phenotypic.tune.score.Scorer method) (phenotypic.tune.score.SupervisedScorer method) (phenotypic.tune.SearchSpace method) (phenotypic.tune.strategy.GridConfig method) (phenotypic.tune.strategy.OptunaConfig method) (phenotypic.tune.strategy.RandomConfig method) (phenotypic.tune.strategy.StrategyConfig method) (phenotypic.tune.Trial method) (phenotypic.tune.TuningSpec method) model_dump() (phenotypic.abc_.BackgroundSubtraction method) (phenotypic.abc_.BaseOperation method) (phenotypic.abc_.ContrastAdjustment method) (phenotypic.abc_.FocusBlob method) (phenotypic.abc_.FocusEdge method) (phenotypic.abc_.GpuDetector method) (phenotypic.abc_.GridCorrector method) (phenotypic.abc_.GridFinder method) (phenotypic.abc_.GridMeasureFeatures method) (phenotypic.abc_.GridObjectDetector method) (phenotypic.abc_.GridObjectRefiner method) (phenotypic.abc_.GridOperation method) (phenotypic.abc_.ImageCorrector method) (phenotypic.abc_.ImageDenoiser method) (phenotypic.abc_.ImageEnhancer method) (phenotypic.abc_.ImageOperation method) (phenotypic.abc_.MeasureFeatures method) (phenotypic.abc_.MorphologicalFiltering method) (phenotypic.abc_.ObjectDetector method) (phenotypic.abc_.ObjectRefiner method) (phenotypic.abc_.PostMeasurement method) (phenotypic.abc_.PrefabPipeline method) (phenotypic.abc_.Smoothing method) (phenotypic.abc_.ThresholdDetector method) (phenotypic.analysis.EdgeCorrector method) (phenotypic.analysis.ErrorCutoffFinder method) (phenotypic.analysis.ExpectedVsDetectedCount method) (phenotypic.analysis.GridOccupancy method) (phenotypic.analysis.ICC method) (phenotypic.analysis.LinearCapAndLagModel method) (phenotypic.analysis.LinearLagModel method) (phenotypic.analysis.LogGrowthModel method) (phenotypic.analysis.MADOutlierRemover method) (phenotypic.analysis.MaxModifiedZScore method) (phenotypic.analysis.RelativeMAD method) (phenotypic.analysis.ReplicateAgreement method) (phenotypic.analysis.TukeyOutlierFraction method) (phenotypic.analysis.TukeyOutlierRemover method) (phenotypic.correction.BayesShrinkCorrector method) (phenotypic.correction.CaptureMetadata method) (phenotypic.correction.ColorCheckerProfile method) (phenotypic.correction.ColorCorrector method) (phenotypic.correction.ColorDenoise method) (phenotypic.correction.DenoiseBlockMatch method) (phenotypic.correction.GridAligner method) (phenotypic.correction.ImageCropper method) (phenotypic.correction.ImagePadder method) (phenotypic.correction.VisuShrinkCorrector method) (phenotypic.detect.CannyDetector method) (phenotypic.detect.ChanVeseDetector method) (phenotypic.detect.CompositeDetector method) (phenotypic.detect.FilamentousFungiDetector method) (phenotypic.detect.HysteresisDetector method) (phenotypic.detect.InoculumDetector method) (phenotypic.detect.IsodataDetector method) (phenotypic.detect.LiDetector method) (phenotypic.detect.MadHysteresisDetector method) (phenotypic.detect.ManualGridPointDetector method) (phenotypic.detect.ManualPointDetector method) (phenotypic.detect.MeanDetector method) (phenotypic.detect.MinimumDetector method) (phenotypic.detect.OtsuDetector method) (phenotypic.detect.RankOtsuDetector method) (phenotypic.detect.RoundPeaksDetector method) (phenotypic.detect.SecondaryOtsuDetector method) (phenotypic.detect.SinePeakDetector method) (phenotypic.detect.TriangleDetector method) (phenotypic.detect.UserThreshold method) (phenotypic.detect.WatershedDetector method) (phenotypic.detect.YenDetector method) (phenotypic.enhance.BayesShrinkEnhancer method) (phenotypic.enhance.CompositeEnhance method) (phenotypic.enhance.ContrastStretching method) (phenotypic.enhance.EnhanceBlockMatch method) (phenotypic.enhance.EnhanceLocalContrast method) (phenotypic.enhance.FlattenIllumination method) (phenotypic.enhance.FocusBlobLoG method) (phenotypic.enhance.FocusEdgeFrangi method) (phenotypic.enhance.FocusEdgeHessian method) (phenotypic.enhance.FocusEdgeLaplace method) (phenotypic.enhance.FocusEdgeMeijering method) (phenotypic.enhance.FocusEdgePhase method) (phenotypic.enhance.FocusEdgeSato method) (phenotypic.enhance.FocusEdgeSobel method) (phenotypic.enhance.GaussianBlur method) (phenotypic.enhance.GrayOpening method) (phenotypic.enhance.ImageInverter method) (phenotypic.enhance.LocalEdgeDenoise method) (phenotypic.enhance.MedianFilter method) (phenotypic.enhance.NonLocalMeansDenoiser method) (phenotypic.enhance.RankMedianEnhancer method) (phenotypic.enhance.SetDetectMode method) (phenotypic.enhance.SharpenEdgeGauss method) (phenotypic.enhance.StructureSmoothing method) (phenotypic.enhance.SubtractGaussian method) (phenotypic.enhance.SubtractOpening method) (phenotypic.enhance.SubtractRollingBall method) (phenotypic.enhance.SubtractWhiteTophat method) (phenotypic.enhance.VisuShrinkEnhancer method) (phenotypic.enhance.WhiteTophatEnhance method) (phenotypic.grid.AutoGridFinder method) (phenotypic.grid.CenteredAutoGridFinder method) (phenotypic.grid.GridApply method) (phenotypic.grid.ManualGridFinder method) (phenotypic.measure.MeasureBounds method) (phenotypic.measure.MeasureColor method) (phenotypic.measure.MeasureGridLinRegStats method) (phenotypic.measure.MeasureGridSpread method) (phenotypic.measure.MeasureIntensity method) (phenotypic.measure.MeasureNeighborDist method) (phenotypic.measure.MeasureOrientationZones method) (phenotypic.measure.MeasureShape method) (phenotypic.measure.MeasureSize method) (phenotypic.measure.MeasureSymmetricZones method) (phenotypic.measure.MeasureTexture method) (phenotypic.prefab.FilamentousFungiPipeline method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.prefab.RoundPeaksPipeline method) (phenotypic.prefab.SpImagerPipeline method) (phenotypic.refine.ExtractColonyCore method) (phenotypic.refine.GridAlignmentRefiner method) (phenotypic.refine.GridOversizedObjectRemover method) (phenotypic.refine.KeepNearestCenter method) (phenotypic.refine.KeepSectionLargest method) (phenotypic.refine.ManualRefine method) (phenotypic.refine.MaskClosing method) (phenotypic.refine.MaskDilation method) (phenotypic.refine.MaskErosion method) (phenotypic.refine.MaskFill method) (phenotypic.refine.MaskGradient method) (phenotypic.refine.MaskOpening method) (phenotypic.refine.MaskWhiteTophat method) (phenotypic.refine.MergeFragmentChains method) (phenotypic.refine.NearestNeighborMerger method) (phenotypic.refine.ReduceSectionsByLine method) (phenotypic.refine.RefineBySineFit method) (phenotypic.refine.RemoveBorderObjects method) (phenotypic.refine.RemoveByFeature method) (phenotypic.refine.RemoveGridOutliers method) (phenotypic.refine.RemoveLowCircularity method) (phenotypic.refine.SeparateObjects method) (phenotypic.refine.Skeletonize method) (phenotypic.refine.SmallObjectRemover method) (phenotypic.refine.SmallToLargeMerger method) (phenotypic.refine.Thinning method) (phenotypic.refine.TrimAsymmetry method) (phenotypic.tune.Budget method) (phenotypic.tune.Categorical method) (phenotypic.tune.EvaluationResult method) (phenotypic.tune.Evaluator method) (phenotypic.tune.Excluded method) (phenotypic.tune.Fixed method) (phenotypic.tune.FloatRange method) (phenotypic.tune.HeldOutConfig method) (phenotypic.tune.ImportanceReport method) (phenotypic.tune.InferredSearchSpace method) (phenotypic.tune.IntRange method) (phenotypic.tune.Knob method) (phenotypic.tune.score.CompositeScorer method) (phenotypic.tune.score.GroundTruthMasks method) (phenotypic.tune.score.QCScorer method) (phenotypic.tune.score.ReferenceFreeScorer method) (phenotypic.tune.score.Scorer method) (phenotypic.tune.score.SupervisedScorer method) (phenotypic.tune.SearchSpace method) (phenotypic.tune.strategy.GridConfig method) (phenotypic.tune.strategy.OptunaConfig method) (phenotypic.tune.strategy.RandomConfig method) (phenotypic.tune.strategy.StrategyConfig method) (phenotypic.tune.Trial method) (phenotypic.tune.TuningSpec method) model_dump_json() (phenotypic.abc_.BackgroundSubtraction method) (phenotypic.abc_.BaseOperation method) (phenotypic.abc_.ContrastAdjustment method) (phenotypic.abc_.FocusBlob method) (phenotypic.abc_.FocusEdge method) (phenotypic.abc_.GpuDetector method) (phenotypic.abc_.GridCorrector method) (phenotypic.abc_.GridFinder method) (phenotypic.abc_.GridMeasureFeatures method) (phenotypic.abc_.GridObjectDetector method) (phenotypic.abc_.GridObjectRefiner method) (phenotypic.abc_.GridOperation method) (phenotypic.abc_.ImageCorrector method) (phenotypic.abc_.ImageDenoiser method) (phenotypic.abc_.ImageEnhancer method) (phenotypic.abc_.ImageOperation method) (phenotypic.abc_.MeasureFeatures method) (phenotypic.abc_.MorphologicalFiltering method) (phenotypic.abc_.ObjectDetector method) (phenotypic.abc_.ObjectRefiner method) (phenotypic.abc_.PostMeasurement method) (phenotypic.abc_.PrefabPipeline method) (phenotypic.abc_.Smoothing method) (phenotypic.abc_.ThresholdDetector method) (phenotypic.analysis.EdgeCorrector method) (phenotypic.analysis.ErrorCutoffFinder method) (phenotypic.analysis.ExpectedVsDetectedCount method) (phenotypic.analysis.GridOccupancy method) (phenotypic.analysis.ICC method) (phenotypic.analysis.LinearCapAndLagModel method) (phenotypic.analysis.LinearLagModel method) (phenotypic.analysis.LogGrowthModel method) (phenotypic.analysis.MADOutlierRemover method) (phenotypic.analysis.MaxModifiedZScore method) (phenotypic.analysis.RelativeMAD method) (phenotypic.analysis.ReplicateAgreement method) (phenotypic.analysis.TukeyOutlierFraction method) (phenotypic.analysis.TukeyOutlierRemover method) (phenotypic.correction.BayesShrinkCorrector method) (phenotypic.correction.CaptureMetadata method) (phenotypic.correction.ColorCheckerProfile method) (phenotypic.correction.ColorCorrector method) (phenotypic.correction.ColorDenoise method) (phenotypic.correction.DenoiseBlockMatch method) (phenotypic.correction.GridAligner method) (phenotypic.correction.ImageCropper method) (phenotypic.correction.ImagePadder method) (phenotypic.correction.VisuShrinkCorrector method) (phenotypic.detect.CannyDetector method) (phenotypic.detect.ChanVeseDetector method) (phenotypic.detect.CompositeDetector method) (phenotypic.detect.FilamentousFungiDetector method) (phenotypic.detect.HysteresisDetector method) (phenotypic.detect.InoculumDetector method) (phenotypic.detect.IsodataDetector method) (phenotypic.detect.LiDetector method) (phenotypic.detect.MadHysteresisDetector method) (phenotypic.detect.ManualGridPointDetector method) (phenotypic.detect.ManualPointDetector method) (phenotypic.detect.MeanDetector method) (phenotypic.detect.MinimumDetector method) (phenotypic.detect.OtsuDetector method) (phenotypic.detect.RankOtsuDetector method) (phenotypic.detect.RoundPeaksDetector method) (phenotypic.detect.SecondaryOtsuDetector method) (phenotypic.detect.SinePeakDetector method) (phenotypic.detect.TriangleDetector method) (phenotypic.detect.UserThreshold method) (phenotypic.detect.WatershedDetector method) (phenotypic.detect.YenDetector method) (phenotypic.enhance.BayesShrinkEnhancer method) (phenotypic.enhance.CompositeEnhance method) (phenotypic.enhance.ContrastStretching method) (phenotypic.enhance.EnhanceBlockMatch method) (phenotypic.enhance.EnhanceLocalContrast method) (phenotypic.enhance.FlattenIllumination method) (phenotypic.enhance.FocusBlobLoG method) (phenotypic.enhance.FocusEdgeFrangi method) (phenotypic.enhance.FocusEdgeHessian method) (phenotypic.enhance.FocusEdgeLaplace method) (phenotypic.enhance.FocusEdgeMeijering method) (phenotypic.enhance.FocusEdgePhase method) (phenotypic.enhance.FocusEdgeSato method) (phenotypic.enhance.FocusEdgeSobel method) (phenotypic.enhance.GaussianBlur method) (phenotypic.enhance.GrayOpening method) (phenotypic.enhance.ImageInverter method) (phenotypic.enhance.LocalEdgeDenoise method) (phenotypic.enhance.MedianFilter method) (phenotypic.enhance.NonLocalMeansDenoiser method) (phenotypic.enhance.RankMedianEnhancer method) (phenotypic.enhance.SetDetectMode method) (phenotypic.enhance.SharpenEdgeGauss method) (phenotypic.enhance.StructureSmoothing method) (phenotypic.enhance.SubtractGaussian method) (phenotypic.enhance.SubtractOpening method) (phenotypic.enhance.SubtractRollingBall method) (phenotypic.enhance.SubtractWhiteTophat method) (phenotypic.enhance.VisuShrinkEnhancer method) (phenotypic.enhance.WhiteTophatEnhance method) (phenotypic.grid.AutoGridFinder method) (phenotypic.grid.CenteredAutoGridFinder method) (phenotypic.grid.GridApply method) (phenotypic.grid.ManualGridFinder method) (phenotypic.measure.MeasureBounds method) (phenotypic.measure.MeasureColor method) (phenotypic.measure.MeasureGridLinRegStats method) (phenotypic.measure.MeasureGridSpread method) (phenotypic.measure.MeasureIntensity method) (phenotypic.measure.MeasureNeighborDist method) (phenotypic.measure.MeasureOrientationZones method) (phenotypic.measure.MeasureShape method) (phenotypic.measure.MeasureSize method) (phenotypic.measure.MeasureSymmetricZones method) (phenotypic.measure.MeasureTexture method) (phenotypic.prefab.FilamentousFungiPipeline method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.prefab.RoundPeaksPipeline method) (phenotypic.prefab.SpImagerPipeline method) (phenotypic.refine.ExtractColonyCore method) (phenotypic.refine.GridAlignmentRefiner method) (phenotypic.refine.GridOversizedObjectRemover method) (phenotypic.refine.KeepNearestCenter method) (phenotypic.refine.KeepSectionLargest method) (phenotypic.refine.ManualRefine method) (phenotypic.refine.MaskClosing method) (phenotypic.refine.MaskDilation method) (phenotypic.refine.MaskErosion method) (phenotypic.refine.MaskFill method) (phenotypic.refine.MaskGradient method) (phenotypic.refine.MaskOpening method) (phenotypic.refine.MaskWhiteTophat method) (phenotypic.refine.MergeFragmentChains method) (phenotypic.refine.NearestNeighborMerger method) (phenotypic.refine.ReduceSectionsByLine method) (phenotypic.refine.RefineBySineFit method) (phenotypic.refine.RemoveBorderObjects method) (phenotypic.refine.RemoveByFeature method) (phenotypic.refine.RemoveGridOutliers method) (phenotypic.refine.RemoveLowCircularity method) (phenotypic.refine.SeparateObjects method) (phenotypic.refine.Skeletonize method) (phenotypic.refine.SmallObjectRemover method) (phenotypic.refine.SmallToLargeMerger method) (phenotypic.refine.Thinning method) (phenotypic.refine.TrimAsymmetry method) (phenotypic.tune.Budget method) (phenotypic.tune.Categorical method) (phenotypic.tune.EvaluationResult method) (phenotypic.tune.Evaluator method) (phenotypic.tune.Excluded method) (phenotypic.tune.Fixed method) (phenotypic.tune.FloatRange method) (phenotypic.tune.HeldOutConfig method) (phenotypic.tune.ImportanceReport method) (phenotypic.tune.InferredSearchSpace method) (phenotypic.tune.IntRange method) (phenotypic.tune.Knob method) (phenotypic.tune.score.CompositeScorer method) (phenotypic.tune.score.GroundTruthMasks method) (phenotypic.tune.score.QCScorer method) (phenotypic.tune.score.ReferenceFreeScorer method) (phenotypic.tune.score.Scorer method) (phenotypic.tune.score.SupervisedScorer method) (phenotypic.tune.SearchSpace method) (phenotypic.tune.strategy.GridConfig method) (phenotypic.tune.strategy.OptunaConfig method) (phenotypic.tune.strategy.RandomConfig method) (phenotypic.tune.strategy.StrategyConfig method) (phenotypic.tune.Trial method) (phenotypic.tune.TuningSpec method) model_extra (phenotypic.abc_.BackgroundSubtraction property) (phenotypic.abc_.BaseOperation property) (phenotypic.abc_.ContrastAdjustment property) (phenotypic.abc_.FocusBlob property) (phenotypic.abc_.FocusEdge property) (phenotypic.abc_.GpuDetector property) (phenotypic.abc_.GridCorrector property) (phenotypic.abc_.GridFinder property) (phenotypic.abc_.GridMeasureFeatures property) (phenotypic.abc_.GridObjectDetector property) (phenotypic.abc_.GridObjectRefiner property) (phenotypic.abc_.GridOperation property) (phenotypic.abc_.ImageCorrector property) (phenotypic.abc_.ImageDenoiser property) (phenotypic.abc_.ImageEnhancer property) (phenotypic.abc_.ImageOperation property) (phenotypic.abc_.MeasureFeatures property) (phenotypic.abc_.MorphologicalFiltering property) (phenotypic.abc_.ObjectDetector property) (phenotypic.abc_.ObjectRefiner property) (phenotypic.abc_.PostMeasurement property) (phenotypic.abc_.PrefabPipeline property) (phenotypic.abc_.Smoothing property) (phenotypic.abc_.ThresholdDetector property) (phenotypic.analysis.EdgeCorrector property) (phenotypic.analysis.ErrorCutoffFinder property) (phenotypic.analysis.ExpectedVsDetectedCount property) (phenotypic.analysis.GridOccupancy property) (phenotypic.analysis.ICC property) (phenotypic.analysis.LinearCapAndLagModel property) (phenotypic.analysis.LinearLagModel property) (phenotypic.analysis.LogGrowthModel property) (phenotypic.analysis.MADOutlierRemover property) (phenotypic.analysis.MaxModifiedZScore property) (phenotypic.analysis.RelativeMAD property) (phenotypic.analysis.ReplicateAgreement property) (phenotypic.analysis.TukeyOutlierFraction property) (phenotypic.analysis.TukeyOutlierRemover property) (phenotypic.correction.BayesShrinkCorrector property) (phenotypic.correction.CaptureMetadata property) (phenotypic.correction.ColorCheckerProfile property) (phenotypic.correction.ColorCorrector property) (phenotypic.correction.ColorDenoise property) (phenotypic.correction.DenoiseBlockMatch property) (phenotypic.correction.GridAligner property) (phenotypic.correction.ImageCropper property) (phenotypic.correction.ImagePadder property) (phenotypic.correction.VisuShrinkCorrector property) (phenotypic.detect.CannyDetector property) (phenotypic.detect.ChanVeseDetector property) (phenotypic.detect.CompositeDetector property) (phenotypic.detect.FilamentousFungiDetector property) (phenotypic.detect.HysteresisDetector property) (phenotypic.detect.InoculumDetector property) (phenotypic.detect.IsodataDetector property) (phenotypic.detect.LiDetector property) (phenotypic.detect.MadHysteresisDetector property) (phenotypic.detect.ManualGridPointDetector property) (phenotypic.detect.ManualPointDetector property) (phenotypic.detect.MeanDetector property) (phenotypic.detect.MinimumDetector property) (phenotypic.detect.OtsuDetector property) (phenotypic.detect.RankOtsuDetector property) (phenotypic.detect.RoundPeaksDetector property) (phenotypic.detect.SecondaryOtsuDetector property) (phenotypic.detect.SinePeakDetector property) (phenotypic.detect.TriangleDetector property) (phenotypic.detect.UserThreshold property) (phenotypic.detect.WatershedDetector property) (phenotypic.detect.YenDetector property) (phenotypic.enhance.BayesShrinkEnhancer property) (phenotypic.enhance.CompositeEnhance property) (phenotypic.enhance.ContrastStretching property) (phenotypic.enhance.EnhanceBlockMatch property) (phenotypic.enhance.EnhanceLocalContrast property) (phenotypic.enhance.FlattenIllumination property) (phenotypic.enhance.FocusBlobLoG property) (phenotypic.enhance.FocusEdgeFrangi property) (phenotypic.enhance.FocusEdgeHessian property) (phenotypic.enhance.FocusEdgeLaplace property) (phenotypic.enhance.FocusEdgeMeijering property) (phenotypic.enhance.FocusEdgePhase property) (phenotypic.enhance.FocusEdgeSato property) (phenotypic.enhance.FocusEdgeSobel property) (phenotypic.enhance.GaussianBlur property) (phenotypic.enhance.GrayOpening property) (phenotypic.enhance.ImageInverter property) (phenotypic.enhance.LocalEdgeDenoise property) (phenotypic.enhance.MedianFilter property) (phenotypic.enhance.NonLocalMeansDenoiser property) (phenotypic.enhance.RankMedianEnhancer property) (phenotypic.enhance.SetDetectMode property) (phenotypic.enhance.SharpenEdgeGauss property) (phenotypic.enhance.StructureSmoothing property) (phenotypic.enhance.SubtractGaussian property) (phenotypic.enhance.SubtractOpening property) (phenotypic.enhance.SubtractRollingBall property) (phenotypic.enhance.SubtractWhiteTophat property) (phenotypic.enhance.VisuShrinkEnhancer property) (phenotypic.enhance.WhiteTophatEnhance property) (phenotypic.grid.AutoGridFinder property) (phenotypic.grid.CenteredAutoGridFinder property) (phenotypic.grid.GridApply property) (phenotypic.grid.ManualGridFinder property) (phenotypic.measure.MeasureBounds property) (phenotypic.measure.MeasureColor property) (phenotypic.measure.MeasureGridLinRegStats property) (phenotypic.measure.MeasureGridSpread property) (phenotypic.measure.MeasureIntensity property) (phenotypic.measure.MeasureNeighborDist property) (phenotypic.measure.MeasureOrientationZones property) (phenotypic.measure.MeasureShape property) (phenotypic.measure.MeasureSize property) (phenotypic.measure.MeasureSymmetricZones property) (phenotypic.measure.MeasureTexture property) (phenotypic.prefab.FilamentousFungiPipeline property) (phenotypic.prefab.GridSectionPipeline property) (phenotypic.prefab.HeavyOtsuPipeline property) (phenotypic.prefab.HeavyRoundPeaksPipeline property) (phenotypic.prefab.HeavyWatershedPipeline property) (phenotypic.prefab.RoundPeaksPipeline property) (phenotypic.prefab.SpImagerPipeline property) (phenotypic.refine.ExtractColonyCore property) (phenotypic.refine.GridAlignmentRefiner property) (phenotypic.refine.GridOversizedObjectRemover property) (phenotypic.refine.KeepNearestCenter property) (phenotypic.refine.KeepSectionLargest property) (phenotypic.refine.ManualRefine property) (phenotypic.refine.MaskClosing property) (phenotypic.refine.MaskDilation property) (phenotypic.refine.MaskErosion property) (phenotypic.refine.MaskFill property) (phenotypic.refine.MaskGradient property) (phenotypic.refine.MaskOpening property) (phenotypic.refine.MaskWhiteTophat property) (phenotypic.refine.MergeFragmentChains property) (phenotypic.refine.NearestNeighborMerger property) (phenotypic.refine.ReduceSectionsByLine property) (phenotypic.refine.RefineBySineFit property) (phenotypic.refine.RemoveBorderObjects property) (phenotypic.refine.RemoveByFeature property) (phenotypic.refine.RemoveGridOutliers property) (phenotypic.refine.RemoveLowCircularity property) (phenotypic.refine.SeparateObjects property) (phenotypic.refine.Skeletonize property) (phenotypic.refine.SmallObjectRemover property) (phenotypic.refine.SmallToLargeMerger property) (phenotypic.refine.Thinning property) (phenotypic.refine.TrimAsymmetry property) (phenotypic.tune.Budget property) (phenotypic.tune.Categorical property) (phenotypic.tune.EvaluationResult property) (phenotypic.tune.Evaluator property) (phenotypic.tune.Excluded property) (phenotypic.tune.Fixed property) (phenotypic.tune.FloatRange property) (phenotypic.tune.HeldOutConfig property) (phenotypic.tune.ImportanceReport property) (phenotypic.tune.InferredSearchSpace property) (phenotypic.tune.IntRange property) (phenotypic.tune.Knob property) (phenotypic.tune.score.CompositeScorer property) (phenotypic.tune.score.GroundTruthMasks property) (phenotypic.tune.score.QCScorer property) (phenotypic.tune.score.ReferenceFreeScorer property) (phenotypic.tune.score.Scorer property) (phenotypic.tune.score.SupervisedScorer property) (phenotypic.tune.SearchSpace property) (phenotypic.tune.strategy.GridConfig property) (phenotypic.tune.strategy.OptunaConfig property) (phenotypic.tune.strategy.RandomConfig property) (phenotypic.tune.strategy.StrategyConfig property) (phenotypic.tune.Trial property) (phenotypic.tune.TuningSpec property) model_fields (phenotypic.abc_.BackgroundSubtraction attribute) (phenotypic.abc_.BaseOperation attribute) (phenotypic.abc_.ContrastAdjustment attribute) (phenotypic.abc_.FocusBlob attribute) (phenotypic.abc_.FocusEdge attribute) (phenotypic.abc_.GpuDetector attribute) (phenotypic.abc_.GridCorrector attribute) (phenotypic.abc_.GridFinder attribute) (phenotypic.abc_.GridMeasureFeatures attribute) (phenotypic.abc_.GridObjectDetector attribute) (phenotypic.abc_.GridObjectRefiner attribute) (phenotypic.abc_.GridOperation attribute) (phenotypic.abc_.ImageCorrector attribute) (phenotypic.abc_.ImageDenoiser attribute) (phenotypic.abc_.ImageEnhancer attribute) (phenotypic.abc_.ImageOperation attribute) (phenotypic.abc_.MeasureFeatures attribute) (phenotypic.abc_.MorphologicalFiltering attribute) (phenotypic.abc_.ObjectDetector attribute) (phenotypic.abc_.ObjectRefiner attribute) (phenotypic.abc_.PostMeasurement attribute) (phenotypic.abc_.PrefabPipeline attribute) (phenotypic.abc_.Smoothing attribute) (phenotypic.abc_.ThresholdDetector attribute) (phenotypic.analysis.EdgeCorrector attribute) (phenotypic.analysis.ErrorCutoffFinder attribute) (phenotypic.analysis.ExpectedVsDetectedCount attribute) (phenotypic.analysis.GridOccupancy attribute) (phenotypic.analysis.ICC attribute) (phenotypic.analysis.LinearCapAndLagModel attribute) (phenotypic.analysis.LinearLagModel attribute) (phenotypic.analysis.LogGrowthModel attribute) (phenotypic.analysis.MADOutlierRemover attribute) (phenotypic.analysis.MaxModifiedZScore attribute) (phenotypic.analysis.RelativeMAD attribute) (phenotypic.analysis.ReplicateAgreement attribute) (phenotypic.analysis.TukeyOutlierFraction attribute) (phenotypic.analysis.TukeyOutlierRemover attribute) (phenotypic.correction.BayesShrinkCorrector attribute) (phenotypic.correction.CaptureMetadata attribute) (phenotypic.correction.ColorCheckerProfile attribute) (phenotypic.correction.ColorCorrector attribute) (phenotypic.correction.ColorDenoise attribute) (phenotypic.correction.DenoiseBlockMatch attribute) (phenotypic.correction.GridAligner attribute) (phenotypic.correction.ImageCropper attribute) (phenotypic.correction.ImagePadder attribute) (phenotypic.correction.VisuShrinkCorrector attribute) (phenotypic.detect.CannyDetector attribute) (phenotypic.detect.ChanVeseDetector attribute) (phenotypic.detect.CompositeDetector attribute) (phenotypic.detect.FilamentousFungiDetector attribute) (phenotypic.detect.HysteresisDetector attribute) (phenotypic.detect.InoculumDetector attribute) (phenotypic.detect.IsodataDetector attribute) (phenotypic.detect.LiDetector attribute) (phenotypic.detect.MadHysteresisDetector attribute) (phenotypic.detect.ManualGridPointDetector attribute) (phenotypic.detect.ManualPointDetector attribute) (phenotypic.detect.MeanDetector attribute) (phenotypic.detect.MinimumDetector attribute) (phenotypic.detect.OtsuDetector attribute) (phenotypic.detect.RankOtsuDetector attribute) (phenotypic.detect.RoundPeaksDetector attribute) (phenotypic.detect.SecondaryOtsuDetector attribute) (phenotypic.detect.SinePeakDetector attribute) (phenotypic.detect.TriangleDetector attribute) (phenotypic.detect.UserThreshold attribute) (phenotypic.detect.WatershedDetector attribute) (phenotypic.detect.YenDetector attribute) (phenotypic.enhance.BayesShrinkEnhancer attribute) (phenotypic.enhance.CompositeEnhance attribute) (phenotypic.enhance.ContrastStretching attribute) (phenotypic.enhance.EnhanceBlockMatch attribute) (phenotypic.enhance.EnhanceLocalContrast attribute) (phenotypic.enhance.FlattenIllumination attribute) (phenotypic.enhance.FocusBlobLoG attribute) (phenotypic.enhance.FocusEdgeFrangi attribute) (phenotypic.enhance.FocusEdgeHessian attribute) (phenotypic.enhance.FocusEdgeLaplace attribute) (phenotypic.enhance.FocusEdgeMeijering attribute) (phenotypic.enhance.FocusEdgePhase attribute) (phenotypic.enhance.FocusEdgeSato attribute) (phenotypic.enhance.FocusEdgeSobel attribute) (phenotypic.enhance.GaussianBlur attribute) (phenotypic.enhance.GrayOpening attribute) (phenotypic.enhance.ImageInverter attribute) (phenotypic.enhance.LocalEdgeDenoise attribute) (phenotypic.enhance.MedianFilter attribute) (phenotypic.enhance.NonLocalMeansDenoiser attribute) (phenotypic.enhance.RankMedianEnhancer attribute) (phenotypic.enhance.SetDetectMode attribute) (phenotypic.enhance.SharpenEdgeGauss attribute) (phenotypic.enhance.StructureSmoothing attribute) (phenotypic.enhance.SubtractGaussian attribute) (phenotypic.enhance.SubtractOpening attribute) (phenotypic.enhance.SubtractRollingBall attribute) (phenotypic.enhance.SubtractWhiteTophat attribute) (phenotypic.enhance.VisuShrinkEnhancer attribute) (phenotypic.enhance.WhiteTophatEnhance attribute) (phenotypic.grid.AutoGridFinder attribute) (phenotypic.grid.CenteredAutoGridFinder attribute) (phenotypic.grid.GridApply attribute) (phenotypic.grid.ManualGridFinder attribute) (phenotypic.measure.MeasureBounds attribute) (phenotypic.measure.MeasureColor attribute) (phenotypic.measure.MeasureGridLinRegStats attribute) (phenotypic.measure.MeasureGridSpread attribute) (phenotypic.measure.MeasureIntensity attribute) (phenotypic.measure.MeasureNeighborDist attribute) (phenotypic.measure.MeasureOrientationZones attribute) (phenotypic.measure.MeasureShape attribute) (phenotypic.measure.MeasureSize attribute) (phenotypic.measure.MeasureSymmetricZones attribute) (phenotypic.measure.MeasureTexture attribute) (phenotypic.prefab.FilamentousFungiPipeline attribute) (phenotypic.prefab.GridSectionPipeline attribute) (phenotypic.prefab.HeavyOtsuPipeline attribute) (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) (phenotypic.prefab.HeavyWatershedPipeline attribute) (phenotypic.prefab.RoundPeaksPipeline attribute) (phenotypic.prefab.SpImagerPipeline attribute) (phenotypic.refine.ExtractColonyCore attribute) (phenotypic.refine.GridAlignmentRefiner attribute) (phenotypic.refine.GridOversizedObjectRemover attribute) (phenotypic.refine.KeepNearestCenter attribute) (phenotypic.refine.KeepSectionLargest attribute) (phenotypic.refine.ManualRefine attribute) (phenotypic.refine.MaskClosing attribute) (phenotypic.refine.MaskDilation attribute) (phenotypic.refine.MaskErosion attribute) (phenotypic.refine.MaskFill attribute) (phenotypic.refine.MaskGradient attribute) (phenotypic.refine.MaskOpening attribute) (phenotypic.refine.MaskWhiteTophat attribute) (phenotypic.refine.MergeFragmentChains attribute) (phenotypic.refine.NearestNeighborMerger attribute) (phenotypic.refine.ReduceSectionsByLine attribute) (phenotypic.refine.RefineBySineFit attribute) (phenotypic.refine.RemoveBorderObjects attribute) (phenotypic.refine.RemoveByFeature attribute) (phenotypic.refine.RemoveGridOutliers attribute) (phenotypic.refine.RemoveLowCircularity attribute) (phenotypic.refine.SeparateObjects attribute) (phenotypic.refine.Skeletonize attribute) (phenotypic.refine.SmallObjectRemover attribute) (phenotypic.refine.SmallToLargeMerger attribute) (phenotypic.refine.Thinning attribute) (phenotypic.refine.TrimAsymmetry attribute) (phenotypic.tune.Budget attribute) (phenotypic.tune.Categorical attribute) (phenotypic.tune.EvaluationResult attribute) (phenotypic.tune.Evaluator attribute) (phenotypic.tune.Excluded attribute) (phenotypic.tune.Fixed attribute) (phenotypic.tune.FloatRange attribute) (phenotypic.tune.HeldOutConfig attribute) (phenotypic.tune.ImportanceReport attribute) (phenotypic.tune.InferredSearchSpace attribute) (phenotypic.tune.IntRange attribute) (phenotypic.tune.Knob attribute) (phenotypic.tune.score.CompositeScorer attribute) (phenotypic.tune.score.GroundTruthMasks attribute) (phenotypic.tune.score.QCScorer attribute) (phenotypic.tune.score.ReferenceFreeScorer attribute) (phenotypic.tune.score.Scorer attribute) (phenotypic.tune.score.SupervisedScorer attribute) (phenotypic.tune.SearchSpace attribute) (phenotypic.tune.strategy.GridConfig attribute) (phenotypic.tune.strategy.OptunaConfig attribute) (phenotypic.tune.strategy.RandomConfig attribute) (phenotypic.tune.strategy.StrategyConfig attribute) (phenotypic.tune.Trial attribute) (phenotypic.tune.TuningSpec attribute) model_fields_set (phenotypic.abc_.BackgroundSubtraction property) (phenotypic.abc_.BaseOperation property) (phenotypic.abc_.ContrastAdjustment property) (phenotypic.abc_.FocusBlob property) (phenotypic.abc_.FocusEdge property) (phenotypic.abc_.GpuDetector property) (phenotypic.abc_.GridCorrector property) (phenotypic.abc_.GridFinder property) (phenotypic.abc_.GridMeasureFeatures property) (phenotypic.abc_.GridObjectDetector property) (phenotypic.abc_.GridObjectRefiner property) (phenotypic.abc_.GridOperation property) (phenotypic.abc_.ImageCorrector property) (phenotypic.abc_.ImageDenoiser property) (phenotypic.abc_.ImageEnhancer property) (phenotypic.abc_.ImageOperation property) (phenotypic.abc_.MeasureFeatures property) (phenotypic.abc_.MorphologicalFiltering property) (phenotypic.abc_.ObjectDetector property) (phenotypic.abc_.ObjectRefiner property) (phenotypic.abc_.PostMeasurement property) (phenotypic.abc_.PrefabPipeline property) (phenotypic.abc_.Smoothing property) (phenotypic.abc_.ThresholdDetector property) (phenotypic.analysis.EdgeCorrector property) (phenotypic.analysis.ErrorCutoffFinder property) (phenotypic.analysis.ExpectedVsDetectedCount property) (phenotypic.analysis.GridOccupancy property) (phenotypic.analysis.ICC property) (phenotypic.analysis.LinearCapAndLagModel property) (phenotypic.analysis.LinearLagModel property) (phenotypic.analysis.LogGrowthModel property) (phenotypic.analysis.MADOutlierRemover property) (phenotypic.analysis.MaxModifiedZScore property) (phenotypic.analysis.RelativeMAD property) (phenotypic.analysis.ReplicateAgreement property) (phenotypic.analysis.TukeyOutlierFraction property) (phenotypic.analysis.TukeyOutlierRemover property) (phenotypic.correction.BayesShrinkCorrector property) (phenotypic.correction.CaptureMetadata property) (phenotypic.correction.ColorCheckerProfile property) (phenotypic.correction.ColorCorrector property) (phenotypic.correction.ColorDenoise property) (phenotypic.correction.DenoiseBlockMatch property) (phenotypic.correction.GridAligner property) (phenotypic.correction.ImageCropper property) (phenotypic.correction.ImagePadder property) (phenotypic.correction.VisuShrinkCorrector property) (phenotypic.detect.CannyDetector property) (phenotypic.detect.ChanVeseDetector property) (phenotypic.detect.CompositeDetector property) (phenotypic.detect.FilamentousFungiDetector property) (phenotypic.detect.HysteresisDetector property) (phenotypic.detect.InoculumDetector property) (phenotypic.detect.IsodataDetector property) (phenotypic.detect.LiDetector property) (phenotypic.detect.MadHysteresisDetector property) (phenotypic.detect.ManualGridPointDetector property) (phenotypic.detect.ManualPointDetector property) (phenotypic.detect.MeanDetector property) (phenotypic.detect.MinimumDetector property) (phenotypic.detect.OtsuDetector property) (phenotypic.detect.RankOtsuDetector property) (phenotypic.detect.RoundPeaksDetector property) (phenotypic.detect.SecondaryOtsuDetector property) (phenotypic.detect.SinePeakDetector property) (phenotypic.detect.TriangleDetector property) (phenotypic.detect.UserThreshold property) (phenotypic.detect.WatershedDetector property) (phenotypic.detect.YenDetector property) (phenotypic.enhance.BayesShrinkEnhancer property) (phenotypic.enhance.CompositeEnhance property) (phenotypic.enhance.ContrastStretching property) (phenotypic.enhance.EnhanceBlockMatch property) (phenotypic.enhance.EnhanceLocalContrast property) (phenotypic.enhance.FlattenIllumination property) (phenotypic.enhance.FocusBlobLoG property) (phenotypic.enhance.FocusEdgeFrangi property) (phenotypic.enhance.FocusEdgeHessian property) (phenotypic.enhance.FocusEdgeLaplace property) (phenotypic.enhance.FocusEdgeMeijering property) (phenotypic.enhance.FocusEdgePhase property) (phenotypic.enhance.FocusEdgeSato property) (phenotypic.enhance.FocusEdgeSobel property) (phenotypic.enhance.GaussianBlur property) (phenotypic.enhance.GrayOpening property) (phenotypic.enhance.ImageInverter property) (phenotypic.enhance.LocalEdgeDenoise property) (phenotypic.enhance.MedianFilter property) (phenotypic.enhance.NonLocalMeansDenoiser property) (phenotypic.enhance.RankMedianEnhancer property) (phenotypic.enhance.SetDetectMode property) (phenotypic.enhance.SharpenEdgeGauss property) (phenotypic.enhance.StructureSmoothing property) (phenotypic.enhance.SubtractGaussian property) (phenotypic.enhance.SubtractOpening property) (phenotypic.enhance.SubtractRollingBall property) (phenotypic.enhance.SubtractWhiteTophat property) (phenotypic.enhance.VisuShrinkEnhancer property) (phenotypic.enhance.WhiteTophatEnhance property) (phenotypic.grid.AutoGridFinder property) (phenotypic.grid.CenteredAutoGridFinder property) (phenotypic.grid.GridApply property) (phenotypic.grid.ManualGridFinder property) (phenotypic.measure.MeasureBounds property) (phenotypic.measure.MeasureColor property) (phenotypic.measure.MeasureGridLinRegStats property) (phenotypic.measure.MeasureGridSpread property) (phenotypic.measure.MeasureIntensity property) (phenotypic.measure.MeasureNeighborDist property) (phenotypic.measure.MeasureOrientationZones property) (phenotypic.measure.MeasureShape property) (phenotypic.measure.MeasureSize property) (phenotypic.measure.MeasureSymmetricZones property) (phenotypic.measure.MeasureTexture property) (phenotypic.prefab.FilamentousFungiPipeline property) (phenotypic.prefab.GridSectionPipeline property) (phenotypic.prefab.HeavyOtsuPipeline property) (phenotypic.prefab.HeavyRoundPeaksPipeline property) (phenotypic.prefab.HeavyWatershedPipeline property) (phenotypic.prefab.RoundPeaksPipeline property) (phenotypic.prefab.SpImagerPipeline property) (phenotypic.refine.ExtractColonyCore property) (phenotypic.refine.GridAlignmentRefiner property) (phenotypic.refine.GridOversizedObjectRemover property) (phenotypic.refine.KeepNearestCenter property) (phenotypic.refine.KeepSectionLargest property) (phenotypic.refine.ManualRefine property) (phenotypic.refine.MaskClosing property) (phenotypic.refine.MaskDilation property) (phenotypic.refine.MaskErosion property) (phenotypic.refine.MaskFill property) (phenotypic.refine.MaskGradient property) (phenotypic.refine.MaskOpening property) (phenotypic.refine.MaskWhiteTophat property) (phenotypic.refine.MergeFragmentChains property) (phenotypic.refine.NearestNeighborMerger property) (phenotypic.refine.ReduceSectionsByLine property) (phenotypic.refine.RefineBySineFit property) (phenotypic.refine.RemoveBorderObjects property) (phenotypic.refine.RemoveByFeature property) (phenotypic.refine.RemoveGridOutliers property) (phenotypic.refine.RemoveLowCircularity property) (phenotypic.refine.SeparateObjects property) (phenotypic.refine.Skeletonize property) (phenotypic.refine.SmallObjectRemover property) (phenotypic.refine.SmallToLargeMerger property) (phenotypic.refine.Thinning property) (phenotypic.refine.TrimAsymmetry property) (phenotypic.tune.Budget property) (phenotypic.tune.Categorical property) (phenotypic.tune.EvaluationResult property) (phenotypic.tune.Evaluator property) (phenotypic.tune.Excluded property) (phenotypic.tune.Fixed property) (phenotypic.tune.FloatRange property) (phenotypic.tune.HeldOutConfig property) (phenotypic.tune.ImportanceReport property) (phenotypic.tune.InferredSearchSpace property) (phenotypic.tune.IntRange property) (phenotypic.tune.Knob property) (phenotypic.tune.score.CompositeScorer property) (phenotypic.tune.score.GroundTruthMasks property) (phenotypic.tune.score.QCScorer property) (phenotypic.tune.score.ReferenceFreeScorer property) (phenotypic.tune.score.Scorer property) (phenotypic.tune.score.SupervisedScorer property) (phenotypic.tune.SearchSpace property) (phenotypic.tune.strategy.GridConfig property) (phenotypic.tune.strategy.OptunaConfig property) (phenotypic.tune.strategy.RandomConfig property) (phenotypic.tune.strategy.StrategyConfig property) (phenotypic.tune.Trial property) (phenotypic.tune.TuningSpec property) model_func() (phenotypic.analysis.LinearCapAndLagModel static method) (phenotypic.analysis.LinearLagModel static method) (phenotypic.analysis.LogGrowthModel static method) model_json_schema() (phenotypic.abc_.BackgroundSubtraction class method) (phenotypic.abc_.BaseOperation class method) (phenotypic.abc_.ContrastAdjustment class method) (phenotypic.abc_.FocusBlob class method) (phenotypic.abc_.FocusEdge class method) (phenotypic.abc_.GpuDetector class method) (phenotypic.abc_.GridCorrector class method) (phenotypic.abc_.GridFinder class method) (phenotypic.abc_.GridMeasureFeatures class method) (phenotypic.abc_.GridObjectDetector class method) (phenotypic.abc_.GridObjectRefiner class method) (phenotypic.abc_.GridOperation class method) (phenotypic.abc_.ImageCorrector class method) (phenotypic.abc_.ImageDenoiser class method) (phenotypic.abc_.ImageEnhancer class method) (phenotypic.abc_.ImageOperation class method) (phenotypic.abc_.MeasureFeatures class method) (phenotypic.abc_.MorphologicalFiltering class method) (phenotypic.abc_.ObjectDetector class method) (phenotypic.abc_.ObjectRefiner class method) (phenotypic.abc_.PostMeasurement class method) (phenotypic.abc_.PrefabPipeline class method) (phenotypic.abc_.Smoothing class method) (phenotypic.abc_.ThresholdDetector class method) (phenotypic.analysis.EdgeCorrector class method) (phenotypic.analysis.ErrorCutoffFinder class method) (phenotypic.analysis.ExpectedVsDetectedCount class method) (phenotypic.analysis.GridOccupancy class method) (phenotypic.analysis.ICC class method) (phenotypic.analysis.LinearCapAndLagModel class method) (phenotypic.analysis.LinearLagModel class method) (phenotypic.analysis.LogGrowthModel class method) (phenotypic.analysis.MADOutlierRemover class method) (phenotypic.analysis.MaxModifiedZScore class method) (phenotypic.analysis.RelativeMAD class method) (phenotypic.analysis.ReplicateAgreement class method) (phenotypic.analysis.TukeyOutlierFraction class method) (phenotypic.analysis.TukeyOutlierRemover class method) (phenotypic.correction.BayesShrinkCorrector class method) (phenotypic.correction.CaptureMetadata class method) (phenotypic.correction.ColorCheckerProfile class method) (phenotypic.correction.ColorCorrector class method) (phenotypic.correction.ColorDenoise class method) (phenotypic.correction.DenoiseBlockMatch class method) (phenotypic.correction.GridAligner class method) (phenotypic.correction.ImageCropper class method) (phenotypic.correction.ImagePadder class method) (phenotypic.correction.VisuShrinkCorrector class method) (phenotypic.detect.CannyDetector class method) (phenotypic.detect.ChanVeseDetector class method) (phenotypic.detect.CompositeDetector class method) (phenotypic.detect.FilamentousFungiDetector class method) (phenotypic.detect.HysteresisDetector class method) (phenotypic.detect.InoculumDetector class method) (phenotypic.detect.IsodataDetector class method) (phenotypic.detect.LiDetector class method) (phenotypic.detect.MadHysteresisDetector class method) (phenotypic.detect.ManualGridPointDetector class method) (phenotypic.detect.ManualPointDetector class method) (phenotypic.detect.MeanDetector class method) (phenotypic.detect.MinimumDetector class method) (phenotypic.detect.OtsuDetector class method) (phenotypic.detect.RankOtsuDetector class method) (phenotypic.detect.RoundPeaksDetector class method) (phenotypic.detect.SecondaryOtsuDetector class method) (phenotypic.detect.SinePeakDetector class method) (phenotypic.detect.TriangleDetector class method) (phenotypic.detect.UserThreshold class method) (phenotypic.detect.WatershedDetector class method) (phenotypic.detect.YenDetector class method) (phenotypic.enhance.BayesShrinkEnhancer class method) (phenotypic.enhance.CompositeEnhance class method) (phenotypic.enhance.ContrastStretching class method) (phenotypic.enhance.EnhanceBlockMatch class method) (phenotypic.enhance.EnhanceLocalContrast class method) (phenotypic.enhance.FlattenIllumination class method) (phenotypic.enhance.FocusBlobLoG class method) (phenotypic.enhance.FocusEdgeFrangi class method) (phenotypic.enhance.FocusEdgeHessian class method) (phenotypic.enhance.FocusEdgeLaplace class method) (phenotypic.enhance.FocusEdgeMeijering class method) (phenotypic.enhance.FocusEdgePhase class method) (phenotypic.enhance.FocusEdgeSato class method) (phenotypic.enhance.FocusEdgeSobel class method) (phenotypic.enhance.GaussianBlur class method) (phenotypic.enhance.GrayOpening class method) (phenotypic.enhance.ImageInverter class method) (phenotypic.enhance.LocalEdgeDenoise class method) (phenotypic.enhance.MedianFilter class method) (phenotypic.enhance.NonLocalMeansDenoiser class method) (phenotypic.enhance.RankMedianEnhancer class method) (phenotypic.enhance.SetDetectMode class method) (phenotypic.enhance.SharpenEdgeGauss class method) (phenotypic.enhance.StructureSmoothing class method) (phenotypic.enhance.SubtractGaussian class method) (phenotypic.enhance.SubtractOpening class method) (phenotypic.enhance.SubtractRollingBall class method) (phenotypic.enhance.SubtractWhiteTophat class method) (phenotypic.enhance.VisuShrinkEnhancer class method) (phenotypic.enhance.WhiteTophatEnhance class method) (phenotypic.grid.AutoGridFinder class method) (phenotypic.grid.CenteredAutoGridFinder class method) (phenotypic.grid.GridApply class method) (phenotypic.grid.ManualGridFinder class method) (phenotypic.measure.MeasureBounds class method) (phenotypic.measure.MeasureColor class method) (phenotypic.measure.MeasureGridLinRegStats class method) (phenotypic.measure.MeasureGridSpread class method) (phenotypic.measure.MeasureIntensity class method) (phenotypic.measure.MeasureNeighborDist class method) (phenotypic.measure.MeasureOrientationZones class method) (phenotypic.measure.MeasureShape class method) (phenotypic.measure.MeasureSize class method) (phenotypic.measure.MeasureSymmetricZones class method) (phenotypic.measure.MeasureTexture class method) (phenotypic.prefab.FilamentousFungiPipeline class method) (phenotypic.prefab.GridSectionPipeline class method) (phenotypic.prefab.HeavyOtsuPipeline class method) (phenotypic.prefab.HeavyRoundPeaksPipeline class method) (phenotypic.prefab.HeavyWatershedPipeline class method) (phenotypic.prefab.RoundPeaksPipeline class method) (phenotypic.prefab.SpImagerPipeline class method) (phenotypic.refine.ExtractColonyCore class method) (phenotypic.refine.GridAlignmentRefiner class method) (phenotypic.refine.GridOversizedObjectRemover class method) (phenotypic.refine.KeepNearestCenter class method) (phenotypic.refine.KeepSectionLargest class method) (phenotypic.refine.ManualRefine class method) (phenotypic.refine.MaskClosing class method) (phenotypic.refine.MaskDilation class method) (phenotypic.refine.MaskErosion class method) (phenotypic.refine.MaskFill class method) (phenotypic.refine.MaskGradient class method) (phenotypic.refine.MaskOpening class method) (phenotypic.refine.MaskWhiteTophat class method) (phenotypic.refine.MergeFragmentChains class method) (phenotypic.refine.NearestNeighborMerger class method) (phenotypic.refine.ReduceSectionsByLine class method) (phenotypic.refine.RefineBySineFit class method) (phenotypic.refine.RemoveBorderObjects class method) (phenotypic.refine.RemoveByFeature class method) (phenotypic.refine.RemoveGridOutliers class method) (phenotypic.refine.RemoveLowCircularity class method) (phenotypic.refine.SeparateObjects class method) (phenotypic.refine.Skeletonize class method) (phenotypic.refine.SmallObjectRemover class method) (phenotypic.refine.SmallToLargeMerger class method) (phenotypic.refine.Thinning class method) (phenotypic.refine.TrimAsymmetry class method) (phenotypic.tune.Budget class method) (phenotypic.tune.Categorical class method) (phenotypic.tune.EvaluationResult class method) (phenotypic.tune.Evaluator class method) (phenotypic.tune.Excluded class method) (phenotypic.tune.Fixed class method) (phenotypic.tune.FloatRange class method) (phenotypic.tune.HeldOutConfig class method) (phenotypic.tune.ImportanceReport class method) (phenotypic.tune.InferredSearchSpace class method) (phenotypic.tune.IntRange class method) (phenotypic.tune.Knob class method) (phenotypic.tune.score.CompositeScorer class method) (phenotypic.tune.score.GroundTruthMasks class method) (phenotypic.tune.score.QCScorer class method) (phenotypic.tune.score.ReferenceFreeScorer class method) (phenotypic.tune.score.Scorer class method) (phenotypic.tune.score.SupervisedScorer class method) (phenotypic.tune.SearchSpace class method) (phenotypic.tune.strategy.GridConfig class method) (phenotypic.tune.strategy.OptunaConfig class method) (phenotypic.tune.strategy.RandomConfig class method) (phenotypic.tune.strategy.StrategyConfig class method) (phenotypic.tune.Trial class method) (phenotypic.tune.TuningSpec class method) model_parametrized_name() (phenotypic.abc_.BackgroundSubtraction class method) (phenotypic.abc_.BaseOperation class method) (phenotypic.abc_.ContrastAdjustment class method) (phenotypic.abc_.FocusBlob class method) (phenotypic.abc_.FocusEdge class method) (phenotypic.abc_.GpuDetector class method) (phenotypic.abc_.GridCorrector class method) (phenotypic.abc_.GridFinder class method) (phenotypic.abc_.GridMeasureFeatures class method) (phenotypic.abc_.GridObjectDetector class method) (phenotypic.abc_.GridObjectRefiner class method) (phenotypic.abc_.GridOperation class method) (phenotypic.abc_.ImageCorrector class method) (phenotypic.abc_.ImageDenoiser class method) (phenotypic.abc_.ImageEnhancer class method) (phenotypic.abc_.ImageOperation class method) (phenotypic.abc_.MeasureFeatures class method) (phenotypic.abc_.MorphologicalFiltering class method) (phenotypic.abc_.ObjectDetector class method) (phenotypic.abc_.ObjectRefiner class method) (phenotypic.abc_.PostMeasurement class method) (phenotypic.abc_.PrefabPipeline class method) (phenotypic.abc_.Smoothing class method) (phenotypic.abc_.ThresholdDetector class method) (phenotypic.analysis.EdgeCorrector class method) (phenotypic.analysis.ErrorCutoffFinder class method) (phenotypic.analysis.ExpectedVsDetectedCount class method) (phenotypic.analysis.GridOccupancy class method) (phenotypic.analysis.ICC class method) (phenotypic.analysis.LinearCapAndLagModel class method) (phenotypic.analysis.LinearLagModel class method) (phenotypic.analysis.LogGrowthModel class method) (phenotypic.analysis.MADOutlierRemover class method) (phenotypic.analysis.MaxModifiedZScore class method) (phenotypic.analysis.RelativeMAD class method) (phenotypic.analysis.ReplicateAgreement class method) (phenotypic.analysis.TukeyOutlierFraction class method) (phenotypic.analysis.TukeyOutlierRemover class method) (phenotypic.correction.BayesShrinkCorrector class method) (phenotypic.correction.CaptureMetadata class method) (phenotypic.correction.ColorCheckerProfile class method) (phenotypic.correction.ColorCorrector class method) (phenotypic.correction.ColorDenoise class method) (phenotypic.correction.DenoiseBlockMatch class method) (phenotypic.correction.GridAligner class method) (phenotypic.correction.ImageCropper class method) (phenotypic.correction.ImagePadder class method) (phenotypic.correction.VisuShrinkCorrector class method) (phenotypic.detect.CannyDetector class method) (phenotypic.detect.ChanVeseDetector class method) (phenotypic.detect.CompositeDetector class method) (phenotypic.detect.FilamentousFungiDetector class method) (phenotypic.detect.HysteresisDetector class method) (phenotypic.detect.InoculumDetector class method) (phenotypic.detect.IsodataDetector class method) (phenotypic.detect.LiDetector class method) (phenotypic.detect.MadHysteresisDetector class method) (phenotypic.detect.ManualGridPointDetector class method) (phenotypic.detect.ManualPointDetector class method) (phenotypic.detect.MeanDetector class method) (phenotypic.detect.MinimumDetector class method) (phenotypic.detect.OtsuDetector class method) (phenotypic.detect.RankOtsuDetector class method) (phenotypic.detect.RoundPeaksDetector class method) (phenotypic.detect.SecondaryOtsuDetector class method) (phenotypic.detect.SinePeakDetector class method) (phenotypic.detect.TriangleDetector class method) (phenotypic.detect.UserThreshold class method) (phenotypic.detect.WatershedDetector class method) (phenotypic.detect.YenDetector class method) (phenotypic.enhance.BayesShrinkEnhancer class method) (phenotypic.enhance.CompositeEnhance class method) (phenotypic.enhance.ContrastStretching class method) (phenotypic.enhance.EnhanceBlockMatch class method) (phenotypic.enhance.EnhanceLocalContrast class method) (phenotypic.enhance.FlattenIllumination class method) (phenotypic.enhance.FocusBlobLoG class method) (phenotypic.enhance.FocusEdgeFrangi class method) (phenotypic.enhance.FocusEdgeHessian class method) (phenotypic.enhance.FocusEdgeLaplace class method) (phenotypic.enhance.FocusEdgeMeijering class method) (phenotypic.enhance.FocusEdgePhase class method) (phenotypic.enhance.FocusEdgeSato class method) (phenotypic.enhance.FocusEdgeSobel class method) (phenotypic.enhance.GaussianBlur class method) (phenotypic.enhance.GrayOpening class method) (phenotypic.enhance.ImageInverter class method) (phenotypic.enhance.LocalEdgeDenoise class method) (phenotypic.enhance.MedianFilter class method) (phenotypic.enhance.NonLocalMeansDenoiser class method) (phenotypic.enhance.RankMedianEnhancer class method) (phenotypic.enhance.SetDetectMode class method) (phenotypic.enhance.SharpenEdgeGauss class method) (phenotypic.enhance.StructureSmoothing class method) (phenotypic.enhance.SubtractGaussian class method) (phenotypic.enhance.SubtractOpening class method) (phenotypic.enhance.SubtractRollingBall class method) (phenotypic.enhance.SubtractWhiteTophat class method) (phenotypic.enhance.VisuShrinkEnhancer class method) (phenotypic.enhance.WhiteTophatEnhance class method) (phenotypic.grid.AutoGridFinder class method) (phenotypic.grid.CenteredAutoGridFinder class method) (phenotypic.grid.GridApply class method) (phenotypic.grid.ManualGridFinder class method) (phenotypic.measure.MeasureBounds class method) (phenotypic.measure.MeasureColor class method) (phenotypic.measure.MeasureGridLinRegStats class method) (phenotypic.measure.MeasureGridSpread class method) (phenotypic.measure.MeasureIntensity class method) (phenotypic.measure.MeasureNeighborDist class method) (phenotypic.measure.MeasureOrientationZones class method) (phenotypic.measure.MeasureShape class method) (phenotypic.measure.MeasureSize class method) (phenotypic.measure.MeasureSymmetricZones class method) (phenotypic.measure.MeasureTexture class method) (phenotypic.prefab.FilamentousFungiPipeline class method) (phenotypic.prefab.GridSectionPipeline class method) (phenotypic.prefab.HeavyOtsuPipeline class method) (phenotypic.prefab.HeavyRoundPeaksPipeline class method) (phenotypic.prefab.HeavyWatershedPipeline class method) (phenotypic.prefab.RoundPeaksPipeline class method) (phenotypic.prefab.SpImagerPipeline class method) (phenotypic.refine.ExtractColonyCore class method) (phenotypic.refine.GridAlignmentRefiner class method) (phenotypic.refine.GridOversizedObjectRemover class method) (phenotypic.refine.KeepNearestCenter class method) (phenotypic.refine.KeepSectionLargest class method) (phenotypic.refine.ManualRefine class method) (phenotypic.refine.MaskClosing class method) (phenotypic.refine.MaskDilation class method) (phenotypic.refine.MaskErosion class method) (phenotypic.refine.MaskFill class method) (phenotypic.refine.MaskGradient class method) (phenotypic.refine.MaskOpening class method) (phenotypic.refine.MaskWhiteTophat class method) (phenotypic.refine.MergeFragmentChains class method) (phenotypic.refine.NearestNeighborMerger class method) (phenotypic.refine.ReduceSectionsByLine class method) (phenotypic.refine.RefineBySineFit class method) (phenotypic.refine.RemoveBorderObjects class method) (phenotypic.refine.RemoveByFeature class method) (phenotypic.refine.RemoveGridOutliers class method) (phenotypic.refine.RemoveLowCircularity class method) (phenotypic.refine.SeparateObjects class method) (phenotypic.refine.Skeletonize class method) (phenotypic.refine.SmallObjectRemover class method) (phenotypic.refine.SmallToLargeMerger class method) (phenotypic.refine.Thinning class method) (phenotypic.refine.TrimAsymmetry class method) (phenotypic.tune.Budget class method) (phenotypic.tune.Categorical class method) (phenotypic.tune.EvaluationResult class method) (phenotypic.tune.Evaluator class method) (phenotypic.tune.Excluded class method) (phenotypic.tune.Fixed class method) (phenotypic.tune.FloatRange class method) (phenotypic.tune.HeldOutConfig class method) (phenotypic.tune.ImportanceReport class method) (phenotypic.tune.InferredSearchSpace class method) (phenotypic.tune.IntRange class method) (phenotypic.tune.Knob class method) (phenotypic.tune.score.CompositeScorer class method) (phenotypic.tune.score.GroundTruthMasks class method) (phenotypic.tune.score.QCScorer class method) (phenotypic.tune.score.ReferenceFreeScorer class method) (phenotypic.tune.score.Scorer class method) (phenotypic.tune.score.SupervisedScorer class method) (phenotypic.tune.SearchSpace class method) (phenotypic.tune.strategy.GridConfig class method) (phenotypic.tune.strategy.OptunaConfig class method) (phenotypic.tune.strategy.RandomConfig class method) (phenotypic.tune.strategy.StrategyConfig class method) (phenotypic.tune.Trial class method) (phenotypic.tune.TuningSpec class method) model_post_init() (phenotypic.abc_.BackgroundSubtraction method) (phenotypic.abc_.BaseOperation method) (phenotypic.abc_.ContrastAdjustment method) (phenotypic.abc_.FocusBlob method) (phenotypic.abc_.FocusEdge method) (phenotypic.abc_.GpuDetector method) (phenotypic.abc_.GridCorrector method) (phenotypic.abc_.GridFinder method) (phenotypic.abc_.GridMeasureFeatures method) (phenotypic.abc_.GridObjectDetector method) (phenotypic.abc_.GridObjectRefiner method) (phenotypic.abc_.GridOperation method) (phenotypic.abc_.ImageCorrector method) (phenotypic.abc_.ImageDenoiser method) (phenotypic.abc_.ImageEnhancer method) (phenotypic.abc_.ImageOperation method) (phenotypic.abc_.MeasureFeatures method) (phenotypic.abc_.MorphologicalFiltering method) (phenotypic.abc_.ObjectDetector method) (phenotypic.abc_.ObjectRefiner method) (phenotypic.abc_.PostMeasurement method) (phenotypic.abc_.PrefabPipeline method) (phenotypic.abc_.Smoothing method) (phenotypic.abc_.ThresholdDetector method) (phenotypic.analysis.EdgeCorrector method) (phenotypic.analysis.ErrorCutoffFinder method) (phenotypic.analysis.ExpectedVsDetectedCount method) (phenotypic.analysis.GridOccupancy method) (phenotypic.analysis.ICC method) (phenotypic.analysis.LinearCapAndLagModel method) (phenotypic.analysis.LinearLagModel method) (phenotypic.analysis.LogGrowthModel method) (phenotypic.analysis.MADOutlierRemover method) (phenotypic.analysis.MaxModifiedZScore method) (phenotypic.analysis.RelativeMAD method) (phenotypic.analysis.ReplicateAgreement method) (phenotypic.analysis.TukeyOutlierFraction method) (phenotypic.analysis.TukeyOutlierRemover method) (phenotypic.correction.BayesShrinkCorrector method) (phenotypic.correction.CaptureMetadata method) (phenotypic.correction.ColorCheckerProfile method) (phenotypic.correction.ColorCorrector method) (phenotypic.correction.ColorDenoise method) (phenotypic.correction.DenoiseBlockMatch method) (phenotypic.correction.GridAligner method) (phenotypic.correction.ImageCropper method) (phenotypic.correction.ImagePadder method) (phenotypic.correction.VisuShrinkCorrector method) (phenotypic.detect.CannyDetector method) (phenotypic.detect.ChanVeseDetector method) (phenotypic.detect.CompositeDetector method) (phenotypic.detect.FilamentousFungiDetector method) (phenotypic.detect.HysteresisDetector method) (phenotypic.detect.InoculumDetector method) (phenotypic.detect.IsodataDetector method) (phenotypic.detect.LiDetector method) (phenotypic.detect.MadHysteresisDetector method) (phenotypic.detect.ManualGridPointDetector method) (phenotypic.detect.ManualPointDetector method) (phenotypic.detect.MeanDetector method) (phenotypic.detect.MinimumDetector method) (phenotypic.detect.OtsuDetector method) (phenotypic.detect.RankOtsuDetector method) (phenotypic.detect.RoundPeaksDetector method) (phenotypic.detect.SecondaryOtsuDetector method) (phenotypic.detect.SinePeakDetector method) (phenotypic.detect.TriangleDetector method) (phenotypic.detect.UserThreshold method) (phenotypic.detect.WatershedDetector method) (phenotypic.detect.YenDetector method) (phenotypic.enhance.BayesShrinkEnhancer method) (phenotypic.enhance.CompositeEnhance method) (phenotypic.enhance.ContrastStretching method) (phenotypic.enhance.EnhanceBlockMatch method) (phenotypic.enhance.EnhanceLocalContrast method) (phenotypic.enhance.FlattenIllumination method) (phenotypic.enhance.FocusBlobLoG method) (phenotypic.enhance.FocusEdgeFrangi method) (phenotypic.enhance.FocusEdgeHessian method) (phenotypic.enhance.FocusEdgeLaplace method) (phenotypic.enhance.FocusEdgeMeijering method) (phenotypic.enhance.FocusEdgePhase method) (phenotypic.enhance.FocusEdgeSato method) (phenotypic.enhance.FocusEdgeSobel method) (phenotypic.enhance.GaussianBlur method) (phenotypic.enhance.GrayOpening method) (phenotypic.enhance.ImageInverter method) (phenotypic.enhance.LocalEdgeDenoise method) (phenotypic.enhance.MedianFilter method) (phenotypic.enhance.NonLocalMeansDenoiser method) (phenotypic.enhance.RankMedianEnhancer method) (phenotypic.enhance.SetDetectMode method) (phenotypic.enhance.SharpenEdgeGauss method) (phenotypic.enhance.StructureSmoothing method) (phenotypic.enhance.SubtractGaussian method) (phenotypic.enhance.SubtractOpening method) (phenotypic.enhance.SubtractRollingBall method) (phenotypic.enhance.SubtractWhiteTophat method) (phenotypic.enhance.VisuShrinkEnhancer method) (phenotypic.enhance.WhiteTophatEnhance method) (phenotypic.grid.AutoGridFinder method) (phenotypic.grid.CenteredAutoGridFinder method) (phenotypic.grid.GridApply method) (phenotypic.grid.ManualGridFinder method) (phenotypic.measure.MeasureBounds method) (phenotypic.measure.MeasureColor method) (phenotypic.measure.MeasureGridLinRegStats method) (phenotypic.measure.MeasureGridSpread method) (phenotypic.measure.MeasureIntensity method) (phenotypic.measure.MeasureNeighborDist method) (phenotypic.measure.MeasureOrientationZones method) (phenotypic.measure.MeasureShape method) (phenotypic.measure.MeasureSize method) (phenotypic.measure.MeasureSymmetricZones method) (phenotypic.measure.MeasureTexture method) (phenotypic.prefab.FilamentousFungiPipeline method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.prefab.RoundPeaksPipeline method) (phenotypic.prefab.SpImagerPipeline method) (phenotypic.refine.ExtractColonyCore method) (phenotypic.refine.GridAlignmentRefiner method) (phenotypic.refine.GridOversizedObjectRemover method) (phenotypic.refine.KeepNearestCenter method) (phenotypic.refine.KeepSectionLargest method) (phenotypic.refine.ManualRefine method) (phenotypic.refine.MaskClosing method) (phenotypic.refine.MaskDilation method) (phenotypic.refine.MaskErosion method) (phenotypic.refine.MaskFill method) (phenotypic.refine.MaskGradient method) (phenotypic.refine.MaskOpening method) (phenotypic.refine.MaskWhiteTophat method) (phenotypic.refine.MergeFragmentChains method) (phenotypic.refine.NearestNeighborMerger method) (phenotypic.refine.ReduceSectionsByLine method) (phenotypic.refine.RefineBySineFit method) (phenotypic.refine.RemoveBorderObjects method) (phenotypic.refine.RemoveByFeature method) (phenotypic.refine.RemoveGridOutliers method) (phenotypic.refine.RemoveLowCircularity method) (phenotypic.refine.SeparateObjects method) (phenotypic.refine.Skeletonize method) (phenotypic.refine.SmallObjectRemover method) (phenotypic.refine.SmallToLargeMerger method) (phenotypic.refine.Thinning method) (phenotypic.refine.TrimAsymmetry method) (phenotypic.tune.Budget method) (phenotypic.tune.Categorical method) (phenotypic.tune.EvaluationResult method) (phenotypic.tune.Evaluator method) (phenotypic.tune.Excluded method) (phenotypic.tune.Fixed method) (phenotypic.tune.FloatRange method) (phenotypic.tune.HeldOutConfig method) (phenotypic.tune.ImportanceReport method) (phenotypic.tune.InferredSearchSpace method) (phenotypic.tune.IntRange method) (phenotypic.tune.Knob method) (phenotypic.tune.score.CompositeScorer method) (phenotypic.tune.score.GroundTruthMasks method) (phenotypic.tune.score.QCScorer method) (phenotypic.tune.score.ReferenceFreeScorer method) (phenotypic.tune.score.Scorer method) (phenotypic.tune.score.SupervisedScorer method) (phenotypic.tune.SearchSpace method) (phenotypic.tune.strategy.GridConfig method) (phenotypic.tune.strategy.OptunaConfig method) (phenotypic.tune.strategy.RandomConfig method) (phenotypic.tune.strategy.StrategyConfig method) (phenotypic.tune.Trial method) (phenotypic.tune.TuningSpec method) model_rebuild() (phenotypic.abc_.BackgroundSubtraction class method) (phenotypic.abc_.BaseOperation class method) (phenotypic.abc_.ContrastAdjustment class method) (phenotypic.abc_.FocusBlob class method) (phenotypic.abc_.FocusEdge class method) (phenotypic.abc_.GpuDetector class method) (phenotypic.abc_.GridCorrector class method) (phenotypic.abc_.GridFinder class method) (phenotypic.abc_.GridMeasureFeatures class method) (phenotypic.abc_.GridObjectDetector class method) (phenotypic.abc_.GridObjectRefiner class method) (phenotypic.abc_.GridOperation class method) (phenotypic.abc_.ImageCorrector class method) (phenotypic.abc_.ImageDenoiser class method) (phenotypic.abc_.ImageEnhancer class method) (phenotypic.abc_.ImageOperation class method) (phenotypic.abc_.MeasureFeatures class method) (phenotypic.abc_.MorphologicalFiltering class method) (phenotypic.abc_.ObjectDetector class method) (phenotypic.abc_.ObjectRefiner class method) (phenotypic.abc_.PostMeasurement class method) (phenotypic.abc_.PrefabPipeline class method) (phenotypic.abc_.Smoothing class method) (phenotypic.abc_.ThresholdDetector class method) (phenotypic.analysis.EdgeCorrector class method) (phenotypic.analysis.ErrorCutoffFinder class method) (phenotypic.analysis.ExpectedVsDetectedCount class method) (phenotypic.analysis.GridOccupancy class method) (phenotypic.analysis.ICC class method) (phenotypic.analysis.LinearCapAndLagModel class method) (phenotypic.analysis.LinearLagModel class method) (phenotypic.analysis.LogGrowthModel class method) (phenotypic.analysis.MADOutlierRemover class method) (phenotypic.analysis.MaxModifiedZScore class method) (phenotypic.analysis.RelativeMAD class method) (phenotypic.analysis.ReplicateAgreement class method) (phenotypic.analysis.TukeyOutlierFraction class method) (phenotypic.analysis.TukeyOutlierRemover class method) (phenotypic.correction.BayesShrinkCorrector class method) (phenotypic.correction.CaptureMetadata class method) (phenotypic.correction.ColorCheckerProfile class method) (phenotypic.correction.ColorCorrector class method) (phenotypic.correction.ColorDenoise class method) (phenotypic.correction.DenoiseBlockMatch class method) (phenotypic.correction.GridAligner class method) (phenotypic.correction.ImageCropper class method) (phenotypic.correction.ImagePadder class method) (phenotypic.correction.VisuShrinkCorrector class method) (phenotypic.detect.CannyDetector class method) (phenotypic.detect.ChanVeseDetector class method) (phenotypic.detect.CompositeDetector class method) (phenotypic.detect.FilamentousFungiDetector class method) (phenotypic.detect.HysteresisDetector class method) (phenotypic.detect.InoculumDetector class method) (phenotypic.detect.IsodataDetector class method) (phenotypic.detect.LiDetector class method) (phenotypic.detect.MadHysteresisDetector class method) (phenotypic.detect.ManualGridPointDetector class method) (phenotypic.detect.ManualPointDetector class method) (phenotypic.detect.MeanDetector class method) (phenotypic.detect.MinimumDetector class method) (phenotypic.detect.OtsuDetector class method) (phenotypic.detect.RankOtsuDetector class method) (phenotypic.detect.RoundPeaksDetector class method) (phenotypic.detect.SecondaryOtsuDetector class method) (phenotypic.detect.SinePeakDetector class method) (phenotypic.detect.TriangleDetector class method) (phenotypic.detect.UserThreshold class method) (phenotypic.detect.WatershedDetector class method) (phenotypic.detect.YenDetector class method) (phenotypic.enhance.BayesShrinkEnhancer class method) (phenotypic.enhance.CompositeEnhance class method) (phenotypic.enhance.ContrastStretching class method) (phenotypic.enhance.EnhanceBlockMatch class method) (phenotypic.enhance.EnhanceLocalContrast class method) (phenotypic.enhance.FlattenIllumination class method) (phenotypic.enhance.FocusBlobLoG class method) (phenotypic.enhance.FocusEdgeFrangi class method) (phenotypic.enhance.FocusEdgeHessian class method) (phenotypic.enhance.FocusEdgeLaplace class method) (phenotypic.enhance.FocusEdgeMeijering class method) (phenotypic.enhance.FocusEdgePhase class method) (phenotypic.enhance.FocusEdgeSato class method) (phenotypic.enhance.FocusEdgeSobel class method) (phenotypic.enhance.GaussianBlur class method) (phenotypic.enhance.GrayOpening class method) (phenotypic.enhance.ImageInverter class method) (phenotypic.enhance.LocalEdgeDenoise class method) (phenotypic.enhance.MedianFilter class method) (phenotypic.enhance.NonLocalMeansDenoiser class method) (phenotypic.enhance.RankMedianEnhancer class method) (phenotypic.enhance.SetDetectMode class method) (phenotypic.enhance.SharpenEdgeGauss class method) (phenotypic.enhance.StructureSmoothing class method) (phenotypic.enhance.SubtractGaussian class method) (phenotypic.enhance.SubtractOpening class method) (phenotypic.enhance.SubtractRollingBall class method) (phenotypic.enhance.SubtractWhiteTophat class method) (phenotypic.enhance.VisuShrinkEnhancer class method) (phenotypic.enhance.WhiteTophatEnhance class method) (phenotypic.grid.AutoGridFinder class method) (phenotypic.grid.CenteredAutoGridFinder class method) (phenotypic.grid.GridApply class method) (phenotypic.grid.ManualGridFinder class method) (phenotypic.measure.MeasureBounds class method) (phenotypic.measure.MeasureColor class method) (phenotypic.measure.MeasureGridLinRegStats class method) (phenotypic.measure.MeasureGridSpread class method) (phenotypic.measure.MeasureIntensity class method) (phenotypic.measure.MeasureNeighborDist class method) (phenotypic.measure.MeasureOrientationZones class method) (phenotypic.measure.MeasureShape class method) (phenotypic.measure.MeasureSize class method) (phenotypic.measure.MeasureSymmetricZones class method) (phenotypic.measure.MeasureTexture class method) (phenotypic.prefab.FilamentousFungiPipeline class method) (phenotypic.prefab.GridSectionPipeline class method) (phenotypic.prefab.HeavyOtsuPipeline class method) (phenotypic.prefab.HeavyRoundPeaksPipeline class method) (phenotypic.prefab.HeavyWatershedPipeline class method) (phenotypic.prefab.RoundPeaksPipeline class method) (phenotypic.prefab.SpImagerPipeline class method) (phenotypic.refine.ExtractColonyCore class method) (phenotypic.refine.GridAlignmentRefiner class method) (phenotypic.refine.GridOversizedObjectRemover class method) (phenotypic.refine.KeepNearestCenter class method) (phenotypic.refine.KeepSectionLargest class method) (phenotypic.refine.ManualRefine class method) (phenotypic.refine.MaskClosing class method) (phenotypic.refine.MaskDilation class method) (phenotypic.refine.MaskErosion class method) (phenotypic.refine.MaskFill class method) (phenotypic.refine.MaskGradient class method) (phenotypic.refine.MaskOpening class method) (phenotypic.refine.MaskWhiteTophat class method) (phenotypic.refine.MergeFragmentChains class method) (phenotypic.refine.NearestNeighborMerger class method) (phenotypic.refine.ReduceSectionsByLine class method) (phenotypic.refine.RefineBySineFit class method) (phenotypic.refine.RemoveBorderObjects class method) (phenotypic.refine.RemoveByFeature class method) (phenotypic.refine.RemoveGridOutliers class method) (phenotypic.refine.RemoveLowCircularity class method) (phenotypic.refine.SeparateObjects class method) (phenotypic.refine.Skeletonize class method) (phenotypic.refine.SmallObjectRemover class method) (phenotypic.refine.SmallToLargeMerger class method) (phenotypic.refine.Thinning class method) (phenotypic.refine.TrimAsymmetry class method) (phenotypic.tune.Budget class method) (phenotypic.tune.Categorical class method) (phenotypic.tune.EvaluationResult class method) (phenotypic.tune.Evaluator class method) (phenotypic.tune.Excluded class method) (phenotypic.tune.Fixed class method) (phenotypic.tune.FloatRange class method) (phenotypic.tune.HeldOutConfig class method) (phenotypic.tune.ImportanceReport class method) (phenotypic.tune.InferredSearchSpace class method) (phenotypic.tune.IntRange class method) (phenotypic.tune.Knob class method) (phenotypic.tune.score.CompositeScorer class method) (phenotypic.tune.score.GroundTruthMasks class method) (phenotypic.tune.score.QCScorer class method) (phenotypic.tune.score.ReferenceFreeScorer class method) (phenotypic.tune.score.Scorer class method) (phenotypic.tune.score.SupervisedScorer class method) (phenotypic.tune.SearchSpace class method) (phenotypic.tune.strategy.GridConfig class method) (phenotypic.tune.strategy.OptunaConfig class method) (phenotypic.tune.strategy.RandomConfig class method) (phenotypic.tune.strategy.StrategyConfig class method) (phenotypic.tune.Trial class method) (phenotypic.tune.TuningSpec class method) model_validate() (phenotypic.abc_.BackgroundSubtraction class method) (phenotypic.abc_.BaseOperation class method) (phenotypic.abc_.ContrastAdjustment class method) (phenotypic.abc_.FocusBlob class method) (phenotypic.abc_.FocusEdge class method) (phenotypic.abc_.GpuDetector class method) (phenotypic.abc_.GridCorrector class method) (phenotypic.abc_.GridFinder class method) (phenotypic.abc_.GridMeasureFeatures class method) (phenotypic.abc_.GridObjectDetector class method) (phenotypic.abc_.GridObjectRefiner class method) (phenotypic.abc_.GridOperation class method) (phenotypic.abc_.ImageCorrector class method) (phenotypic.abc_.ImageDenoiser class method) (phenotypic.abc_.ImageEnhancer class method) (phenotypic.abc_.ImageOperation class method) (phenotypic.abc_.MeasureFeatures class method) (phenotypic.abc_.MorphologicalFiltering class method) (phenotypic.abc_.ObjectDetector class method) (phenotypic.abc_.ObjectRefiner class method) (phenotypic.abc_.PostMeasurement class method) (phenotypic.abc_.PrefabPipeline class method) (phenotypic.abc_.Smoothing class method) (phenotypic.abc_.ThresholdDetector class method) (phenotypic.analysis.EdgeCorrector class method) (phenotypic.analysis.ErrorCutoffFinder class method) (phenotypic.analysis.ExpectedVsDetectedCount class method) (phenotypic.analysis.GridOccupancy class method) (phenotypic.analysis.ICC class method) (phenotypic.analysis.LinearCapAndLagModel class method) (phenotypic.analysis.LinearLagModel class method) (phenotypic.analysis.LogGrowthModel class method) (phenotypic.analysis.MADOutlierRemover class method) (phenotypic.analysis.MaxModifiedZScore class method) (phenotypic.analysis.RelativeMAD class method) (phenotypic.analysis.ReplicateAgreement class method) (phenotypic.analysis.TukeyOutlierFraction class method) (phenotypic.analysis.TukeyOutlierRemover class method) (phenotypic.correction.BayesShrinkCorrector class method) (phenotypic.correction.CaptureMetadata class method) (phenotypic.correction.ColorCheckerProfile class method) (phenotypic.correction.ColorCorrector class method) (phenotypic.correction.ColorDenoise class method) (phenotypic.correction.DenoiseBlockMatch class method) (phenotypic.correction.GridAligner class method) (phenotypic.correction.ImageCropper class method) (phenotypic.correction.ImagePadder class method) (phenotypic.correction.VisuShrinkCorrector class method) (phenotypic.detect.CannyDetector class method) (phenotypic.detect.ChanVeseDetector class method) (phenotypic.detect.CompositeDetector class method) (phenotypic.detect.FilamentousFungiDetector class method) (phenotypic.detect.HysteresisDetector class method) (phenotypic.detect.InoculumDetector class method) (phenotypic.detect.IsodataDetector class method) (phenotypic.detect.LiDetector class method) (phenotypic.detect.MadHysteresisDetector class method) (phenotypic.detect.ManualGridPointDetector class method) (phenotypic.detect.ManualPointDetector class method) (phenotypic.detect.MeanDetector class method) (phenotypic.detect.MinimumDetector class method) (phenotypic.detect.OtsuDetector class method) (phenotypic.detect.RankOtsuDetector class method) (phenotypic.detect.RoundPeaksDetector class method) (phenotypic.detect.SecondaryOtsuDetector class method) (phenotypic.detect.SinePeakDetector class method) (phenotypic.detect.TriangleDetector class method) (phenotypic.detect.UserThreshold class method) (phenotypic.detect.WatershedDetector class method) (phenotypic.detect.YenDetector class method) (phenotypic.enhance.BayesShrinkEnhancer class method) (phenotypic.enhance.CompositeEnhance class method) (phenotypic.enhance.ContrastStretching class method) (phenotypic.enhance.EnhanceBlockMatch class method) (phenotypic.enhance.EnhanceLocalContrast class method) (phenotypic.enhance.FlattenIllumination class method) (phenotypic.enhance.FocusBlobLoG class method) (phenotypic.enhance.FocusEdgeFrangi class method) (phenotypic.enhance.FocusEdgeHessian class method) (phenotypic.enhance.FocusEdgeLaplace class method) (phenotypic.enhance.FocusEdgeMeijering class method) (phenotypic.enhance.FocusEdgePhase class method) (phenotypic.enhance.FocusEdgeSato class method) (phenotypic.enhance.FocusEdgeSobel class method) (phenotypic.enhance.GaussianBlur class method) (phenotypic.enhance.GrayOpening class method) (phenotypic.enhance.ImageInverter class method) (phenotypic.enhance.LocalEdgeDenoise class method) (phenotypic.enhance.MedianFilter class method) (phenotypic.enhance.NonLocalMeansDenoiser class method) (phenotypic.enhance.RankMedianEnhancer class method) (phenotypic.enhance.SetDetectMode class method) (phenotypic.enhance.SharpenEdgeGauss class method) (phenotypic.enhance.StructureSmoothing class method) (phenotypic.enhance.SubtractGaussian class method) (phenotypic.enhance.SubtractOpening class method) (phenotypic.enhance.SubtractRollingBall class method) (phenotypic.enhance.SubtractWhiteTophat class method) (phenotypic.enhance.VisuShrinkEnhancer class method) (phenotypic.enhance.WhiteTophatEnhance class method) (phenotypic.grid.AutoGridFinder class method) (phenotypic.grid.CenteredAutoGridFinder class method) (phenotypic.grid.GridApply class method) (phenotypic.grid.ManualGridFinder class method) (phenotypic.measure.MeasureBounds class method) (phenotypic.measure.MeasureColor class method) (phenotypic.measure.MeasureGridLinRegStats class method) (phenotypic.measure.MeasureGridSpread class method) (phenotypic.measure.MeasureIntensity class method) (phenotypic.measure.MeasureNeighborDist class method) (phenotypic.measure.MeasureOrientationZones class method) (phenotypic.measure.MeasureShape class method) (phenotypic.measure.MeasureSize class method) (phenotypic.measure.MeasureSymmetricZones class method) (phenotypic.measure.MeasureTexture class method) (phenotypic.prefab.FilamentousFungiPipeline class method) (phenotypic.prefab.GridSectionPipeline class method) (phenotypic.prefab.HeavyOtsuPipeline class method) (phenotypic.prefab.HeavyRoundPeaksPipeline class method) (phenotypic.prefab.HeavyWatershedPipeline class method) (phenotypic.prefab.RoundPeaksPipeline class method) (phenotypic.prefab.SpImagerPipeline class method) (phenotypic.refine.ExtractColonyCore class method) (phenotypic.refine.GridAlignmentRefiner class method) (phenotypic.refine.GridOversizedObjectRemover class method) (phenotypic.refine.KeepNearestCenter class method) (phenotypic.refine.KeepSectionLargest class method) (phenotypic.refine.ManualRefine class method) (phenotypic.refine.MaskClosing class method) (phenotypic.refine.MaskDilation class method) (phenotypic.refine.MaskErosion class method) (phenotypic.refine.MaskFill class method) (phenotypic.refine.MaskGradient class method) (phenotypic.refine.MaskOpening class method) (phenotypic.refine.MaskWhiteTophat class method) (phenotypic.refine.MergeFragmentChains class method) (phenotypic.refine.NearestNeighborMerger class method) (phenotypic.refine.ReduceSectionsByLine class method) (phenotypic.refine.RefineBySineFit class method) (phenotypic.refine.RemoveBorderObjects class method) (phenotypic.refine.RemoveByFeature class method) (phenotypic.refine.RemoveGridOutliers class method) (phenotypic.refine.RemoveLowCircularity class method) (phenotypic.refine.SeparateObjects class method) (phenotypic.refine.Skeletonize class method) (phenotypic.refine.SmallObjectRemover class method) (phenotypic.refine.SmallToLargeMerger class method) (phenotypic.refine.Thinning class method) (phenotypic.refine.TrimAsymmetry class method) (phenotypic.tune.Budget class method) (phenotypic.tune.Categorical class method) (phenotypic.tune.EvaluationResult class method) (phenotypic.tune.Evaluator class method) (phenotypic.tune.Excluded class method) (phenotypic.tune.Fixed class method) (phenotypic.tune.FloatRange class method) (phenotypic.tune.HeldOutConfig class method) (phenotypic.tune.ImportanceReport class method) (phenotypic.tune.InferredSearchSpace class method) (phenotypic.tune.IntRange class method) (phenotypic.tune.Knob class method) (phenotypic.tune.score.CompositeScorer class method) (phenotypic.tune.score.GroundTruthMasks class method) (phenotypic.tune.score.QCScorer class method) (phenotypic.tune.score.ReferenceFreeScorer class method) (phenotypic.tune.score.Scorer class method) (phenotypic.tune.score.SupervisedScorer class method) (phenotypic.tune.SearchSpace class method) (phenotypic.tune.strategy.GridConfig class method) (phenotypic.tune.strategy.OptunaConfig class method) (phenotypic.tune.strategy.RandomConfig class method) (phenotypic.tune.strategy.StrategyConfig class method) (phenotypic.tune.Trial class method) (phenotypic.tune.TuningSpec class method) model_validate_json() (phenotypic.abc_.BackgroundSubtraction class method) (phenotypic.abc_.BaseOperation class method) (phenotypic.abc_.ContrastAdjustment class method) (phenotypic.abc_.FocusBlob class method) (phenotypic.abc_.FocusEdge class method) (phenotypic.abc_.GpuDetector class method) (phenotypic.abc_.GridCorrector class method) (phenotypic.abc_.GridFinder class method) (phenotypic.abc_.GridMeasureFeatures class method) (phenotypic.abc_.GridObjectDetector class method) (phenotypic.abc_.GridObjectRefiner class method) (phenotypic.abc_.GridOperation class method) (phenotypic.abc_.ImageCorrector class method) (phenotypic.abc_.ImageDenoiser class method) (phenotypic.abc_.ImageEnhancer class method) (phenotypic.abc_.ImageOperation class method) (phenotypic.abc_.MeasureFeatures class method) (phenotypic.abc_.MorphologicalFiltering class method) (phenotypic.abc_.ObjectDetector class method) (phenotypic.abc_.ObjectRefiner class method) (phenotypic.abc_.PostMeasurement class method) (phenotypic.abc_.PrefabPipeline class method) (phenotypic.abc_.Smoothing class method) (phenotypic.abc_.ThresholdDetector class method) (phenotypic.analysis.EdgeCorrector class method) (phenotypic.analysis.ErrorCutoffFinder class method) (phenotypic.analysis.ExpectedVsDetectedCount class method) (phenotypic.analysis.GridOccupancy class method) (phenotypic.analysis.ICC class method) (phenotypic.analysis.LinearCapAndLagModel class method) (phenotypic.analysis.LinearLagModel class method) (phenotypic.analysis.LogGrowthModel class method) (phenotypic.analysis.MADOutlierRemover class method) (phenotypic.analysis.MaxModifiedZScore class method) (phenotypic.analysis.RelativeMAD class method) (phenotypic.analysis.ReplicateAgreement class method) (phenotypic.analysis.TukeyOutlierFraction class method) (phenotypic.analysis.TukeyOutlierRemover class method) (phenotypic.correction.BayesShrinkCorrector class method) (phenotypic.correction.CaptureMetadata class method) (phenotypic.correction.ColorCheckerProfile class method) (phenotypic.correction.ColorCorrector class method) (phenotypic.correction.ColorDenoise class method) (phenotypic.correction.DenoiseBlockMatch class method) (phenotypic.correction.GridAligner class method) (phenotypic.correction.ImageCropper class method) (phenotypic.correction.ImagePadder class method) (phenotypic.correction.VisuShrinkCorrector class method) (phenotypic.detect.CannyDetector class method) (phenotypic.detect.ChanVeseDetector class method) (phenotypic.detect.CompositeDetector class method) (phenotypic.detect.FilamentousFungiDetector class method) (phenotypic.detect.HysteresisDetector class method) (phenotypic.detect.InoculumDetector class method) (phenotypic.detect.IsodataDetector class method) (phenotypic.detect.LiDetector class method) (phenotypic.detect.MadHysteresisDetector class method) (phenotypic.detect.ManualGridPointDetector class method) (phenotypic.detect.ManualPointDetector class method) (phenotypic.detect.MeanDetector class method) (phenotypic.detect.MinimumDetector class method) (phenotypic.detect.OtsuDetector class method) (phenotypic.detect.RankOtsuDetector class method) (phenotypic.detect.RoundPeaksDetector class method) (phenotypic.detect.SecondaryOtsuDetector class method) (phenotypic.detect.SinePeakDetector class method) (phenotypic.detect.TriangleDetector class method) (phenotypic.detect.UserThreshold class method) (phenotypic.detect.WatershedDetector class method) (phenotypic.detect.YenDetector class method) (phenotypic.enhance.BayesShrinkEnhancer class method) (phenotypic.enhance.CompositeEnhance class method) (phenotypic.enhance.ContrastStretching class method) (phenotypic.enhance.EnhanceBlockMatch class method) (phenotypic.enhance.EnhanceLocalContrast class method) (phenotypic.enhance.FlattenIllumination class method) (phenotypic.enhance.FocusBlobLoG class method) (phenotypic.enhance.FocusEdgeFrangi class method) (phenotypic.enhance.FocusEdgeHessian class method) (phenotypic.enhance.FocusEdgeLaplace class method) (phenotypic.enhance.FocusEdgeMeijering class method) (phenotypic.enhance.FocusEdgePhase class method) (phenotypic.enhance.FocusEdgeSato class method) (phenotypic.enhance.FocusEdgeSobel class method) (phenotypic.enhance.GaussianBlur class method) (phenotypic.enhance.GrayOpening class method) (phenotypic.enhance.ImageInverter class method) (phenotypic.enhance.LocalEdgeDenoise class method) (phenotypic.enhance.MedianFilter class method) (phenotypic.enhance.NonLocalMeansDenoiser class method) (phenotypic.enhance.RankMedianEnhancer class method) (phenotypic.enhance.SetDetectMode class method) (phenotypic.enhance.SharpenEdgeGauss class method) (phenotypic.enhance.StructureSmoothing class method) (phenotypic.enhance.SubtractGaussian class method) (phenotypic.enhance.SubtractOpening class method) (phenotypic.enhance.SubtractRollingBall class method) (phenotypic.enhance.SubtractWhiteTophat class method) (phenotypic.enhance.VisuShrinkEnhancer class method) (phenotypic.enhance.WhiteTophatEnhance class method) (phenotypic.grid.AutoGridFinder class method) (phenotypic.grid.CenteredAutoGridFinder class method) (phenotypic.grid.GridApply class method) (phenotypic.grid.ManualGridFinder class method) (phenotypic.measure.MeasureBounds class method) (phenotypic.measure.MeasureColor class method) (phenotypic.measure.MeasureGridLinRegStats class method) (phenotypic.measure.MeasureGridSpread class method) (phenotypic.measure.MeasureIntensity class method) (phenotypic.measure.MeasureNeighborDist class method) (phenotypic.measure.MeasureOrientationZones class method) (phenotypic.measure.MeasureShape class method) (phenotypic.measure.MeasureSize class method) (phenotypic.measure.MeasureSymmetricZones class method) (phenotypic.measure.MeasureTexture class method) (phenotypic.prefab.FilamentousFungiPipeline class method) (phenotypic.prefab.GridSectionPipeline class method) (phenotypic.prefab.HeavyOtsuPipeline class method) (phenotypic.prefab.HeavyRoundPeaksPipeline class method) (phenotypic.prefab.HeavyWatershedPipeline class method) (phenotypic.prefab.RoundPeaksPipeline class method) (phenotypic.prefab.SpImagerPipeline class method) (phenotypic.refine.ExtractColonyCore class method) (phenotypic.refine.GridAlignmentRefiner class method) (phenotypic.refine.GridOversizedObjectRemover class method) (phenotypic.refine.KeepNearestCenter class method) (phenotypic.refine.KeepSectionLargest class method) (phenotypic.refine.ManualRefine class method) (phenotypic.refine.MaskClosing class method) (phenotypic.refine.MaskDilation class method) (phenotypic.refine.MaskErosion class method) (phenotypic.refine.MaskFill class method) (phenotypic.refine.MaskGradient class method) (phenotypic.refine.MaskOpening class method) (phenotypic.refine.MaskWhiteTophat class method) (phenotypic.refine.MergeFragmentChains class method) (phenotypic.refine.NearestNeighborMerger class method) (phenotypic.refine.ReduceSectionsByLine class method) (phenotypic.refine.RefineBySineFit class method) (phenotypic.refine.RemoveBorderObjects class method) (phenotypic.refine.RemoveByFeature class method) (phenotypic.refine.RemoveGridOutliers class method) (phenotypic.refine.RemoveLowCircularity class method) (phenotypic.refine.SeparateObjects class method) (phenotypic.refine.Skeletonize class method) (phenotypic.refine.SmallObjectRemover class method) (phenotypic.refine.SmallToLargeMerger class method) (phenotypic.refine.Thinning class method) (phenotypic.refine.TrimAsymmetry class method) (phenotypic.tune.Budget class method) (phenotypic.tune.Categorical class method) (phenotypic.tune.EvaluationResult class method) (phenotypic.tune.Evaluator class method) (phenotypic.tune.Excluded class method) (phenotypic.tune.Fixed class method) (phenotypic.tune.FloatRange class method) (phenotypic.tune.HeldOutConfig class method) (phenotypic.tune.ImportanceReport class method) (phenotypic.tune.InferredSearchSpace class method) (phenotypic.tune.IntRange class method) (phenotypic.tune.Knob class method) (phenotypic.tune.score.CompositeScorer class method) (phenotypic.tune.score.GroundTruthMasks class method) (phenotypic.tune.score.QCScorer class method) (phenotypic.tune.score.ReferenceFreeScorer class method) (phenotypic.tune.score.Scorer class method) (phenotypic.tune.score.SupervisedScorer class method) (phenotypic.tune.SearchSpace class method) (phenotypic.tune.strategy.GridConfig class method) (phenotypic.tune.strategy.OptunaConfig class method) (phenotypic.tune.strategy.RandomConfig class method) (phenotypic.tune.strategy.StrategyConfig class method) (phenotypic.tune.Trial class method) (phenotypic.tune.TuningSpec class method) model_validate_strings() (phenotypic.abc_.BackgroundSubtraction class method) (phenotypic.abc_.BaseOperation class method) (phenotypic.abc_.ContrastAdjustment class method) (phenotypic.abc_.FocusBlob class method) (phenotypic.abc_.FocusEdge class method) (phenotypic.abc_.GpuDetector class method) (phenotypic.abc_.GridCorrector class method) (phenotypic.abc_.GridFinder class method) (phenotypic.abc_.GridMeasureFeatures class method) (phenotypic.abc_.GridObjectDetector class method) (phenotypic.abc_.GridObjectRefiner class method) (phenotypic.abc_.GridOperation class method) (phenotypic.abc_.ImageCorrector class method) (phenotypic.abc_.ImageDenoiser class method) (phenotypic.abc_.ImageEnhancer class method) (phenotypic.abc_.ImageOperation class method) (phenotypic.abc_.MeasureFeatures class method) (phenotypic.abc_.MorphologicalFiltering class method) (phenotypic.abc_.ObjectDetector class method) (phenotypic.abc_.ObjectRefiner class method) (phenotypic.abc_.PostMeasurement class method) (phenotypic.abc_.PrefabPipeline class method) (phenotypic.abc_.Smoothing class method) (phenotypic.abc_.ThresholdDetector class method) (phenotypic.analysis.EdgeCorrector class method) (phenotypic.analysis.ErrorCutoffFinder class method) (phenotypic.analysis.ExpectedVsDetectedCount class method) (phenotypic.analysis.GridOccupancy class method) (phenotypic.analysis.ICC class method) (phenotypic.analysis.LinearCapAndLagModel class method) (phenotypic.analysis.LinearLagModel class method) (phenotypic.analysis.LogGrowthModel class method) (phenotypic.analysis.MADOutlierRemover class method) (phenotypic.analysis.MaxModifiedZScore class method) (phenotypic.analysis.RelativeMAD class method) (phenotypic.analysis.ReplicateAgreement class method) (phenotypic.analysis.TukeyOutlierFraction class method) (phenotypic.analysis.TukeyOutlierRemover class method) (phenotypic.correction.BayesShrinkCorrector class method) (phenotypic.correction.CaptureMetadata class method) (phenotypic.correction.ColorCheckerProfile class method) (phenotypic.correction.ColorCorrector class method) (phenotypic.correction.ColorDenoise class method) (phenotypic.correction.DenoiseBlockMatch class method) (phenotypic.correction.GridAligner class method) (phenotypic.correction.ImageCropper class method) (phenotypic.correction.ImagePadder class method) (phenotypic.correction.VisuShrinkCorrector class method) (phenotypic.detect.CannyDetector class method) (phenotypic.detect.ChanVeseDetector class method) (phenotypic.detect.CompositeDetector class method) (phenotypic.detect.FilamentousFungiDetector class method) (phenotypic.detect.HysteresisDetector class method) (phenotypic.detect.InoculumDetector class method) (phenotypic.detect.IsodataDetector class method) (phenotypic.detect.LiDetector class method) (phenotypic.detect.MadHysteresisDetector class method) (phenotypic.detect.ManualGridPointDetector class method) (phenotypic.detect.ManualPointDetector class method) (phenotypic.detect.MeanDetector class method) (phenotypic.detect.MinimumDetector class method) (phenotypic.detect.OtsuDetector class method) (phenotypic.detect.RankOtsuDetector class method) (phenotypic.detect.RoundPeaksDetector class method) (phenotypic.detect.SecondaryOtsuDetector class method) (phenotypic.detect.SinePeakDetector class method) (phenotypic.detect.TriangleDetector class method) (phenotypic.detect.UserThreshold class method) (phenotypic.detect.WatershedDetector class method) (phenotypic.detect.YenDetector class method) (phenotypic.enhance.BayesShrinkEnhancer class method) (phenotypic.enhance.CompositeEnhance class method) (phenotypic.enhance.ContrastStretching class method) (phenotypic.enhance.EnhanceBlockMatch class method) (phenotypic.enhance.EnhanceLocalContrast class method) (phenotypic.enhance.FlattenIllumination class method) (phenotypic.enhance.FocusBlobLoG class method) (phenotypic.enhance.FocusEdgeFrangi class method) (phenotypic.enhance.FocusEdgeHessian class method) (phenotypic.enhance.FocusEdgeLaplace class method) (phenotypic.enhance.FocusEdgeMeijering class method) (phenotypic.enhance.FocusEdgePhase class method) (phenotypic.enhance.FocusEdgeSato class method) (phenotypic.enhance.FocusEdgeSobel class method) (phenotypic.enhance.GaussianBlur class method) (phenotypic.enhance.GrayOpening class method) (phenotypic.enhance.ImageInverter class method) (phenotypic.enhance.LocalEdgeDenoise class method) (phenotypic.enhance.MedianFilter class method) (phenotypic.enhance.NonLocalMeansDenoiser class method) (phenotypic.enhance.RankMedianEnhancer class method) (phenotypic.enhance.SetDetectMode class method) (phenotypic.enhance.SharpenEdgeGauss class method) (phenotypic.enhance.StructureSmoothing class method) (phenotypic.enhance.SubtractGaussian class method) (phenotypic.enhance.SubtractOpening class method) (phenotypic.enhance.SubtractRollingBall class method) (phenotypic.enhance.SubtractWhiteTophat class method) (phenotypic.enhance.VisuShrinkEnhancer class method) (phenotypic.enhance.WhiteTophatEnhance class method) (phenotypic.grid.AutoGridFinder class method) (phenotypic.grid.CenteredAutoGridFinder class method) (phenotypic.grid.GridApply class method) (phenotypic.grid.ManualGridFinder class method) (phenotypic.measure.MeasureBounds class method) (phenotypic.measure.MeasureColor class method) (phenotypic.measure.MeasureGridLinRegStats class method) (phenotypic.measure.MeasureGridSpread class method) (phenotypic.measure.MeasureIntensity class method) (phenotypic.measure.MeasureNeighborDist class method) (phenotypic.measure.MeasureOrientationZones class method) (phenotypic.measure.MeasureShape class method) (phenotypic.measure.MeasureSize class method) (phenotypic.measure.MeasureSymmetricZones class method) (phenotypic.measure.MeasureTexture class method) (phenotypic.prefab.FilamentousFungiPipeline class method) (phenotypic.prefab.GridSectionPipeline class method) (phenotypic.prefab.HeavyOtsuPipeline class method) (phenotypic.prefab.HeavyRoundPeaksPipeline class method) (phenotypic.prefab.HeavyWatershedPipeline class method) (phenotypic.prefab.RoundPeaksPipeline class method) (phenotypic.prefab.SpImagerPipeline class method) (phenotypic.refine.ExtractColonyCore class method) (phenotypic.refine.GridAlignmentRefiner class method) (phenotypic.refine.GridOversizedObjectRemover class method) (phenotypic.refine.KeepNearestCenter class method) (phenotypic.refine.KeepSectionLargest class method) (phenotypic.refine.ManualRefine class method) (phenotypic.refine.MaskClosing class method) (phenotypic.refine.MaskDilation class method) (phenotypic.refine.MaskErosion class method) (phenotypic.refine.MaskFill class method) (phenotypic.refine.MaskGradient class method) (phenotypic.refine.MaskOpening class method) (phenotypic.refine.MaskWhiteTophat class method) (phenotypic.refine.MergeFragmentChains class method) (phenotypic.refine.NearestNeighborMerger class method) (phenotypic.refine.ReduceSectionsByLine class method) (phenotypic.refine.RefineBySineFit class method) (phenotypic.refine.RemoveBorderObjects class method) (phenotypic.refine.RemoveByFeature class method) (phenotypic.refine.RemoveGridOutliers class method) (phenotypic.refine.RemoveLowCircularity class method) (phenotypic.refine.SeparateObjects class method) (phenotypic.refine.Skeletonize class method) (phenotypic.refine.SmallObjectRemover class method) (phenotypic.refine.SmallToLargeMerger class method) (phenotypic.refine.Thinning class method) (phenotypic.refine.TrimAsymmetry class method) (phenotypic.tune.Budget class method) (phenotypic.tune.Categorical class method) (phenotypic.tune.EvaluationResult class method) (phenotypic.tune.Evaluator class method) (phenotypic.tune.Excluded class method) (phenotypic.tune.Fixed class method) (phenotypic.tune.FloatRange class method) (phenotypic.tune.HeldOutConfig class method) (phenotypic.tune.ImportanceReport class method) (phenotypic.tune.InferredSearchSpace class method) (phenotypic.tune.IntRange class method) (phenotypic.tune.Knob class method) (phenotypic.tune.score.CompositeScorer class method) (phenotypic.tune.score.GroundTruthMasks class method) (phenotypic.tune.score.QCScorer class method) (phenotypic.tune.score.ReferenceFreeScorer class method) (phenotypic.tune.score.Scorer class method) (phenotypic.tune.score.SupervisedScorer class method) (phenotypic.tune.SearchSpace class method) (phenotypic.tune.strategy.GridConfig class method) (phenotypic.tune.strategy.OptunaConfig class method) (phenotypic.tune.strategy.RandomConfig class method) (phenotypic.tune.strategy.StrategyConfig class method) (phenotypic.tune.Trial class method) (phenotypic.tune.TuningSpec class method) module phenotypic ModulePath (class in phenotypic.sdk_) morph_close_radius (phenotypic.refine.ExtractColonyCore attribute) morph_open_radius (phenotypic.refine.ExtractColonyCore attribute) morph_progression() (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) MorphologicalFiltering (class in phenotypic.abc_) mu (phenotypic.correction.DenoiseBlockMatch attribute) (phenotypic.detect.ChanVeseDetector attribute) mult (phenotypic.enhance.FocusEdgePhase attribute) multi_objective (phenotypic.tune.score.CompositeScorer attribute) mycelium N n_angular_bins (phenotypic.measure.MeasureOrientationZones attribute) (phenotypic.measure.MeasureSymmetricZones attribute) (phenotypic.refine.TrimAsymmetry attribute) n_annuli (phenotypic.measure.MeasureOrientationZones attribute) (phenotypic.measure.MeasureSymmetricZones attribute) (phenotypic.refine.TrimAsymmetry attribute) n_components (phenotypic.refine.ExtractColonyCore attribute) n_excluded (phenotypic.tune.InferredSearchSpace property) n_images (phenotypic.tune.EvaluationResult attribute) (phenotypic.tune.Trial attribute) n_iter (phenotypic.enhance.GrayOpening attribute) (phenotypic.enhance.SharpenEdgeGauss attribute) (phenotypic.enhance.SubtractGaussian attribute) (phenotypic.enhance.SubtractOpening attribute) (phenotypic.refine.MaskClosing attribute) (phenotypic.refine.MaskDilation attribute) (phenotypic.refine.MaskErosion attribute) (phenotypic.refine.MaskOpening attribute) n_jobs (phenotypic.analysis.EdgeCorrector attribute) (phenotypic.analysis.ExpectedVsDetectedCount attribute) (phenotypic.analysis.GridOccupancy attribute) (phenotypic.analysis.ICC attribute) (phenotypic.analysis.LinearCapAndLagModel attribute) (phenotypic.analysis.LinearLagModel attribute) (phenotypic.analysis.LogGrowthModel attribute) (phenotypic.analysis.MADOutlierRemover attribute), [1] (phenotypic.analysis.MaxModifiedZScore attribute) (phenotypic.analysis.RelativeMAD attribute) (phenotypic.analysis.ReplicateAgreement attribute) (phenotypic.analysis.TukeyOutlierFraction attribute) (phenotypic.analysis.TukeyOutlierRemover attribute), [1] n_knobs (phenotypic.tune.InferredSearchSpace property) n_needs_review (phenotypic.tune.InferredSearchSpace property) n_orient (phenotypic.enhance.FocusEdgePhase attribute) n_pitch_samples (phenotypic.grid.CenteredAutoGridFinder attribute) n_scale (phenotypic.enhance.FocusEdgePhase attribute) n_trials (phenotypic.tune.Budget attribute) (phenotypic.tune.strategy.OptunaConfig attribute) (phenotypic.tune.strategy.RandomConfig attribute) name (phenotypic.abc_.DetectionMode property) (phenotypic.abc_.FigureSpec attribute), [1] (phenotypic.abc_.PrefabPipeline attribute) (phenotypic.analysis.ExpectedVsDetectedCount attribute) (phenotypic.analysis.GridOccupancy attribute) (phenotypic.analysis.ICC attribute) (phenotypic.analysis.MaxModifiedZScore attribute) (phenotypic.analysis.RelativeMAD attribute) (phenotypic.analysis.ReplicateAgreement attribute) (phenotypic.analysis.TukeyOutlierFraction attribute) (phenotypic.gui.builder._state._DagBuilderScope attribute), [1] (phenotypic.prefab.FilamentousFungiPipeline attribute) (phenotypic.prefab.GridSectionPipeline attribute) (phenotypic.prefab.HeavyOtsuPipeline attribute) (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) (phenotypic.prefab.HeavyWatershedPipeline attribute) (phenotypic.prefab.RoundPeaksPipeline attribute) (phenotypic.prefab.SpImagerPipeline attribute) NAME (phenotypic.sdk_.ChunkManifestKey attribute) name (phenotypic.sdk_.exceptions_.DataIntegrityError attribute) (phenotypic.sdk_.exceptions_.EmptyImageError attribute) (phenotypic.sdk_.exceptions_.IllegalElementAssignmentError attribute) (phenotypic.sdk_.exceptions_.ImmutableComponentError attribute) (phenotypic.sdk_.exceptions_.InvalidHsvSchemaError attribute) (phenotypic.sdk_.exceptions_.NoArrayError attribute) (phenotypic.sdk_.exceptions_.NoComponentError attribute) (phenotypic.sdk_.exceptions_.NoImageDataError attribute) (phenotypic.sdk_.exceptions_.NoObjectsError attribute) (phenotypic.sdk_.exceptions_.ObjectNotFoundError attribute) (phenotypic.sdk_.exceptions_.OperationIntegrityError attribute) (phenotypic.sdk_.exceptions_.UuidAssignmentError attribute) (phenotypic.sdk_.exceptions_.UUIDReassignmentError attribute) (phenotypic.sdk_.HDF attribute), [1] nansafe (phenotypic.enhance.SubtractRollingBall attribute) 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) (phenotypic.detect.ManualPointDetector method) (phenotypic.refine.ManualRefine 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) (phenotypic.abc_.PrefabPipeline attribute) (phenotypic.analysis.EdgeCorrector attribute) (phenotypic.grid.AutoGridFinder attribute) (phenotypic.grid.CenteredAutoGridFinder attribute) (phenotypic.grid.ManualGridFinder attribute), [1] (phenotypic.gui.builder._state._DagBuilderScope attribute), [1] (phenotypic.prefab.FilamentousFungiPipeline attribute) (phenotypic.prefab.GridSectionPipeline attribute) (phenotypic.prefab.HeavyOtsuPipeline attribute) (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) (phenotypic.prefab.HeavyWatershedPipeline attribute) (phenotypic.prefab.RoundPeaksPipeline attribute) (phenotypic.prefab.SpImagerPipeline attribute) 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) needs_review (phenotypic.tune.InferredSearchSpace property) (phenotypic.tune.Knob attribute) nested (phenotypic.gui.builder._state.BlockNode attribute), [1] NEXT_CHUNK_ID (phenotypic.sdk_.ChunkStateKey attribute) NO_QC (phenotypic.sdk_.JobMetadataKey attribute) NoArrayError NoComponentError NoImageDataError noise_method (phenotypic.enhance.FocusEdgePhase attribute) noise_radius (phenotypic.detect.RoundPeaksDetector attribute) (phenotypic.detect.SinePeakDetector attribute) NoiseMetrics (class in phenotypic.util) None (phenotypic.abc_.FootprintMixin attribute) (phenotypic.abc_.ImageOperation attribute) (phenotypic.abc_.ObjectDetector attribute) NONE (phenotypic.sdk_.constants_.IMAGE_MODE attribute) None (phenotypic.sdk_.FootprintMixin attribute) NonLocalMeansDenoiser (class in phenotypic.enhance) nonuniformity_ratio (phenotypic.util.BackgroundMetrics attribute) NoObjectsError NoOpChannel (class in phenotypic.tune.strategy) NoOutputError normed() (phenotypic._core._image_parts.accessors._rgb_accessor.ImageRGB method) nrows (phenotypic.abc_.GridFinder attribute) (phenotypic.abc_.PrefabPipeline attribute) (phenotypic.analysis.EdgeCorrector attribute) (phenotypic.grid.AutoGridFinder attribute) (phenotypic.grid.CenteredAutoGridFinder attribute) (phenotypic.grid.ManualGridFinder attribute), [1] (phenotypic.gui.builder._state._DagBuilderScope attribute), [1] (phenotypic.prefab.FilamentousFungiPipeline attribute) (phenotypic.prefab.GridSectionPipeline attribute) (phenotypic.prefab.HeavyOtsuPipeline attribute) (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) (phenotypic.prefab.HeavyWatershedPipeline attribute) (phenotypic.prefab.RoundPeaksPipeline attribute) (phenotypic.prefab.SpImagerPipeline attribute) num_iter (phenotypic.enhance.StructureSmoothing attribute) num_objects (phenotypic._core._image_parts.accessors._objects_accessor.ObjectsAccessor property) num_scales (phenotypic.enhance.FocusBlobLoG attribute) number (phenotypic.tune.Trial attribute) O obj (phenotypic.sdk_.exceptions_.DataIntegrityError attribute) (phenotypic.sdk_.exceptions_.EmptyImageError attribute) (phenotypic.sdk_.exceptions_.IllegalElementAssignmentError attribute) (phenotypic.sdk_.exceptions_.ImmutableComponentError attribute) (phenotypic.sdk_.exceptions_.InvalidHsvSchemaError attribute) (phenotypic.sdk_.exceptions_.NoArrayError attribute) (phenotypic.sdk_.exceptions_.NoComponentError attribute) (phenotypic.sdk_.exceptions_.NoImageDataError attribute) (phenotypic.sdk_.exceptions_.NoObjectsError attribute) (phenotypic.sdk_.exceptions_.ObjectNotFoundError attribute) (phenotypic.sdk_.exceptions_.OperationIntegrityError attribute) (phenotypic.sdk_.exceptions_.UuidAssignmentError attribute) (phenotypic.sdk_.exceptions_.UUIDReassignmentError attribute) OBJECT (phenotypic.sdk_.constants_.IMAGE_TYPES attribute) ObjectDetector (class in phenotypic.abc_) objective_names() (phenotypic.tune.score.CompositeScorer method) objectives (phenotypic.tune.EvaluationResult attribute) (phenotypic.tune.Trial attribute) ObjectMap (class in phenotypic._core._image_parts.accessors._objmap_accessor) ObjectMask (class in phenotypic._core._image_parts.accessors._objmask_accessor) ObjectNotFoundError ObjectRefiner (class in phenotypic.abc_) 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.EdgeCorrector attribute) (phenotypic.analysis.ExpectedVsDetectedCount attribute) (phenotypic.analysis.GridOccupancy attribute) (phenotypic.analysis.ICC attribute) (phenotypic.analysis.LinearCapAndLagModel attribute) (phenotypic.analysis.LinearLagModel attribute) (phenotypic.analysis.LogGrowthModel attribute) (phenotypic.analysis.MADOutlierRemover attribute), [1] (phenotypic.analysis.MaxModifiedZScore attribute) (phenotypic.analysis.RelativeMAD attribute) (phenotypic.analysis.ReplicateAgreement attribute) (phenotypic.analysis.TukeyOutlierFraction attribute) (phenotypic.analysis.TukeyOutlierRemover attribute), [1] open_port_menu (phenotypic.gui.builder._state._DagBuilderState attribute) OperationFailedError OperationIntegrityError ops (phenotypic.abc_.PrefabPipeline attribute) (phenotypic.detect.CompositeDetector attribute) (phenotypic.enhance.CompositeEnhance attribute) (phenotypic.prefab.FilamentousFungiPipeline attribute) (phenotypic.prefab.GridSectionPipeline attribute) (phenotypic.prefab.HeavyOtsuPipeline attribute) (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) (phenotypic.prefab.HeavyWatershedPipeline attribute) (phenotypic.prefab.RoundPeaksPipeline attribute) (phenotypic.prefab.SpImagerPipeline attribute) optimal_scale (phenotypic.util.StructureMetrics attribute) optimize() (phenotypic.tune.TuningEngine method) options (phenotypic.abc_.Control attribute) OptunaConfig (class in phenotypic.tune.strategy) order (phenotypic.abc_.FigureSpec attribute), [1] order_measurement_columns() (in module phenotypic.sdk_) origin (phenotypic.refine.MaskFill attribute) OtsuDetector (class in phenotypic.detect) outlier_sigma (phenotypic.correction.ColorCheckerProfile attribute) output (phenotypic.enhance.FocusEdgePhase attribute) OUTPUT_DIR (phenotypic.sdk_.ProcessingStateKey attribute) output_illuminant (phenotypic.correction.ColorCorrector attribute) output_kind (phenotypic.abc_.GpuDetector attribute) output_root (phenotypic.sdk_.BundleLayout attribute), [1] OutputValueError overlay_manifest_path() (in module phenotypic.sdk_) overlay_path() (phenotypic.sdk_.BundleLayout method) overlays_dir() (in module phenotypic.sdk_) (phenotypic.sdk_.BundleLayout method) owns_header() (phenotypic.abc_.MeasurementInfo class method) (phenotypic.sdk_.constants_.ConstantLabels class method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS class method) (phenotypic.sdk_.constants_.PIPE_STATUS class method) P p1 (phenotypic.util.ContrastMetrics attribute) p99 (phenotypic.util.ContrastMetrics attribute) pad_checker (phenotypic.correction.ColorCheckerProfile attribute) pair (phenotypic.abc_.MeasurementInfo attribute), [1] (phenotypic.sdk_.constants_.ConstantLabels attribute) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS attribute) (phenotypic.sdk_.constants_.PIPE_STATUS attribute) param_importance_path() (in module phenotypic.sdk_) param_importances() (phenotypic.tune.JournalStudyStore method) params (phenotypic.gui.builder._state.BlockNode attribute), [1] (phenotypic.tune.Trial attribute) pareto_best_pipeline_path() (in module phenotypic.sdk_) pareto_dir() (in module phenotypic.sdk_) pareto_front() (phenotypic.tune.JournalStudyStore method) pareto_front_parquet_path() (in module phenotypic.sdk_) pareto_importance_path() (in module phenotypic.sdk_) parse_file() (phenotypic.abc_.BackgroundSubtraction class method) (phenotypic.abc_.BaseOperation class method) (phenotypic.abc_.ContrastAdjustment class method) (phenotypic.abc_.FocusBlob class method) (phenotypic.abc_.FocusEdge class method) (phenotypic.abc_.GpuDetector class method) (phenotypic.abc_.GridCorrector class method) (phenotypic.abc_.GridFinder class method) (phenotypic.abc_.GridMeasureFeatures class method) (phenotypic.abc_.GridObjectDetector class method) (phenotypic.abc_.GridObjectRefiner class method) (phenotypic.abc_.GridOperation class method) (phenotypic.abc_.ImageCorrector class method) (phenotypic.abc_.ImageDenoiser class method) (phenotypic.abc_.ImageEnhancer class method) (phenotypic.abc_.ImageOperation class method) (phenotypic.abc_.MeasureFeatures class method) (phenotypic.abc_.MorphologicalFiltering class method) (phenotypic.abc_.ObjectDetector class method) (phenotypic.abc_.ObjectRefiner class method) (phenotypic.abc_.PostMeasurement class method) (phenotypic.abc_.PrefabPipeline class method) (phenotypic.abc_.Smoothing class method) (phenotypic.abc_.ThresholdDetector class method) (phenotypic.analysis.EdgeCorrector class method) (phenotypic.analysis.ErrorCutoffFinder class method) (phenotypic.analysis.ExpectedVsDetectedCount class method) (phenotypic.analysis.GridOccupancy class method) (phenotypic.analysis.ICC class method) (phenotypic.analysis.LinearCapAndLagModel class method) (phenotypic.analysis.LinearLagModel class method) (phenotypic.analysis.LogGrowthModel class method) (phenotypic.analysis.MADOutlierRemover class method) (phenotypic.analysis.MaxModifiedZScore class method) (phenotypic.analysis.RelativeMAD class method) (phenotypic.analysis.ReplicateAgreement class method) (phenotypic.analysis.TukeyOutlierFraction class method) (phenotypic.analysis.TukeyOutlierRemover class method) (phenotypic.correction.BayesShrinkCorrector class method) (phenotypic.correction.CaptureMetadata class method) (phenotypic.correction.ColorCheckerProfile class method) (phenotypic.correction.ColorCorrector class method) (phenotypic.correction.ColorDenoise class method) (phenotypic.correction.DenoiseBlockMatch class method) (phenotypic.correction.GridAligner class method) (phenotypic.correction.ImageCropper class method) (phenotypic.correction.ImagePadder class method) (phenotypic.correction.VisuShrinkCorrector class method) (phenotypic.detect.CannyDetector class method) (phenotypic.detect.ChanVeseDetector class method) (phenotypic.detect.CompositeDetector class method) (phenotypic.detect.FilamentousFungiDetector class method) (phenotypic.detect.HysteresisDetector class method) (phenotypic.detect.InoculumDetector class method) (phenotypic.detect.IsodataDetector class method) (phenotypic.detect.LiDetector class method) (phenotypic.detect.MadHysteresisDetector class method) (phenotypic.detect.ManualGridPointDetector class method) (phenotypic.detect.ManualPointDetector class method) (phenotypic.detect.MeanDetector class method) (phenotypic.detect.MinimumDetector class method) (phenotypic.detect.OtsuDetector class method) (phenotypic.detect.RankOtsuDetector class method) (phenotypic.detect.RoundPeaksDetector class method) (phenotypic.detect.SecondaryOtsuDetector class method) (phenotypic.detect.SinePeakDetector class method) (phenotypic.detect.TriangleDetector class method) (phenotypic.detect.UserThreshold class method) (phenotypic.detect.WatershedDetector class method) (phenotypic.detect.YenDetector class method) (phenotypic.enhance.BayesShrinkEnhancer class method) (phenotypic.enhance.CompositeEnhance class method) (phenotypic.enhance.ContrastStretching class method) (phenotypic.enhance.EnhanceBlockMatch class method) (phenotypic.enhance.EnhanceLocalContrast class method) (phenotypic.enhance.FlattenIllumination class method) (phenotypic.enhance.FocusBlobLoG class method) (phenotypic.enhance.FocusEdgeFrangi class method) (phenotypic.enhance.FocusEdgeHessian class method) (phenotypic.enhance.FocusEdgeLaplace class method) (phenotypic.enhance.FocusEdgeMeijering class method) (phenotypic.enhance.FocusEdgePhase class method) (phenotypic.enhance.FocusEdgeSato class method) (phenotypic.enhance.FocusEdgeSobel class method) (phenotypic.enhance.GaussianBlur class method) (phenotypic.enhance.GrayOpening class method) (phenotypic.enhance.ImageInverter class method) (phenotypic.enhance.LocalEdgeDenoise class method) (phenotypic.enhance.MedianFilter class method) (phenotypic.enhance.NonLocalMeansDenoiser class method) (phenotypic.enhance.RankMedianEnhancer class method) (phenotypic.enhance.SetDetectMode class method) (phenotypic.enhance.SharpenEdgeGauss class method) (phenotypic.enhance.StructureSmoothing class method) (phenotypic.enhance.SubtractGaussian class method) (phenotypic.enhance.SubtractOpening class method) (phenotypic.enhance.SubtractRollingBall class method) (phenotypic.enhance.SubtractWhiteTophat class method) (phenotypic.enhance.VisuShrinkEnhancer class method) (phenotypic.enhance.WhiteTophatEnhance class method) (phenotypic.grid.AutoGridFinder class method) (phenotypic.grid.CenteredAutoGridFinder class method) (phenotypic.grid.GridApply class method) (phenotypic.grid.ManualGridFinder class method) (phenotypic.measure.MeasureBounds class method) (phenotypic.measure.MeasureColor class method) (phenotypic.measure.MeasureGridLinRegStats class method) (phenotypic.measure.MeasureGridSpread class method) (phenotypic.measure.MeasureIntensity class method) (phenotypic.measure.MeasureNeighborDist class method) (phenotypic.measure.MeasureOrientationZones class method) (phenotypic.measure.MeasureShape class method) (phenotypic.measure.MeasureSize class method) (phenotypic.measure.MeasureSymmetricZones class method) (phenotypic.measure.MeasureTexture class method) (phenotypic.prefab.FilamentousFungiPipeline class method) (phenotypic.prefab.GridSectionPipeline class method) (phenotypic.prefab.HeavyOtsuPipeline class method) (phenotypic.prefab.HeavyRoundPeaksPipeline class method) (phenotypic.prefab.HeavyWatershedPipeline class method) (phenotypic.prefab.RoundPeaksPipeline class method) (phenotypic.prefab.SpImagerPipeline class method) (phenotypic.refine.ExtractColonyCore class method) (phenotypic.refine.GridAlignmentRefiner class method) (phenotypic.refine.GridOversizedObjectRemover class method) (phenotypic.refine.KeepNearestCenter class method) (phenotypic.refine.KeepSectionLargest class method) (phenotypic.refine.ManualRefine class method) (phenotypic.refine.MaskClosing class method) (phenotypic.refine.MaskDilation class method) (phenotypic.refine.MaskErosion class method) (phenotypic.refine.MaskFill class method) (phenotypic.refine.MaskGradient class method) (phenotypic.refine.MaskOpening class method) (phenotypic.refine.MaskWhiteTophat class method) (phenotypic.refine.MergeFragmentChains class method) (phenotypic.refine.NearestNeighborMerger class method) (phenotypic.refine.ReduceSectionsByLine class method) (phenotypic.refine.RefineBySineFit class method) (phenotypic.refine.RemoveBorderObjects class method) (phenotypic.refine.RemoveByFeature class method) (phenotypic.refine.RemoveGridOutliers class method) (phenotypic.refine.RemoveLowCircularity class method) (phenotypic.refine.SeparateObjects class method) (phenotypic.refine.Skeletonize class method) (phenotypic.refine.SmallObjectRemover class method) (phenotypic.refine.SmallToLargeMerger class method) (phenotypic.refine.Thinning class method) (phenotypic.refine.TrimAsymmetry class method) (phenotypic.tune.Budget class method) (phenotypic.tune.Categorical class method) (phenotypic.tune.EvaluationResult class method) (phenotypic.tune.Evaluator class method) (phenotypic.tune.Excluded class method) (phenotypic.tune.Fixed class method) (phenotypic.tune.FloatRange class method) (phenotypic.tune.HeldOutConfig class method) (phenotypic.tune.ImportanceReport class method) (phenotypic.tune.InferredSearchSpace class method) (phenotypic.tune.IntRange class method) (phenotypic.tune.Knob class method) (phenotypic.tune.score.CompositeScorer class method) (phenotypic.tune.score.GroundTruthMasks class method) (phenotypic.tune.score.QCScorer class method) (phenotypic.tune.score.ReferenceFreeScorer class method) (phenotypic.tune.score.Scorer class method) (phenotypic.tune.score.SupervisedScorer class method) (phenotypic.tune.SearchSpace class method) (phenotypic.tune.strategy.GridConfig class method) (phenotypic.tune.strategy.OptunaConfig class method) (phenotypic.tune.strategy.RandomConfig class method) (phenotypic.tune.strategy.StrategyConfig class method) (phenotypic.tune.Trial class method) (phenotypic.tune.TuningSpec class method) parse_job_id() (in module phenotypic.sdk_.slurm) parse_obj() (phenotypic.abc_.BackgroundSubtraction class method) (phenotypic.abc_.BaseOperation class method) (phenotypic.abc_.ContrastAdjustment class method) (phenotypic.abc_.FocusBlob class method) (phenotypic.abc_.FocusEdge class method) (phenotypic.abc_.GpuDetector class method) (phenotypic.abc_.GridCorrector class method) (phenotypic.abc_.GridFinder class method) (phenotypic.abc_.GridMeasureFeatures class method) (phenotypic.abc_.GridObjectDetector class method) (phenotypic.abc_.GridObjectRefiner class method) (phenotypic.abc_.GridOperation class method) (phenotypic.abc_.ImageCorrector class method) (phenotypic.abc_.ImageDenoiser class method) (phenotypic.abc_.ImageEnhancer class method) (phenotypic.abc_.ImageOperation class method) (phenotypic.abc_.MeasureFeatures class method) (phenotypic.abc_.MorphologicalFiltering class method) (phenotypic.abc_.ObjectDetector class method) (phenotypic.abc_.ObjectRefiner class method) (phenotypic.abc_.PostMeasurement class method) (phenotypic.abc_.PrefabPipeline class method) (phenotypic.abc_.Smoothing class method) (phenotypic.abc_.ThresholdDetector class method) (phenotypic.analysis.EdgeCorrector class method) (phenotypic.analysis.ErrorCutoffFinder class method) (phenotypic.analysis.ExpectedVsDetectedCount class method) (phenotypic.analysis.GridOccupancy class method) (phenotypic.analysis.ICC class method) (phenotypic.analysis.LinearCapAndLagModel class method) (phenotypic.analysis.LinearLagModel class method) (phenotypic.analysis.LogGrowthModel class method) (phenotypic.analysis.MADOutlierRemover class method) (phenotypic.analysis.MaxModifiedZScore class method) (phenotypic.analysis.RelativeMAD class method) (phenotypic.analysis.ReplicateAgreement class method) (phenotypic.analysis.TukeyOutlierFraction class method) (phenotypic.analysis.TukeyOutlierRemover class method) (phenotypic.correction.BayesShrinkCorrector class method) (phenotypic.correction.CaptureMetadata class method) (phenotypic.correction.ColorCheckerProfile class method) (phenotypic.correction.ColorCorrector class method) (phenotypic.correction.ColorDenoise class method) (phenotypic.correction.DenoiseBlockMatch class method) (phenotypic.correction.GridAligner class method) (phenotypic.correction.ImageCropper class method) (phenotypic.correction.ImagePadder class method) (phenotypic.correction.VisuShrinkCorrector class method) (phenotypic.detect.CannyDetector class method) (phenotypic.detect.ChanVeseDetector class method) (phenotypic.detect.CompositeDetector class method) (phenotypic.detect.FilamentousFungiDetector class method) (phenotypic.detect.HysteresisDetector class method) (phenotypic.detect.InoculumDetector class method) (phenotypic.detect.IsodataDetector class method) (phenotypic.detect.LiDetector class method) (phenotypic.detect.MadHysteresisDetector class method) (phenotypic.detect.ManualGridPointDetector class method) (phenotypic.detect.ManualPointDetector class method) (phenotypic.detect.MeanDetector class method) (phenotypic.detect.MinimumDetector class method) (phenotypic.detect.OtsuDetector class method) (phenotypic.detect.RankOtsuDetector class method) (phenotypic.detect.RoundPeaksDetector class method) (phenotypic.detect.SecondaryOtsuDetector class method) (phenotypic.detect.SinePeakDetector class method) (phenotypic.detect.TriangleDetector class method) (phenotypic.detect.UserThreshold class method) (phenotypic.detect.WatershedDetector class method) (phenotypic.detect.YenDetector class method) (phenotypic.enhance.BayesShrinkEnhancer class method) (phenotypic.enhance.CompositeEnhance class method) (phenotypic.enhance.ContrastStretching class method) (phenotypic.enhance.EnhanceBlockMatch class method) (phenotypic.enhance.EnhanceLocalContrast class method) (phenotypic.enhance.FlattenIllumination class method) (phenotypic.enhance.FocusBlobLoG class method) (phenotypic.enhance.FocusEdgeFrangi class method) (phenotypic.enhance.FocusEdgeHessian class method) (phenotypic.enhance.FocusEdgeLaplace class method) (phenotypic.enhance.FocusEdgeMeijering class method) (phenotypic.enhance.FocusEdgePhase class method) (phenotypic.enhance.FocusEdgeSato class method) (phenotypic.enhance.FocusEdgeSobel class method) (phenotypic.enhance.GaussianBlur class method) (phenotypic.enhance.GrayOpening class method) (phenotypic.enhance.ImageInverter class method) (phenotypic.enhance.LocalEdgeDenoise class method) (phenotypic.enhance.MedianFilter class method) (phenotypic.enhance.NonLocalMeansDenoiser class method) (phenotypic.enhance.RankMedianEnhancer class method) (phenotypic.enhance.SetDetectMode class method) (phenotypic.enhance.SharpenEdgeGauss class method) (phenotypic.enhance.StructureSmoothing class method) (phenotypic.enhance.SubtractGaussian class method) (phenotypic.enhance.SubtractOpening class method) (phenotypic.enhance.SubtractRollingBall class method) (phenotypic.enhance.SubtractWhiteTophat class method) (phenotypic.enhance.VisuShrinkEnhancer class method) (phenotypic.enhance.WhiteTophatEnhance class method) (phenotypic.grid.AutoGridFinder class method) (phenotypic.grid.CenteredAutoGridFinder class method) (phenotypic.grid.GridApply class method) (phenotypic.grid.ManualGridFinder class method) (phenotypic.measure.MeasureBounds class method) (phenotypic.measure.MeasureColor class method) (phenotypic.measure.MeasureGridLinRegStats class method) (phenotypic.measure.MeasureGridSpread class method) (phenotypic.measure.MeasureIntensity class method) (phenotypic.measure.MeasureNeighborDist class method) (phenotypic.measure.MeasureOrientationZones class method) (phenotypic.measure.MeasureShape class method) (phenotypic.measure.MeasureSize class method) (phenotypic.measure.MeasureSymmetricZones class method) (phenotypic.measure.MeasureTexture class method) (phenotypic.prefab.FilamentousFungiPipeline class method) (phenotypic.prefab.GridSectionPipeline class method) (phenotypic.prefab.HeavyOtsuPipeline class method) (phenotypic.prefab.HeavyRoundPeaksPipeline class method) (phenotypic.prefab.HeavyWatershedPipeline class method) (phenotypic.prefab.RoundPeaksPipeline class method) (phenotypic.prefab.SpImagerPipeline class method) (phenotypic.refine.ExtractColonyCore class method) (phenotypic.refine.GridAlignmentRefiner class method) (phenotypic.refine.GridOversizedObjectRemover class method) (phenotypic.refine.KeepNearestCenter class method) (phenotypic.refine.KeepSectionLargest class method) (phenotypic.refine.ManualRefine class method) (phenotypic.refine.MaskClosing class method) (phenotypic.refine.MaskDilation class method) (phenotypic.refine.MaskErosion class method) (phenotypic.refine.MaskFill class method) (phenotypic.refine.MaskGradient class method) (phenotypic.refine.MaskOpening class method) (phenotypic.refine.MaskWhiteTophat class method) (phenotypic.refine.MergeFragmentChains class method) (phenotypic.refine.NearestNeighborMerger class method) (phenotypic.refine.ReduceSectionsByLine class method) (phenotypic.refine.RefineBySineFit class method) (phenotypic.refine.RemoveBorderObjects class method) (phenotypic.refine.RemoveByFeature class method) (phenotypic.refine.RemoveGridOutliers class method) (phenotypic.refine.RemoveLowCircularity class method) (phenotypic.refine.SeparateObjects class method) (phenotypic.refine.Skeletonize class method) (phenotypic.refine.SmallObjectRemover class method) (phenotypic.refine.SmallToLargeMerger class method) (phenotypic.refine.Thinning class method) (phenotypic.refine.TrimAsymmetry class method) (phenotypic.tune.Budget class method) (phenotypic.tune.Categorical class method) (phenotypic.tune.EvaluationResult class method) (phenotypic.tune.Evaluator class method) (phenotypic.tune.Excluded class method) (phenotypic.tune.Fixed class method) (phenotypic.tune.FloatRange class method) (phenotypic.tune.HeldOutConfig class method) (phenotypic.tune.ImportanceReport class method) (phenotypic.tune.InferredSearchSpace class method) (phenotypic.tune.IntRange class method) (phenotypic.tune.Knob class method) (phenotypic.tune.score.CompositeScorer class method) (phenotypic.tune.score.GroundTruthMasks class method) (phenotypic.tune.score.QCScorer class method) (phenotypic.tune.score.ReferenceFreeScorer class method) (phenotypic.tune.score.Scorer class method) (phenotypic.tune.score.SupervisedScorer class method) (phenotypic.tune.SearchSpace class method) (phenotypic.tune.strategy.GridConfig class method) (phenotypic.tune.strategy.OptunaConfig class method) (phenotypic.tune.strategy.RandomConfig class method) (phenotypic.tune.strategy.StrategyConfig class method) (phenotypic.tune.Trial class method) (phenotypic.tune.TuningSpec class method) parse_raw() (phenotypic.abc_.BackgroundSubtraction class method) (phenotypic.abc_.BaseOperation class method) (phenotypic.abc_.ContrastAdjustment class method) (phenotypic.abc_.FocusBlob class method) (phenotypic.abc_.FocusEdge class method) (phenotypic.abc_.GpuDetector class method) (phenotypic.abc_.GridCorrector class method) (phenotypic.abc_.GridFinder class method) (phenotypic.abc_.GridMeasureFeatures class method) (phenotypic.abc_.GridObjectDetector class method) (phenotypic.abc_.GridObjectRefiner class method) (phenotypic.abc_.GridOperation class method) (phenotypic.abc_.ImageCorrector class method) (phenotypic.abc_.ImageDenoiser class method) (phenotypic.abc_.ImageEnhancer class method) (phenotypic.abc_.ImageOperation class method) (phenotypic.abc_.MeasureFeatures class method) (phenotypic.abc_.MorphologicalFiltering class method) (phenotypic.abc_.ObjectDetector class method) (phenotypic.abc_.ObjectRefiner class method) (phenotypic.abc_.PostMeasurement class method) (phenotypic.abc_.PrefabPipeline class method) (phenotypic.abc_.Smoothing class method) (phenotypic.abc_.ThresholdDetector class method) (phenotypic.analysis.EdgeCorrector class method) (phenotypic.analysis.ErrorCutoffFinder class method) (phenotypic.analysis.ExpectedVsDetectedCount class method) (phenotypic.analysis.GridOccupancy class method) (phenotypic.analysis.ICC class method) (phenotypic.analysis.LinearCapAndLagModel class method) (phenotypic.analysis.LinearLagModel class method) (phenotypic.analysis.LogGrowthModel class method) (phenotypic.analysis.MADOutlierRemover class method) (phenotypic.analysis.MaxModifiedZScore class method) (phenotypic.analysis.RelativeMAD class method) (phenotypic.analysis.ReplicateAgreement class method) (phenotypic.analysis.TukeyOutlierFraction class method) (phenotypic.analysis.TukeyOutlierRemover class method) (phenotypic.correction.BayesShrinkCorrector class method) (phenotypic.correction.CaptureMetadata class method) (phenotypic.correction.ColorCheckerProfile class method) (phenotypic.correction.ColorCorrector class method) (phenotypic.correction.ColorDenoise class method) (phenotypic.correction.DenoiseBlockMatch class method) (phenotypic.correction.GridAligner class method) (phenotypic.correction.ImageCropper class method) (phenotypic.correction.ImagePadder class method) (phenotypic.correction.VisuShrinkCorrector class method) (phenotypic.detect.CannyDetector class method) (phenotypic.detect.ChanVeseDetector class method) (phenotypic.detect.CompositeDetector class method) (phenotypic.detect.FilamentousFungiDetector class method) (phenotypic.detect.HysteresisDetector class method) (phenotypic.detect.InoculumDetector class method) (phenotypic.detect.IsodataDetector class method) (phenotypic.detect.LiDetector class method) (phenotypic.detect.MadHysteresisDetector class method) (phenotypic.detect.ManualGridPointDetector class method) (phenotypic.detect.ManualPointDetector class method) (phenotypic.detect.MeanDetector class method) (phenotypic.detect.MinimumDetector class method) (phenotypic.detect.OtsuDetector class method) (phenotypic.detect.RankOtsuDetector class method) (phenotypic.detect.RoundPeaksDetector class method) (phenotypic.detect.SecondaryOtsuDetector class method) (phenotypic.detect.SinePeakDetector class method) (phenotypic.detect.TriangleDetector class method) (phenotypic.detect.UserThreshold class method) (phenotypic.detect.WatershedDetector class method) (phenotypic.detect.YenDetector class method) (phenotypic.enhance.BayesShrinkEnhancer class method) (phenotypic.enhance.CompositeEnhance class method) (phenotypic.enhance.ContrastStretching class method) (phenotypic.enhance.EnhanceBlockMatch class method) (phenotypic.enhance.EnhanceLocalContrast class method) (phenotypic.enhance.FlattenIllumination class method) (phenotypic.enhance.FocusBlobLoG class method) (phenotypic.enhance.FocusEdgeFrangi class method) (phenotypic.enhance.FocusEdgeHessian class method) (phenotypic.enhance.FocusEdgeLaplace class method) (phenotypic.enhance.FocusEdgeMeijering class method) (phenotypic.enhance.FocusEdgePhase class method) (phenotypic.enhance.FocusEdgeSato class method) (phenotypic.enhance.FocusEdgeSobel class method) (phenotypic.enhance.GaussianBlur class method) (phenotypic.enhance.GrayOpening class method) (phenotypic.enhance.ImageInverter class method) (phenotypic.enhance.LocalEdgeDenoise class method) (phenotypic.enhance.MedianFilter class method) (phenotypic.enhance.NonLocalMeansDenoiser class method) (phenotypic.enhance.RankMedianEnhancer class method) (phenotypic.enhance.SetDetectMode class method) (phenotypic.enhance.SharpenEdgeGauss class method) (phenotypic.enhance.StructureSmoothing class method) (phenotypic.enhance.SubtractGaussian class method) (phenotypic.enhance.SubtractOpening class method) (phenotypic.enhance.SubtractRollingBall class method) (phenotypic.enhance.SubtractWhiteTophat class method) (phenotypic.enhance.VisuShrinkEnhancer class method) (phenotypic.enhance.WhiteTophatEnhance class method) (phenotypic.grid.AutoGridFinder class method) (phenotypic.grid.CenteredAutoGridFinder class method) (phenotypic.grid.GridApply class method) (phenotypic.grid.ManualGridFinder class method) (phenotypic.measure.MeasureBounds class method) (phenotypic.measure.MeasureColor class method) (phenotypic.measure.MeasureGridLinRegStats class method) (phenotypic.measure.MeasureGridSpread class method) (phenotypic.measure.MeasureIntensity class method) (phenotypic.measure.MeasureNeighborDist class method) (phenotypic.measure.MeasureOrientationZones class method) (phenotypic.measure.MeasureShape class method) (phenotypic.measure.MeasureSize class method) (phenotypic.measure.MeasureSymmetricZones class method) (phenotypic.measure.MeasureTexture class method) (phenotypic.prefab.FilamentousFungiPipeline class method) (phenotypic.prefab.GridSectionPipeline class method) (phenotypic.prefab.HeavyOtsuPipeline class method) (phenotypic.prefab.HeavyRoundPeaksPipeline class method) (phenotypic.prefab.HeavyWatershedPipeline class method) (phenotypic.prefab.RoundPeaksPipeline class method) (phenotypic.prefab.SpImagerPipeline class method) (phenotypic.refine.ExtractColonyCore class method) (phenotypic.refine.GridAlignmentRefiner class method) (phenotypic.refine.GridOversizedObjectRemover class method) (phenotypic.refine.KeepNearestCenter class method) (phenotypic.refine.KeepSectionLargest class method) (phenotypic.refine.ManualRefine class method) (phenotypic.refine.MaskClosing class method) (phenotypic.refine.MaskDilation class method) (phenotypic.refine.MaskErosion class method) (phenotypic.refine.MaskFill class method) (phenotypic.refine.MaskGradient class method) (phenotypic.refine.MaskOpening class method) (phenotypic.refine.MaskWhiteTophat class method) (phenotypic.refine.MergeFragmentChains class method) (phenotypic.refine.NearestNeighborMerger class method) (phenotypic.refine.ReduceSectionsByLine class method) (phenotypic.refine.RefineBySineFit class method) (phenotypic.refine.RemoveBorderObjects class method) (phenotypic.refine.RemoveByFeature class method) (phenotypic.refine.RemoveGridOutliers class method) (phenotypic.refine.RemoveLowCircularity class method) (phenotypic.refine.SeparateObjects class method) (phenotypic.refine.Skeletonize class method) (phenotypic.refine.SmallObjectRemover class method) (phenotypic.refine.SmallToLargeMerger class method) (phenotypic.refine.Thinning class method) (phenotypic.refine.TrimAsymmetry class method) (phenotypic.tune.Budget class method) (phenotypic.tune.Categorical class method) (phenotypic.tune.EvaluationResult class method) (phenotypic.tune.Evaluator class method) (phenotypic.tune.Excluded class method) (phenotypic.tune.Fixed class method) (phenotypic.tune.FloatRange class method) (phenotypic.tune.HeldOutConfig class method) (phenotypic.tune.ImportanceReport class method) (phenotypic.tune.InferredSearchSpace class method) (phenotypic.tune.IntRange class method) (phenotypic.tune.Knob class method) (phenotypic.tune.score.CompositeScorer class method) (phenotypic.tune.score.GroundTruthMasks class method) (phenotypic.tune.score.QCScorer class method) (phenotypic.tune.score.ReferenceFreeScorer class method) (phenotypic.tune.score.Scorer class method) (phenotypic.tune.score.SupervisedScorer class method) (phenotypic.tune.SearchSpace class method) (phenotypic.tune.strategy.GridConfig class method) (phenotypic.tune.strategy.OptunaConfig class method) (phenotypic.tune.strategy.RandomConfig class method) (phenotypic.tune.strategy.StrategyConfig class method) (phenotypic.tune.Trial class method) (phenotypic.tune.TuningSpec class method) partition() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) patch_size (phenotypic.enhance.NonLocalMeansDenoiser attribute) path_dilation_radius (phenotypic.detect.FilamentousFungiDetector attribute) pct_min_wavelength (phenotypic.detect.FilamentousFungiDetector attribute) pct_n_orient (phenotypic.detect.FilamentousFungiDetector attribute) peak_prominence (phenotypic.detect.RoundPeaksDetector attribute) (phenotypic.detect.SinePeakDetector attribute) (phenotypic.refine.GridAlignmentRefiner attribute) (phenotypic.refine.RefineBySineFit attribute) peak_response (phenotypic.util.StructureMetrics attribute) pelt_penalty (phenotypic.measure.MeasureOrientationZones attribute) (phenotypic.measure.MeasureSymmetricZones attribute) (phenotypic.refine.TrimAsymmetry attribute) PENDING (phenotypic.sdk_.DashboardManifestKey attribute) PENDING_CHUNKS (phenotypic.sdk_.DashboardManifestSlurmInfoKey attribute) pending_delete_block_id (phenotypic.gui.builder._state._DagBuilderState attribute), [1] phenotypic module phenotypic_cache_dir() (in module phenotypic.sdk_) phenotypic_cache_pipeline_json_path() (in module phenotypic.sdk_) PHENOTYPIC_CLASS (phenotypic.sdk_.HdfAttr attribute) PHENOTYPIC_METADATA_KEY (phenotypic.sdk_.constants_.IO attribute) phenotypic_version (phenotypic.tune.TuningSpec attribute) PhenoTypicError PIPE_STATUS (class in phenotypic.sdk_.constants_) pipeline (phenotypic.tune.TuningSpec attribute) PIPELINE_CLASS_NAME (in module phenotypic.gui.builder._state) pipeline_config_path (phenotypic.sdk_.BundleLayout property) pipeline_json_path() (in module phenotypic.sdk_) PIPELINE_PATH (phenotypic.sdk_.ProcessingStateKey attribute) PlotAccessor (class in phenotypic._core._image_parts.accessors._plot_accessor) PlotterRegistry (class in phenotypic.sdk_.register) PNG_FILE_EXTENSIONS (phenotypic.sdk_.constants_.IO attribute) PointPickerWidget (class in phenotypic.sdk_.napari_) pop() (phenotypic._core._image_parts.accessors._metadata_accessor.MetadataAccessor method) (phenotypic.util.BackgroundMetrics method) (phenotypic.util.ContrastMetrics method) (phenotypic.util.NoiseMetrics method) (phenotypic.util.QualityScores method) (phenotypic.util.StructureMetrics method) popitem() (phenotypic.util.BackgroundMetrics method) (phenotypic.util.ContrastMetrics method) (phenotypic.util.NoiseMetrics method) (phenotypic.util.QualityScores method) (phenotypic.util.StructureMetrics method) post (phenotypic.abc_.PrefabPipeline attribute) (phenotypic.prefab.FilamentousFungiPipeline attribute) (phenotypic.prefab.GridSectionPipeline attribute) (phenotypic.prefab.HeavyOtsuPipeline attribute) (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) (phenotypic.prefab.HeavyWatershedPipeline attribute) (phenotypic.prefab.RoundPeaksPipeline attribute) (phenotypic.prefab.SpImagerPipeline attribute) POST (phenotypic.sdk_.ModulePath attribute) PostMeasurement (class in phenotypic.abc_) preallocate_frame_layout() (phenotypic.sdk_.HDF static method) preallocate_series_layout() (phenotypic.sdk_.HDF static method) PRED_CC (phenotypic.sdk_.constants_.GRID_LINREG_STATS_EXTRACTOR attribute) PRED_RR (phenotypic.sdk_.constants_.GRID_LINREG_STATS_EXTRACTOR attribute) prefab pipeline PrefabPipeline (class in phenotypic.abc_) preserve_range (phenotypic.enhance.SharpenEdgeGauss attribute) (phenotypic.enhance.SubtractGaussian attribute) preview_modes() (phenotypic._core._image_parts.accessors._detect_mat_accessor.DetectMatAccessor method) primary (phenotypic.abc_.FigureSpec attribute), [1] PROCESSED (phenotypic.sdk_.constants_.PIPE_STATUS attribute) processing_report_html_path() (in module phenotypic.sdk_) processing_state_path() (in module phenotypic.sdk_) ProcessingStateKey (class in phenotypic.sdk_) profile (phenotypic.correction.ColorCorrector attribute) progress_dir() (in module phenotypic.sdk_) props (phenotypic._core._image_parts.accessors._objects_accessor.ObjectsAccessor property) PROTECTED_METADATA_SUBGROUP_KEY (phenotypic.sdk_.HDF attribute) prune (phenotypic.tune.strategy.OptunaConfig attribute) prune_saturated (phenotypic.analysis.LinearLagModel attribute) pruned (phenotypic.tune.EvaluationResult attribute) (phenotypic.tune.Trial attribute) PruningChannel (class in phenotypic.tune.strategy) PUBLIC_METADATA_SUBGROUP_KEY (phenotypic.sdk_.HDF attribute) pvalue (phenotypic.analysis.EdgeCorrector attribute) Q qc (phenotypic.abc_.PrefabPipeline attribute) (phenotypic.prefab.FilamentousFungiPipeline attribute) (phenotypic.prefab.GridSectionPipeline attribute) (phenotypic.prefab.HeavyOtsuPipeline attribute) (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) (phenotypic.prefab.HeavyWatershedPipeline attribute) (phenotypic.prefab.RoundPeaksPipeline attribute) (phenotypic.prefab.SpImagerPipeline attribute) qc_dir (phenotypic.sdk_.BundleLayout property) qc_dir() (in module phenotypic.sdk_) qc_duckdb (phenotypic.sdk_.BundleLayout property) qc_duckdb_path() (in module phenotypic.sdk_) qc_review_state_path (phenotypic.sdk_.BundleLayout property) qc_review_state_path() (in module phenotypic.sdk_) QCScorer (class in phenotypic.tune.score) QualityScores (class in phenotypic.util) quant_lvl (phenotypic.measure.MeasureTexture attribute) quiver_block (phenotypic.measure.MeasureOrientationZones attribute) R radius (phenotypic.enhance.SharpenEdgeGauss attribute) (phenotypic.enhance.SubtractRollingBall attribute) random_seed (phenotypic.measure.MeasureColor attribute) RandomConfig (class in phenotypic.tune.strategy) RandomStrategy (class in phenotypic.tune.strategy) RankMedianEnhancer (class in phenotypic.enhance) RankOtsuDetector (class in phenotypic.detect) rater_label (phenotypic.analysis.ICC attribute) RAW_FILE_EXTENSIONS (phenotypic.sdk_.constants_.IO attribute) read_run_manifest() (in module phenotypic.sdk_) reader() (phenotypic.sdk_.HDF method) readme_md_path() (in module phenotypic.sdk_) reason (phenotypic.tune.Excluded attribute) recommendation (phenotypic.tune.ScreeningResult attribute) recompile_dir() (in module phenotypic.sdk_) recompile_status_dir() (in module phenotypic.sdk_) reconnection_tolerance (phenotypic.detect.FilamentousFungiDetector attribute) reduced_space (phenotypic.tune.ScreeningResult attribute) ReduceSectionsByLine (class in phenotypic.refine) ReferenceFreeScorer (class in phenotypic.tune.score) RefineBySineFit (class in phenotypic.refine) region_metric (phenotypic.tune.score.SupervisedScorer attribute) region_term_name (phenotypic.tune.score.SupervisedScorer attribute) register() (phenotypic.sdk_.register.AnalysisPluginRegistry class method) (phenotypic.sdk_.register.BaseRegistry class method) (phenotypic.sdk_.register.PlotterRegistry class method) register_analysis() (in module phenotypic.sdk_.register) register_detection_mode() (in module phenotypic.abc_) register_plotter() (in module phenotypic.sdk_.register) register_result() (phenotypic.tune.strategy.GridStrategy method) (phenotypic.tune.strategy.RandomStrategy method) (phenotypic.tune.strategy.SearchStrategy method) relabel (phenotypic.detect.WatershedDetector attribute) 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) RelativeMAD (class in phenotypic.analysis) rembi_manifest_path() (in module phenotypic.sdk_) rembi_module() (phenotypic.abc_.MeasurementInfo class method) (phenotypic.sdk_.constants_.ConstantLabels class method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS class method) (phenotypic.sdk_.constants_.PIPE_STATUS class method) rembi_module_override (phenotypic.abc_.MeasurementInfo attribute) (phenotypic.sdk_.constants_.ConstantLabels attribute) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS attribute) (phenotypic.sdk_.constants_.PIPE_STATUS attribute) remove_noise (phenotypic.detect.RoundPeaksDetector attribute) (phenotypic.detect.SinePeakDetector attribute) RemoveBorderObjects (class in phenotypic.refine) RemoveByFeature (class in phenotypic.refine) RemoveGridOutliers (class in phenotypic.refine) RemoveLowCircularity (class in phenotypic.refine) removeprefix() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) removesuffix() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) render() (phenotypic.abc_.BoundFigures method) render_error_analysis_html() (in module phenotypic.analysis) render_error_analysis_report() (in module phenotypic.analysis) replace() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) replicate_groupby (phenotypic.tune.score.ReferenceFreeScorer attribute) ReplicateAgreement (class in phenotypic.analysis) report() (phenotypic.tune.strategy.NoOpChannel method) (phenotypic.tune.strategy.PruningChannel method) requires_rgb (phenotypic.abc_.DetectionMode property) rescale_sigma (phenotypic.correction.BayesShrinkCorrector attribute) (phenotypic.correction.VisuShrinkCorrector attribute) (phenotypic.enhance.BayesShrinkEnhancer attribute) (phenotypic.enhance.VisuShrinkEnhancer attribute) reset (phenotypic.abc_.PrefabPipeline attribute) (phenotypic.prefab.FilamentousFungiPipeline attribute) (phenotypic.prefab.GridSectionPipeline attribute) (phenotypic.prefab.HeavyOtsuPipeline attribute) (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) (phenotypic.prefab.HeavyWatershedPipeline attribute) (phenotypic.prefab.RoundPeaksPipeline attribute) (phenotypic.prefab.SpImagerPipeline attribute) 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) RESIDUAL_ERR (phenotypic.sdk_.constants_.GRID_LINREG_STATS_EXTRACTOR attribute) residual_fraction (phenotypic.grid.AutoGridFinder attribute) (phenotypic.grid.CenteredAutoGridFinder attribute) resolve_best_pipeline_path() (in module phenotypic.sdk_) resolve_event_log_path() (in module phenotypic.sdk_) resolve_execution_mode() (in module phenotypic.sdk_) resolve_manifest_json_path() (in module phenotypic.sdk_) resolve_pipeline_config_path() (in module phenotypic.sdk_) resolve_processing_state_path() (in module phenotypic.sdk_) resolve_progress_dir() (in module phenotypic.sdk_) resolve_qc_dir() (in module phenotypic.sdk_) resolve_split_assignment_path() (in module phenotypic.sdk_) resolve_study_db_path() (in module phenotypic.sdk_) resolve_tuning_spec_path() (in module phenotypic.sdk_) resolved_kind (phenotypic.abc_.MeasurementInfo property) (phenotypic.sdk_.constants_.ConstantLabels property) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS property) (phenotypic.sdk_.constants_.PIPE_STATUS property) resolved_pipeline_config_path (phenotypic.sdk_.BundleLayout property) resolved_rembi_module (phenotypic.abc_.MeasurementInfo property) (phenotypic.sdk_.constants_.ConstantLabels property) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS property) (phenotypic.sdk_.constants_.PIPE_STATUS property) resolved_tier (phenotypic.abc_.MeasurementInfo property) (phenotypic.sdk_.constants_.ConstantLabels property) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS property) (phenotypic.sdk_.constants_.PIPE_STATUS property) response_floor (phenotypic.grid.CenteredAutoGridFinder attribute) results() (phenotypic.analysis.EdgeCorrector method) (phenotypic.analysis.ExpectedVsDetectedCount method) (phenotypic.analysis.GridOccupancy method) (phenotypic.analysis.ICC method) (phenotypic.analysis.LinearCapAndLagModel method) (phenotypic.analysis.LinearLagModel method) (phenotypic.analysis.LogGrowthModel method) (phenotypic.analysis.MADOutlierRemover method) (phenotypic.analysis.MaxModifiedZScore method) (phenotypic.analysis.RelativeMAD method) (phenotypic.analysis.ReplicateAgreement method) (phenotypic.analysis.TukeyOutlierFraction method) (phenotypic.analysis.TukeyOutlierRemover method) results_dir (phenotypic.sdk_.BundleLayout property) results_dir() (in module phenotypic.sdk_) rfind() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) rgb (phenotypic.Image property) RGB (phenotypic.sdk_.constants_.IMAGE_MODE attribute) RGB_OR_BGR (phenotypic.sdk_.constants_.IMAGE_MODE attribute) RGBA (phenotypic.sdk_.constants_.IMAGE_MODE attribute) RGBA_OR_BGRA (phenotypic.sdk_.constants_.IMAGE_MODE attribute) rho (phenotypic.enhance.StructureSmoothing attribute) (phenotypic.tune.score.CompositeScorer attribute) ridge_lambda (phenotypic.correction.ColorCheckerProfile attribute) ridge_method (phenotypic.util.StructureMetrics attribute) ridge_responses (phenotypic.util.StructureMetrics attribute) right (phenotypic.correction.ImageCropper attribute) (phenotypic.correction.ImagePadder attribute) rindex() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) rjust() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) rms_contrast (phenotypic.util.ContrastMetrics attribute) robust_color_center() (in module phenotypic.util) rois (phenotypic.correction.ColorCheckerProfile attribute) root (phenotypic.gui.builder._state._DagBuilderState attribute), [1] root_posix (phenotypic.sdk_.HDF attribute), [1] rotate() (phenotypic.Image method) RoundPeaksDetector (class in phenotypic.detect) RoundPeaksPipeline (class in phenotypic.prefab) row_edges (phenotypic.grid.ManualGridFinder attribute), [1] ROW_LINREG_B (phenotypic.sdk_.constants_.GRID_LINREG_STATS_EXTRACTOR attribute) ROW_LINREG_M (phenotypic.sdk_.constants_.GRID_LINREG_STATS_EXTRACTOR attribute) ROWS (phenotypic.sdk_.ChunkManifestKey attribute) rpartition() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) rsplit() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) rst_table() (phenotypic.abc_.MeasurementInfo class method) (phenotypic.sdk_.constants_.ConstantLabels class method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS class method) (phenotypic.sdk_.constants_.PIPE_STATUS class method) rstrip() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) run() (phenotypic.sdk_.napari_.LabelEditorWidget method) (phenotypic.sdk_.napari_.PointPickerWidget method) (phenotypic.tune.ScreeningController method) run_auto_space() (in module phenotypic.tune) run_held_out() (in module phenotypic.tune) run_tuning() (in module phenotypic.tune) rung_factor (phenotypic.tune.Evaluator attribute) rung_floor (phenotypic.tune.Evaluator attribute) S s0_prior (phenotypic.analysis.LinearCapAndLagModel attribute) (phenotypic.analysis.LinearLagModel attribute) s0_prior_cv (phenotypic.analysis.LinearCapAndLagModel attribute) (phenotypic.analysis.LinearLagModel attribute) s0_prior_groupby (phenotypic.analysis.LinearCapAndLagModel attribute) (phenotypic.analysis.LinearLagModel attribute) s0_prior_sigma (phenotypic.analysis.LinearCapAndLagModel attribute) (phenotypic.analysis.LinearLagModel attribute) safe_writer() (phenotypic.sdk_.HDF method) sampler (phenotypic.tune.strategy.OptunaConfig attribute) save2hdf5() (phenotypic.Image method) save2pickle() (phenotypic.Image method) save_array2hdf5() (phenotypic.sdk_.HDF static method) save_frame_append() (phenotypic.sdk_.HDF static method) save_frame_new() (phenotypic.sdk_.HDF static method) save_frame_update() (phenotypic.sdk_.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) save_series_new() (phenotypic.sdk_.HDF static method) save_series_update() (phenotypic.sdk_.HDF static method) scale (phenotypic.measure.MeasureTexture attribute) scale_factor (phenotypic.correction.DenoiseBlockMatch attribute) scales (phenotypic.util.StructureMetrics attribute) schema() (phenotypic.abc_.BackgroundSubtraction class method) (phenotypic.abc_.BaseOperation class method) (phenotypic.abc_.ContrastAdjustment class method) (phenotypic.abc_.FocusBlob class method) (phenotypic.abc_.FocusEdge class method) (phenotypic.abc_.GpuDetector class method) (phenotypic.abc_.GridCorrector class method) (phenotypic.abc_.GridFinder class method) (phenotypic.abc_.GridMeasureFeatures class method) (phenotypic.abc_.GridObjectDetector class method) (phenotypic.abc_.GridObjectRefiner class method) (phenotypic.abc_.GridOperation class method) (phenotypic.abc_.ImageCorrector class method) (phenotypic.abc_.ImageDenoiser class method) (phenotypic.abc_.ImageEnhancer class method) (phenotypic.abc_.ImageOperation class method) (phenotypic.abc_.MeasureFeatures class method) (phenotypic.abc_.MorphologicalFiltering class method) (phenotypic.abc_.ObjectDetector class method) (phenotypic.abc_.ObjectRefiner class method) (phenotypic.abc_.PostMeasurement class method) (phenotypic.abc_.PrefabPipeline class method) (phenotypic.abc_.Smoothing class method) (phenotypic.abc_.ThresholdDetector class method) (phenotypic.analysis.EdgeCorrector class method) (phenotypic.analysis.ErrorCutoffFinder class method) (phenotypic.analysis.ExpectedVsDetectedCount class method) (phenotypic.analysis.GridOccupancy class method) (phenotypic.analysis.ICC class method) (phenotypic.analysis.LinearCapAndLagModel class method) (phenotypic.analysis.LinearLagModel class method) (phenotypic.analysis.LogGrowthModel class method) (phenotypic.analysis.MADOutlierRemover class method) (phenotypic.analysis.MaxModifiedZScore class method) (phenotypic.analysis.RelativeMAD class method) (phenotypic.analysis.ReplicateAgreement class method) (phenotypic.analysis.TukeyOutlierFraction class method) (phenotypic.analysis.TukeyOutlierRemover class method) (phenotypic.correction.BayesShrinkCorrector class method) (phenotypic.correction.CaptureMetadata class method) (phenotypic.correction.ColorCheckerProfile class method) (phenotypic.correction.ColorCorrector class method) (phenotypic.correction.ColorDenoise class method) (phenotypic.correction.DenoiseBlockMatch class method) (phenotypic.correction.GridAligner class method) (phenotypic.correction.ImageCropper class method) (phenotypic.correction.ImagePadder class method) (phenotypic.correction.VisuShrinkCorrector class method) (phenotypic.detect.CannyDetector class method) (phenotypic.detect.ChanVeseDetector class method) (phenotypic.detect.CompositeDetector class method) (phenotypic.detect.FilamentousFungiDetector class method) (phenotypic.detect.HysteresisDetector class method) (phenotypic.detect.InoculumDetector class method) (phenotypic.detect.IsodataDetector class method) (phenotypic.detect.LiDetector class method) (phenotypic.detect.MadHysteresisDetector class method) (phenotypic.detect.ManualGridPointDetector class method) (phenotypic.detect.ManualPointDetector class method) (phenotypic.detect.MeanDetector class method) (phenotypic.detect.MinimumDetector class method) (phenotypic.detect.OtsuDetector class method) (phenotypic.detect.RankOtsuDetector class method) (phenotypic.detect.RoundPeaksDetector class method) (phenotypic.detect.SecondaryOtsuDetector class method) (phenotypic.detect.SinePeakDetector class method) (phenotypic.detect.TriangleDetector class method) (phenotypic.detect.UserThreshold class method) (phenotypic.detect.WatershedDetector class method) (phenotypic.detect.YenDetector class method) (phenotypic.enhance.BayesShrinkEnhancer class method) (phenotypic.enhance.CompositeEnhance class method) (phenotypic.enhance.ContrastStretching class method) (phenotypic.enhance.EnhanceBlockMatch class method) (phenotypic.enhance.EnhanceLocalContrast class method) (phenotypic.enhance.FlattenIllumination class method) (phenotypic.enhance.FocusBlobLoG class method) (phenotypic.enhance.FocusEdgeFrangi class method) (phenotypic.enhance.FocusEdgeHessian class method) (phenotypic.enhance.FocusEdgeLaplace class method) (phenotypic.enhance.FocusEdgeMeijering class method) (phenotypic.enhance.FocusEdgePhase class method) (phenotypic.enhance.FocusEdgeSato class method) (phenotypic.enhance.FocusEdgeSobel class method) (phenotypic.enhance.GaussianBlur class method) (phenotypic.enhance.GrayOpening class method) (phenotypic.enhance.ImageInverter class method) (phenotypic.enhance.LocalEdgeDenoise class method) (phenotypic.enhance.MedianFilter class method) (phenotypic.enhance.NonLocalMeansDenoiser class method) (phenotypic.enhance.RankMedianEnhancer class method) (phenotypic.enhance.SetDetectMode class method) (phenotypic.enhance.SharpenEdgeGauss class method) (phenotypic.enhance.StructureSmoothing class method) (phenotypic.enhance.SubtractGaussian class method) (phenotypic.enhance.SubtractOpening class method) (phenotypic.enhance.SubtractRollingBall class method) (phenotypic.enhance.SubtractWhiteTophat class method) (phenotypic.enhance.VisuShrinkEnhancer class method) (phenotypic.enhance.WhiteTophatEnhance class method) (phenotypic.grid.AutoGridFinder class method) (phenotypic.grid.CenteredAutoGridFinder class method) (phenotypic.grid.GridApply class method) (phenotypic.grid.ManualGridFinder class method) (phenotypic.measure.MeasureBounds class method) (phenotypic.measure.MeasureColor class method) (phenotypic.measure.MeasureGridLinRegStats class method) (phenotypic.measure.MeasureGridSpread class method) (phenotypic.measure.MeasureIntensity class method) (phenotypic.measure.MeasureNeighborDist class method) (phenotypic.measure.MeasureOrientationZones class method) (phenotypic.measure.MeasureShape class method) (phenotypic.measure.MeasureSize class method) (phenotypic.measure.MeasureSymmetricZones class method) (phenotypic.measure.MeasureTexture class method) (phenotypic.prefab.FilamentousFungiPipeline class method) (phenotypic.prefab.GridSectionPipeline class method) (phenotypic.prefab.HeavyOtsuPipeline class method) (phenotypic.prefab.HeavyRoundPeaksPipeline class method) (phenotypic.prefab.HeavyWatershedPipeline class method) (phenotypic.prefab.RoundPeaksPipeline class method) (phenotypic.prefab.SpImagerPipeline class method) (phenotypic.refine.ExtractColonyCore class method) (phenotypic.refine.GridAlignmentRefiner class method) (phenotypic.refine.GridOversizedObjectRemover class method) (phenotypic.refine.KeepNearestCenter class method) (phenotypic.refine.KeepSectionLargest class method) (phenotypic.refine.ManualRefine class method) (phenotypic.refine.MaskClosing class method) (phenotypic.refine.MaskDilation class method) (phenotypic.refine.MaskErosion class method) (phenotypic.refine.MaskFill class method) (phenotypic.refine.MaskGradient class method) (phenotypic.refine.MaskOpening class method) (phenotypic.refine.MaskWhiteTophat class method) (phenotypic.refine.MergeFragmentChains class method) (phenotypic.refine.NearestNeighborMerger class method) (phenotypic.refine.ReduceSectionsByLine class method) (phenotypic.refine.RefineBySineFit class method) (phenotypic.refine.RemoveBorderObjects class method) (phenotypic.refine.RemoveByFeature class method) (phenotypic.refine.RemoveGridOutliers class method) (phenotypic.refine.RemoveLowCircularity class method) (phenotypic.refine.SeparateObjects class method) (phenotypic.refine.Skeletonize class method) (phenotypic.refine.SmallObjectRemover class method) (phenotypic.refine.SmallToLargeMerger class method) (phenotypic.refine.Thinning class method) (phenotypic.refine.TrimAsymmetry class method) (phenotypic.tune.Budget class method) (phenotypic.tune.Categorical class method) (phenotypic.tune.EvaluationResult class method) (phenotypic.tune.Evaluator class method) (phenotypic.tune.Excluded class method) (phenotypic.tune.Fixed class method) (phenotypic.tune.FloatRange class method) (phenotypic.tune.HeldOutConfig class method) (phenotypic.tune.ImportanceReport class method) (phenotypic.tune.InferredSearchSpace class method) (phenotypic.tune.IntRange class method) (phenotypic.tune.Knob class method) (phenotypic.tune.score.CompositeScorer class method) (phenotypic.tune.score.GroundTruthMasks class method) (phenotypic.tune.score.QCScorer class method) (phenotypic.tune.score.ReferenceFreeScorer class method) (phenotypic.tune.score.Scorer class method) (phenotypic.tune.score.SupervisedScorer class method) (phenotypic.tune.SearchSpace class method) (phenotypic.tune.strategy.GridConfig class method) (phenotypic.tune.strategy.OptunaConfig class method) (phenotypic.tune.strategy.RandomConfig class method) (phenotypic.tune.strategy.StrategyConfig class method) (phenotypic.tune.Trial class method) (phenotypic.tune.TuningSpec class method) schema_json() (phenotypic.abc_.BackgroundSubtraction class method) (phenotypic.abc_.BaseOperation class method) (phenotypic.abc_.ContrastAdjustment class method) (phenotypic.abc_.FocusBlob class method) (phenotypic.abc_.FocusEdge class method) (phenotypic.abc_.GpuDetector class method) (phenotypic.abc_.GridCorrector class method) (phenotypic.abc_.GridFinder class method) (phenotypic.abc_.GridMeasureFeatures class method) (phenotypic.abc_.GridObjectDetector class method) (phenotypic.abc_.GridObjectRefiner class method) (phenotypic.abc_.GridOperation class method) (phenotypic.abc_.ImageCorrector class method) (phenotypic.abc_.ImageDenoiser class method) (phenotypic.abc_.ImageEnhancer class method) (phenotypic.abc_.ImageOperation class method) (phenotypic.abc_.MeasureFeatures class method) (phenotypic.abc_.MorphologicalFiltering class method) (phenotypic.abc_.ObjectDetector class method) (phenotypic.abc_.ObjectRefiner class method) (phenotypic.abc_.PostMeasurement class method) (phenotypic.abc_.PrefabPipeline class method) (phenotypic.abc_.Smoothing class method) (phenotypic.abc_.ThresholdDetector class method) (phenotypic.analysis.EdgeCorrector class method) (phenotypic.analysis.ErrorCutoffFinder class method) (phenotypic.analysis.ExpectedVsDetectedCount class method) (phenotypic.analysis.GridOccupancy class method) (phenotypic.analysis.ICC class method) (phenotypic.analysis.LinearCapAndLagModel class method) (phenotypic.analysis.LinearLagModel class method) (phenotypic.analysis.LogGrowthModel class method) (phenotypic.analysis.MADOutlierRemover class method) (phenotypic.analysis.MaxModifiedZScore class method) (phenotypic.analysis.RelativeMAD class method) (phenotypic.analysis.ReplicateAgreement class method) (phenotypic.analysis.TukeyOutlierFraction class method) (phenotypic.analysis.TukeyOutlierRemover class method) (phenotypic.correction.BayesShrinkCorrector class method) (phenotypic.correction.CaptureMetadata class method) (phenotypic.correction.ColorCheckerProfile class method) (phenotypic.correction.ColorCorrector class method) (phenotypic.correction.ColorDenoise class method) (phenotypic.correction.DenoiseBlockMatch class method) (phenotypic.correction.GridAligner class method) (phenotypic.correction.ImageCropper class method) (phenotypic.correction.ImagePadder class method) (phenotypic.correction.VisuShrinkCorrector class method) (phenotypic.detect.CannyDetector class method) (phenotypic.detect.ChanVeseDetector class method) (phenotypic.detect.CompositeDetector class method) (phenotypic.detect.FilamentousFungiDetector class method) (phenotypic.detect.HysteresisDetector class method) (phenotypic.detect.InoculumDetector class method) (phenotypic.detect.IsodataDetector class method) (phenotypic.detect.LiDetector class method) (phenotypic.detect.MadHysteresisDetector class method) (phenotypic.detect.ManualGridPointDetector class method) (phenotypic.detect.ManualPointDetector class method) (phenotypic.detect.MeanDetector class method) (phenotypic.detect.MinimumDetector class method) (phenotypic.detect.OtsuDetector class method) (phenotypic.detect.RankOtsuDetector class method) (phenotypic.detect.RoundPeaksDetector class method) (phenotypic.detect.SecondaryOtsuDetector class method) (phenotypic.detect.SinePeakDetector class method) (phenotypic.detect.TriangleDetector class method) (phenotypic.detect.UserThreshold class method) (phenotypic.detect.WatershedDetector class method) (phenotypic.detect.YenDetector class method) (phenotypic.enhance.BayesShrinkEnhancer class method) (phenotypic.enhance.CompositeEnhance class method) (phenotypic.enhance.ContrastStretching class method) (phenotypic.enhance.EnhanceBlockMatch class method) (phenotypic.enhance.EnhanceLocalContrast class method) (phenotypic.enhance.FlattenIllumination class method) (phenotypic.enhance.FocusBlobLoG class method) (phenotypic.enhance.FocusEdgeFrangi class method) (phenotypic.enhance.FocusEdgeHessian class method) (phenotypic.enhance.FocusEdgeLaplace class method) (phenotypic.enhance.FocusEdgeMeijering class method) (phenotypic.enhance.FocusEdgePhase class method) (phenotypic.enhance.FocusEdgeSato class method) (phenotypic.enhance.FocusEdgeSobel class method) (phenotypic.enhance.GaussianBlur class method) (phenotypic.enhance.GrayOpening class method) (phenotypic.enhance.ImageInverter class method) (phenotypic.enhance.LocalEdgeDenoise class method) (phenotypic.enhance.MedianFilter class method) (phenotypic.enhance.NonLocalMeansDenoiser class method) (phenotypic.enhance.RankMedianEnhancer class method) (phenotypic.enhance.SetDetectMode class method) (phenotypic.enhance.SharpenEdgeGauss class method) (phenotypic.enhance.StructureSmoothing class method) (phenotypic.enhance.SubtractGaussian class method) (phenotypic.enhance.SubtractOpening class method) (phenotypic.enhance.SubtractRollingBall class method) (phenotypic.enhance.SubtractWhiteTophat class method) (phenotypic.enhance.VisuShrinkEnhancer class method) (phenotypic.enhance.WhiteTophatEnhance class method) (phenotypic.grid.AutoGridFinder class method) (phenotypic.grid.CenteredAutoGridFinder class method) (phenotypic.grid.GridApply class method) (phenotypic.grid.ManualGridFinder class method) (phenotypic.measure.MeasureBounds class method) (phenotypic.measure.MeasureColor class method) (phenotypic.measure.MeasureGridLinRegStats class method) (phenotypic.measure.MeasureGridSpread class method) (phenotypic.measure.MeasureIntensity class method) (phenotypic.measure.MeasureNeighborDist class method) (phenotypic.measure.MeasureOrientationZones class method) (phenotypic.measure.MeasureShape class method) (phenotypic.measure.MeasureSize class method) (phenotypic.measure.MeasureSymmetricZones class method) (phenotypic.measure.MeasureTexture class method) (phenotypic.prefab.FilamentousFungiPipeline class method) (phenotypic.prefab.GridSectionPipeline class method) (phenotypic.prefab.HeavyOtsuPipeline class method) (phenotypic.prefab.HeavyRoundPeaksPipeline class method) (phenotypic.prefab.HeavyWatershedPipeline class method) (phenotypic.prefab.RoundPeaksPipeline class method) (phenotypic.prefab.SpImagerPipeline class method) (phenotypic.refine.ExtractColonyCore class method) (phenotypic.refine.GridAlignmentRefiner class method) (phenotypic.refine.GridOversizedObjectRemover class method) (phenotypic.refine.KeepNearestCenter class method) (phenotypic.refine.KeepSectionLargest class method) (phenotypic.refine.ManualRefine class method) (phenotypic.refine.MaskClosing class method) (phenotypic.refine.MaskDilation class method) (phenotypic.refine.MaskErosion class method) (phenotypic.refine.MaskFill class method) (phenotypic.refine.MaskGradient class method) (phenotypic.refine.MaskOpening class method) (phenotypic.refine.MaskWhiteTophat class method) (phenotypic.refine.MergeFragmentChains class method) (phenotypic.refine.NearestNeighborMerger class method) (phenotypic.refine.ReduceSectionsByLine class method) (phenotypic.refine.RefineBySineFit class method) (phenotypic.refine.RemoveBorderObjects class method) (phenotypic.refine.RemoveByFeature class method) (phenotypic.refine.RemoveGridOutliers class method) (phenotypic.refine.RemoveLowCircularity class method) (phenotypic.refine.SeparateObjects class method) (phenotypic.refine.Skeletonize class method) (phenotypic.refine.SmallObjectRemover class method) (phenotypic.refine.SmallToLargeMerger class method) (phenotypic.refine.Thinning class method) (phenotypic.refine.TrimAsymmetry class method) (phenotypic.tune.Budget class method) (phenotypic.tune.Categorical class method) (phenotypic.tune.EvaluationResult class method) (phenotypic.tune.Evaluator class method) (phenotypic.tune.Excluded class method) (phenotypic.tune.Fixed class method) (phenotypic.tune.FloatRange class method) (phenotypic.tune.HeldOutConfig class method) (phenotypic.tune.ImportanceReport class method) (phenotypic.tune.InferredSearchSpace class method) (phenotypic.tune.IntRange class method) (phenotypic.tune.Knob class method) (phenotypic.tune.score.CompositeScorer class method) (phenotypic.tune.score.GroundTruthMasks class method) (phenotypic.tune.score.QCScorer class method) (phenotypic.tune.score.ReferenceFreeScorer class method) (phenotypic.tune.score.Scorer class method) (phenotypic.tune.score.SupervisedScorer class method) (phenotypic.tune.SearchSpace class method) (phenotypic.tune.strategy.GridConfig class method) (phenotypic.tune.strategy.OptunaConfig class method) (phenotypic.tune.strategy.RandomConfig class method) (phenotypic.tune.strategy.StrategyConfig class method) (phenotypic.tune.Trial class method) (phenotypic.tune.TuningSpec class method) scope_path (phenotypic.gui.builder._validation.Issue attribute), [1] score (phenotypic.tune.EvaluationResult attribute) (phenotypic.tune.Trial attribute) score_image() (phenotypic.tune.score.CompositeScorer method) (phenotypic.tune.score.QCScorer method) (phenotypic.tune.score.ReferenceFreeScorer method) (phenotypic.tune.score.Scorer method) (phenotypic.tune.score.SupervisedScorer method) Scorer (class in phenotypic.tune.score) scorer (phenotypic.tune.TuningSpec attribute) scorers (phenotypic.tune.score.CompositeScorer attribute) SCRATCH (phenotypic.sdk_.EnvVar attribute) screened (phenotypic.tune.ScreeningResult attribute) screening_warmup_floor() (in module phenotypic.tune) ScreeningConfig (class in phenotypic.tune) ScreeningController (class in phenotypic.tune) ScreeningResult (class in phenotypic.tune) search_dist (phenotypic.enhance.NonLocalMeansDenoiser attribute) search_space (phenotypic.tune.TuningSpec attribute) SearchSpace (class in phenotypic.tune) SearchStrategy (class in phenotypic.tune.strategy) SecondaryOtsuDetector (class in phenotypic.detect) section (phenotypic.abc_.FigureSpec attribute), [1] section_num (phenotypic.measure.MeasureGridLinRegStats attribute) seed (phenotypic.tune.strategy.GridConfig attribute) (phenotypic.tune.strategy.OptunaConfig attribute) (phenotypic.tune.strategy.RandomConfig attribute) (phenotypic.tune.strategy.StrategyConfig attribute) select_params_to_freeze() (in module phenotypic.tune) 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_mode (phenotypic.detect.RoundPeaksDetector attribute) (phenotypic.detect.SinePeakDetector attribute) (phenotypic.refine.GridAlignmentRefiner attribute) (phenotypic.refine.RefineBySineFit attribute) sentinel_resubmitted_path() (in module phenotypic.sdk_) SeparateObjects (class in phenotypic.refine) separation_threshold (phenotypic.refine.ExtractColonyCore attribute) set_active_set() (phenotypic.tune.score.CompositeScorer method) set_data_posix (phenotypic.sdk_.HDF attribute), [1] set_filters() (phenotypic.abc_.PrefabPipeline method) (phenotypic.prefab.FilamentousFungiPipeline method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.prefab.RoundPeaksPipeline method) (phenotypic.prefab.SpImagerPipeline method) set_meas() (phenotypic.abc_.PrefabPipeline method) (phenotypic.ImagePipeline method) (phenotypic.prefab.FilamentousFungiPipeline method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.prefab.RoundPeaksPipeline method) (phenotypic.prefab.SpImagerPipeline method) set_model() (phenotypic.abc_.PrefabPipeline method) (phenotypic.prefab.FilamentousFungiPipeline method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.prefab.RoundPeaksPipeline method) (phenotypic.prefab.SpImagerPipeline method) set_ops() (phenotypic.abc_.PrefabPipeline method) (phenotypic.ImagePipeline method) (phenotypic.prefab.FilamentousFungiPipeline method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.prefab.RoundPeaksPipeline method) (phenotypic.prefab.SpImagerPipeline method) set_post() (phenotypic.abc_.PrefabPipeline method) (phenotypic.prefab.FilamentousFungiPipeline method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.prefab.RoundPeaksPipeline method) (phenotypic.prefab.SpImagerPipeline method) set_qc() (phenotypic.abc_.PrefabPipeline method) (phenotypic.prefab.FilamentousFungiPipeline method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.prefab.RoundPeaksPipeline method) (phenotypic.prefab.SpImagerPipeline method) setdefault() (phenotypic.util.BackgroundMetrics method) (phenotypic.util.ContrastMetrics method) (phenotypic.util.NoiseMetrics method) (phenotypic.util.QualityScores method) (phenotypic.util.StructureMetrics method) SetDetectMode (class in phenotypic.enhance) severity (phenotypic.gui.builder._validation.Issue attribute), [1] 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) (phenotypic.detect.ManualPointDetector attribute) (phenotypic.detect.RankOtsuDetector attribute) (phenotypic.enhance.GrayOpening attribute) (phenotypic.enhance.MedianFilter attribute) (phenotypic.enhance.RankMedianEnhancer attribute) (phenotypic.enhance.SubtractOpening attribute) (phenotypic.enhance.SubtractWhiteTophat attribute) (phenotypic.enhance.WhiteTophatEnhance attribute) (phenotypic.refine.ManualRefine attribute) (phenotypic.refine.MaskClosing attribute) (phenotypic.refine.MaskDilation attribute) (phenotypic.refine.MaskErosion attribute) (phenotypic.refine.MaskGradient attribute) (phenotypic.refine.MaskOpening attribute) (phenotypic.refine.MaskWhiteTophat attribute) shard_parquet_filename() (in module phenotypic.sdk_) SharpenEdgeGauss (class in phenotypic.enhance) Sharpness (phenotypic.util.QualityScores attribute) shift_x (phenotypic.enhance.RankMedianEnhancer attribute) shift_y (phenotypic.enhance.RankMedianEnhancer attribute) should_prune() (phenotypic.tune.strategy.NoOpChannel method) (phenotypic.tune.strategy.PruningChannel method) shoulder_slope_ratio (phenotypic.analysis.LinearCapAndLagModel attribute) 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.EdgeCorrector method) (phenotypic.analysis.ExpectedVsDetectedCount method) (phenotypic.analysis.GridOccupancy method) (phenotypic.analysis.ICC method) (phenotypic.analysis.LinearCapAndLagModel method) (phenotypic.analysis.LinearLagModel method) (phenotypic.analysis.LogGrowthModel method) (phenotypic.analysis.MADOutlierRemover method) (phenotypic.analysis.MaxModifiedZScore method) (phenotypic.analysis.RelativeMAD method) (phenotypic.analysis.ReplicateAgreement method) (phenotypic.analysis.TukeyOutlierFraction method) (phenotypic.analysis.TukeyOutlierRemover method) (phenotypic.Image method) sigma (phenotypic.correction.BayesShrinkCorrector attribute) (phenotypic.correction.DenoiseBlockMatch attribute) (phenotypic.correction.VisuShrinkCorrector attribute) (phenotypic.detect.CannyDetector attribute) (phenotypic.enhance.BayesShrinkEnhancer attribute) (phenotypic.enhance.FlattenIllumination attribute) (phenotypic.enhance.GaussianBlur attribute) (phenotypic.enhance.NonLocalMeansDenoiser attribute) (phenotypic.enhance.StructureSmoothing attribute) (phenotypic.enhance.SubtractGaussian attribute) (phenotypic.enhance.VisuShrinkEnhancer attribute) sigma_color (phenotypic.enhance.LocalEdgeDenoise attribute) sigma_d (phenotypic.measure.MeasureOrientationZones attribute) sigma_i (phenotypic.measure.MeasureOrientationZones attribute) sigma_mad (phenotypic.util.NoiseMetrics attribute) sigma_onf (phenotypic.enhance.FocusEdgePhase attribute) sigma_psd (phenotypic.correction.ColorDenoise attribute) (phenotypic.enhance.EnhanceBlockMatch attribute) sigma_spatial (phenotypic.enhance.LocalEdgeDenoise attribute) sigmas (phenotypic.enhance.FocusEdgeFrangi attribute) (phenotypic.enhance.FocusEdgeHessian attribute) (phenotypic.enhance.FocusEdgeMeijering attribute) (phenotypic.enhance.FocusEdgeSato attribute) SinePeakDetector (class in phenotypic.detect) SINGLE_IMAGE_HDF5_PARENT_GROUP (phenotypic.sdk_.constants_.IO attribute) SINGLE_IMAGE_ROOT_POSIX (phenotypic.sdk_.HDF attribute), [1] 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) size_viewer() (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) Skeletonize (class in phenotypic.refine) slices (phenotypic._core._image_parts.accessors._objects_accessor.ObjectsAccessor property) SLURM_ARRAY_JOB_ID (phenotypic.sdk_.EnvVar attribute) SLURM_ARRAY_TASK_COUNT (phenotypic.sdk_.EnvVar attribute) SLURM_ARRAY_TASK_ID (phenotypic.sdk_.EnvVar attribute) SLURM_CPUS_PER_TASK (phenotypic.sdk_.EnvVar attribute) SLURM_INFO (phenotypic.sdk_.DashboardManifestKey attribute) SLURM_JOB_ID (phenotypic.sdk_.EnvVar attribute) SLURM_JOB_IDS (phenotypic.sdk_.JobMetadataKey attribute) SLURM_MEM_PER_NODE (phenotypic.sdk_.EnvVar attribute) slurm_scripts_dir() (in module phenotypic.sdk_) small_object_min_size (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) SmallObjectRemover (class in phenotypic.refine) SmallToLargeMerger (class in phenotypic.refine) smax (phenotypic.analysis.LinearCapAndLagModel attribute) Smoothing (class in phenotypic.abc_) smoothing_sigma (phenotypic.detect.RoundPeaksDetector attribute) (phenotypic.detect.SinePeakDetector attribute) (phenotypic.refine.GridAlignmentRefiner attribute) (phenotypic.refine.RefineBySineFit attribute) smoothing_window (phenotypic.measure.MeasureOrientationZones attribute) (phenotypic.measure.MeasureSymmetricZones attribute) (phenotypic.refine.TrimAsymmetry attribute) snr (phenotypic.util.NoiseMetrics attribute) SNR (phenotypic.util.QualityScores attribute) snr_margin (phenotypic.detect.FilamentousFungiDetector attribute) source (phenotypic.tune.Knob attribute) source_block_id (phenotypic.gui.builder._state.Edge attribute), [1] source_port (phenotypic.gui.builder._state.Edge attribute), [1] SPAN_PCT_HIGH (phenotypic.grid.CenteredAutoGridFinder attribute) SPAN_PCT_LOW (phenotypic.grid.CenteredAutoGridFinder attribute) spatial_size_map() (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) specs() (phenotypic.abc_.BoundFigures method) SpImagerPipeline (class in phenotypic.prefab) split() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) split_disconnected_labels (phenotypic.abc_.GpuDetector attribute) split_measurements() (in module phenotypic.util) split_merged (phenotypic.detect.RoundPeaksDetector attribute) (phenotypic.detect.SinePeakDetector attribute) (phenotypic.refine.GridAlignmentRefiner attribute) (phenotypic.refine.RefineBySineFit attribute) splitlines() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) SRGB (phenotypic.sdk_.constants_.GAMMA_ENCODINGS attribute) stability_weight (phenotypic.tune.Evaluator attribute) stage_arg (phenotypic.correction.DenoiseBlockMatch attribute) (phenotypic.enhance.EnhanceBlockMatch attribute) START_TIME (phenotypic.sdk_.DashboardManifestKey attribute) (phenotypic.sdk_.JobMetadataKey attribute) STARTED (phenotypic.sdk_.DashboardManifestKey attribute) (phenotypic.sdk_.ProcessingStateKey attribute) startswith() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) status_col() (phenotypic.analysis.ExpectedVsDetectedCount class method) (phenotypic.analysis.GridOccupancy class method) (phenotypic.analysis.ICC class method) (phenotypic.analysis.MaxModifiedZScore class method) (phenotypic.analysis.RelativeMAD class method) (phenotypic.analysis.ReplicateAgreement class method) (phenotypic.analysis.TukeyOutlierFraction class method) stddev_mag_threshold (phenotypic.correction.ColorCheckerProfile attribute) stderr_label (phenotypic.analysis.LinearCapAndLagModel attribute) (phenotypic.analysis.LinearLagModel attribute) step (phenotypic.abc_.Control attribute) (phenotypic.tune.FloatRange attribute) (phenotypic.tune.IntRange attribute) (phenotypic.tune.TuneSpec attribute) storage_url (phenotypic.tune.strategy.OptunaConfig attribute) store (phenotypic.tune.TuningEngine property) strategy (phenotypic.tune.TuningSpec attribute) StrategyConfig (class in phenotypic.tune.strategy) strict_writer() (phenotypic.sdk_.HDF method) strip() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) structural_response_curve() (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) structure (phenotypic.refine.MaskFill attribute) StructureMetrics (class in phenotypic.util) StructureSmoothing (class in phenotypic.enhance) StudyStore (in module phenotypic.tune) subject (phenotypic.abc_.BoundFigures property) subject_label (phenotypic.analysis.ICC attribute) subject_param (phenotypic.abc_.FigureSpec attribute), [1] submit_drip_feed_start() (in module phenotypic.sdk_.slurm) submit_script() (in module phenotypic.sdk_.slurm) subtract_background (phenotypic.detect.RoundPeaksDetector attribute) (phenotypic.detect.SinePeakDetector attribute) SubtractGaussian (class in phenotypic.enhance) SubtractOpening (class in phenotypic.enhance) SubtractRollingBall (class in phenotypic.enhance) SubtractWhiteTophat (class in phenotypic.enhance) SUCCESS_RATE (phenotypic.sdk_.DashboardManifestKey attribute) suggest() (phenotypic.tune.strategy.GridStrategy method) (phenotypic.tune.strategy.RandomStrategy method) (phenotypic.tune.strategy.SearchStrategy method) summary() (phenotypic.analysis.ExpectedVsDetectedCount method) (phenotypic.analysis.GridOccupancy method) (phenotypic.analysis.ICC method) (phenotypic.analysis.MaxModifiedZScore method) (phenotypic.analysis.RelativeMAD method) (phenotypic.analysis.ReplicateAgreement method) (phenotypic.analysis.TukeyOutlierFraction method) SupervisedScorer (class in phenotypic.tune.score) SUPPORTED_FORMATS (phenotypic.sdk_.constants_.IMAGE_MODE attribute) supports_batching (phenotypic.abc_.GpuDetector attribute) supports_object_curation (phenotypic.analysis.ExpectedVsDetectedCount attribute) (phenotypic.analysis.GridOccupancy attribute) (phenotypic.analysis.ICC attribute) (phenotypic.analysis.MaxModifiedZScore attribute) (phenotypic.analysis.RelativeMAD attribute) (phenotypic.analysis.ReplicateAgreement attribute) (phenotypic.analysis.TukeyOutlierFraction attribute) suspicious (phenotypic.tune.EvaluationResult attribute) (phenotypic.tune.Trial attribute) suspicious_count_floor (phenotypic.tune.Evaluator attribute) suspicious_score_floor (phenotypic.tune.Evaluator attribute) swapcase() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) swmr_reader() (phenotypic.sdk_.HDF method) swmr_writer() (phenotypic.sdk_.HDF method) symmetry_threshold (phenotypic.measure.MeasureOrientationZones attribute) (phenotypic.measure.MeasureSymmetricZones attribute) (phenotypic.refine.TrimAsymmetry attribute) T table() (phenotypic._core._image_parts.accessors._metadata_accessor.MetadataAccessor method) table_spec() (phenotypic.analysis.ExpectedVsDetectedCount method) (phenotypic.analysis.GridOccupancy method) (phenotypic.analysis.ICC method) (phenotypic.analysis.MaxModifiedZScore method) (phenotypic.analysis.RelativeMAD method) (phenotypic.analysis.ReplicateAgreement method) (phenotypic.analysis.TukeyOutlierFraction method) target (phenotypic.tune.Knob attribute) target_block_id (phenotypic.gui.builder._state.Edge attribute), [1] target_illuminant (phenotypic.correction.ColorCheckerProfile attribute) target_port (phenotypic.gui.builder._state.Edge attribute), [1] target_slot (phenotypic.gui.builder._state.Edge attribute), [1] targets() (phenotypic.tune.SearchSpace method) task_status_filename() (in module phenotypic.sdk_) task_status_path() (in module phenotypic.sdk_) tau_core (phenotypic.measure.MeasureOrientationZones attribute) (phenotypic.measure.MeasureSymmetricZones attribute) tau_dense (phenotypic.measure.MeasureOrientationZones attribute) (phenotypic.measure.MeasureSymmetricZones attribute) tau_sparse (phenotypic.measure.MeasureOrientationZones attribute) (phenotypic.measure.MeasureSymmetricZones attribute) term_name (phenotypic.tune.score.QCScorer attribute) terms (phenotypic.tune.EvaluationResult attribute) (phenotypic.tune.Trial attribute) texture_enhance (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) texture_quant_lvl (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) texture_scale (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) texture_warn (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) Thinning (class in phenotypic.refine) thresh_method (phenotypic.detect.InoculumDetector attribute) (phenotypic.detect.RoundPeaksDetector attribute) (phenotypic.detect.SinePeakDetector attribute) threshold (phenotypic.analysis.MADOutlierRemover attribute), [1] (phenotypic.detect.UserThreshold attribute) ThresholdDetector (class in phenotypic.abc_) tier() (phenotypic.abc_.MeasurementInfo class method) (phenotypic.sdk_.constants_.ConstantLabels class method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS class method) (phenotypic.sdk_.constants_.PIPE_STATUS class method) tier_override (phenotypic.abc_.MeasurementInfo attribute) (phenotypic.sdk_.constants_.ConstantLabels attribute) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS attribute) (phenotypic.sdk_.constants_.PIPE_STATUS attribute) TIFF_EXTENSIONS (phenotypic.sdk_.constants_.IO attribute) tile_overlap (phenotypic.detect.FilamentousFungiDetector attribute) tile_size (phenotypic.detect.FilamentousFungiDetector attribute) time_label (phenotypic.analysis.EdgeCorrector attribute) (phenotypic.analysis.LinearCapAndLagModel attribute) (phenotypic.analysis.LinearLagModel attribute) (phenotypic.analysis.LogGrowthModel attribute) (phenotypic.analysis.MaxModifiedZScore attribute) (phenotypic.analysis.RelativeMAD attribute) (phenotypic.analysis.ReplicateAgreement attribute) (phenotypic.analysis.TukeyOutlierFraction attribute) timed_execution() (in module phenotypic.sdk_) TIMESTAMP (phenotypic.sdk_.ProcessingStateKey attribute) title (phenotypic.abc_.FigureSpec attribute), [1] title() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) to_dataframe() (phenotypic.tune.JournalStudyStore method) to_dict() (phenotypic.tune.GeneralizationReport method) to_json() (phenotypic.abc_.BackgroundSubtraction method) (phenotypic.abc_.BaseOperation method) (phenotypic.abc_.ContrastAdjustment method) (phenotypic.abc_.FocusBlob method) (phenotypic.abc_.FocusEdge method) (phenotypic.abc_.GpuDetector method) (phenotypic.abc_.GridCorrector method) (phenotypic.abc_.GridFinder method) (phenotypic.abc_.GridMeasureFeatures method) (phenotypic.abc_.GridObjectDetector method) (phenotypic.abc_.GridObjectRefiner method) (phenotypic.abc_.GridOperation method) (phenotypic.abc_.ImageCorrector method) (phenotypic.abc_.ImageDenoiser method) (phenotypic.abc_.ImageEnhancer method) (phenotypic.abc_.ImageOperation method) (phenotypic.abc_.MeasureFeatures method) (phenotypic.abc_.MorphologicalFiltering method) (phenotypic.abc_.ObjectDetector method) (phenotypic.abc_.ObjectRefiner method) (phenotypic.abc_.PostMeasurement method) (phenotypic.abc_.PrefabPipeline method) (phenotypic.abc_.Smoothing method) (phenotypic.abc_.ThresholdDetector method) (phenotypic.correction.BayesShrinkCorrector method) (phenotypic.correction.ColorCheckerProfile method) (phenotypic.correction.ColorCorrector method) (phenotypic.correction.ColorDenoise method) (phenotypic.correction.DenoiseBlockMatch method) (phenotypic.correction.GridAligner method) (phenotypic.correction.ImageCropper method) (phenotypic.correction.ImagePadder method) (phenotypic.correction.VisuShrinkCorrector method) (phenotypic.detect.CannyDetector method) (phenotypic.detect.ChanVeseDetector method) (phenotypic.detect.CompositeDetector method) (phenotypic.detect.FilamentousFungiDetector method) (phenotypic.detect.HysteresisDetector method) (phenotypic.detect.InoculumDetector method) (phenotypic.detect.IsodataDetector method) (phenotypic.detect.LiDetector method) (phenotypic.detect.MadHysteresisDetector method) (phenotypic.detect.ManualGridPointDetector method) (phenotypic.detect.ManualPointDetector method) (phenotypic.detect.MeanDetector method) (phenotypic.detect.MinimumDetector method) (phenotypic.detect.OtsuDetector method) (phenotypic.detect.RankOtsuDetector method) (phenotypic.detect.RoundPeaksDetector method) (phenotypic.detect.SecondaryOtsuDetector method) (phenotypic.detect.SinePeakDetector method) (phenotypic.detect.TriangleDetector method) (phenotypic.detect.UserThreshold method) (phenotypic.detect.WatershedDetector method) (phenotypic.detect.YenDetector method) (phenotypic.enhance.BayesShrinkEnhancer method) (phenotypic.enhance.CompositeEnhance method) (phenotypic.enhance.ContrastStretching method) (phenotypic.enhance.EnhanceBlockMatch method) (phenotypic.enhance.EnhanceLocalContrast method) (phenotypic.enhance.FlattenIllumination method) (phenotypic.enhance.FocusBlobLoG method) (phenotypic.enhance.FocusEdgeFrangi method) (phenotypic.enhance.FocusEdgeHessian method) (phenotypic.enhance.FocusEdgeLaplace method) (phenotypic.enhance.FocusEdgeMeijering method) (phenotypic.enhance.FocusEdgePhase method) (phenotypic.enhance.FocusEdgeSato method) (phenotypic.enhance.FocusEdgeSobel method) (phenotypic.enhance.GaussianBlur method) (phenotypic.enhance.GrayOpening method) (phenotypic.enhance.ImageInverter method) (phenotypic.enhance.LocalEdgeDenoise method) (phenotypic.enhance.MedianFilter method) (phenotypic.enhance.NonLocalMeansDenoiser method) (phenotypic.enhance.RankMedianEnhancer method) (phenotypic.enhance.SetDetectMode method) (phenotypic.enhance.SharpenEdgeGauss method) (phenotypic.enhance.StructureSmoothing method) (phenotypic.enhance.SubtractGaussian method) (phenotypic.enhance.SubtractOpening method) (phenotypic.enhance.SubtractRollingBall method) (phenotypic.enhance.SubtractWhiteTophat method) (phenotypic.enhance.VisuShrinkEnhancer method) (phenotypic.enhance.WhiteTophatEnhance method) (phenotypic.grid.AutoGridFinder method) (phenotypic.grid.CenteredAutoGridFinder method) (phenotypic.grid.GridApply method) (phenotypic.grid.ManualGridFinder method) (phenotypic.ImagePipeline method) (phenotypic.measure.MeasureBounds method) (phenotypic.measure.MeasureColor method) (phenotypic.measure.MeasureGridLinRegStats method) (phenotypic.measure.MeasureGridSpread method) (phenotypic.measure.MeasureIntensity method) (phenotypic.measure.MeasureNeighborDist method) (phenotypic.measure.MeasureOrientationZones method) (phenotypic.measure.MeasureShape method) (phenotypic.measure.MeasureSize method) (phenotypic.measure.MeasureSymmetricZones method) (phenotypic.measure.MeasureTexture method) (phenotypic.prefab.FilamentousFungiPipeline method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.prefab.RoundPeaksPipeline method) (phenotypic.prefab.SpImagerPipeline method) (phenotypic.refine.ExtractColonyCore method) (phenotypic.refine.GridAlignmentRefiner method) (phenotypic.refine.GridOversizedObjectRemover method) (phenotypic.refine.KeepNearestCenter method) (phenotypic.refine.KeepSectionLargest method) (phenotypic.refine.ManualRefine method) (phenotypic.refine.MaskClosing method) (phenotypic.refine.MaskDilation method) (phenotypic.refine.MaskErosion method) (phenotypic.refine.MaskFill method) (phenotypic.refine.MaskGradient method) (phenotypic.refine.MaskOpening method) (phenotypic.refine.MaskWhiteTophat method) (phenotypic.refine.MergeFragmentChains method) (phenotypic.refine.NearestNeighborMerger method) (phenotypic.refine.ReduceSectionsByLine method) (phenotypic.refine.RefineBySineFit method) (phenotypic.refine.RemoveBorderObjects method) (phenotypic.refine.RemoveByFeature method) (phenotypic.refine.RemoveGridOutliers method) (phenotypic.refine.RemoveLowCircularity method) (phenotypic.refine.SeparateObjects method) (phenotypic.refine.Skeletonize method) (phenotypic.refine.SmallObjectRemover method) (phenotypic.refine.SmallToLargeMerger method) (phenotypic.refine.Thinning method) (phenotypic.refine.TrimAsymmetry method) (phenotypic.tune.TuningSpec method) to_parquet() (phenotypic.tune.JournalStudyStore method) to_pipeline_dag() (in module phenotypic.gui.builder._conversion_dag) to_search_space() (phenotypic.tune.InferredSearchSpace method) to_table() (phenotypic.analysis.ExpectedVsDetectedCount method) (phenotypic.analysis.GridOccupancy method) (phenotypic.analysis.ICC method) (phenotypic.analysis.MaxModifiedZScore method) (phenotypic.analysis.RelativeMAD method) (phenotypic.analysis.ReplicateAgreement method) (phenotypic.analysis.TukeyOutlierFraction method) toast_queue (phenotypic.gui.builder._state._DagBuilderState attribute), [1] tol (phenotypic.detect.ChanVeseDetector attribute) (phenotypic.grid.AutoGridFinder attribute) top (phenotypic.correction.ImageCropper attribute) (phenotypic.correction.ImagePadder attribute) top_k (phenotypic.tune.ScreeningConfig attribute) top_n (phenotypic.analysis.EdgeCorrector attribute) TOTAL_CHUNKS (phenotypic.sdk_.DashboardManifestSlurmInfoKey attribute) TOTAL_IMAGES (phenotypic.sdk_.DashboardManifestKey attribute) TOTAL_ROWS (phenotypic.sdk_.ChunkManifestKey attribute) translate() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) Trial (class in phenotypic.tune) trials (phenotypic.tune.JournalStudyStore property) trials_parquet_path() (in module phenotypic.sdk_) TriangleDetector (class in phenotypic.detect) TrimAsymmetry (class in phenotypic.refine) truncate (phenotypic.enhance.GaussianBlur attribute) (phenotypic.enhance.SubtractGaussian attribute) try_thresh() (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) TukeyOutlierFraction (class in phenotypic.analysis) TukeyOutlierRemover (class in phenotypic.analysis) tunable (phenotypic.tune.TuneSpec attribute) tune_cache_dir() (in module phenotypic.sdk_) tune_cache_run_marker_path() (in module phenotypic.sdk_) tune_cache_split_assignment_path() (in module phenotypic.sdk_) tune_cache_splits_dir() (in module phenotypic.sdk_) tune_cache_study_db_path() (in module phenotypic.sdk_) TuneSpec (class in phenotypic.tune) tuning_spec_path() (in module phenotypic.sdk_) TuningEngine (class in phenotypic.tune) TuningSpec (class in phenotypic.tune) U Uniformity (phenotypic.util.QualityScores attribute) UnknownError unmatched_groups (phenotypic.analysis.ExpectedVsDetectedCount attribute) (phenotypic.analysis.GridOccupancy attribute) (phenotypic.analysis.ICC attribute) (phenotypic.analysis.MaxModifiedZScore attribute) (phenotypic.analysis.RelativeMAD attribute) (phenotypic.analysis.ReplicateAgreement attribute) (phenotypic.analysis.TukeyOutlierFraction attribute) UnsupportedFileTypeError UnsupportedImageFormat update() (phenotypic.util.BackgroundMetrics method) (phenotypic.util.ContrastMetrics method) (phenotypic.util.NoiseMetrics method) (phenotypic.util.QualityScores method) (phenotypic.util.StructureMetrics method) update_forward_refs() (phenotypic.abc_.BackgroundSubtraction class method) (phenotypic.abc_.BaseOperation class method) (phenotypic.abc_.ContrastAdjustment class method) (phenotypic.abc_.FocusBlob class method) (phenotypic.abc_.FocusEdge class method) (phenotypic.abc_.GpuDetector class method) (phenotypic.abc_.GridCorrector class method) (phenotypic.abc_.GridFinder class method) (phenotypic.abc_.GridMeasureFeatures class method) (phenotypic.abc_.GridObjectDetector class method) (phenotypic.abc_.GridObjectRefiner class method) (phenotypic.abc_.GridOperation class method) (phenotypic.abc_.ImageCorrector class method) (phenotypic.abc_.ImageDenoiser class method) (phenotypic.abc_.ImageEnhancer class method) (phenotypic.abc_.ImageOperation class method) (phenotypic.abc_.MeasureFeatures class method) (phenotypic.abc_.MorphologicalFiltering class method) (phenotypic.abc_.ObjectDetector class method) (phenotypic.abc_.ObjectRefiner class method) (phenotypic.abc_.PostMeasurement class method) (phenotypic.abc_.PrefabPipeline class method) (phenotypic.abc_.Smoothing class method) (phenotypic.abc_.ThresholdDetector class method) (phenotypic.analysis.EdgeCorrector class method) (phenotypic.analysis.ErrorCutoffFinder class method) (phenotypic.analysis.ExpectedVsDetectedCount class method) (phenotypic.analysis.GridOccupancy class method) (phenotypic.analysis.ICC class method) (phenotypic.analysis.LinearCapAndLagModel class method) (phenotypic.analysis.LinearLagModel class method) (phenotypic.analysis.LogGrowthModel class method) (phenotypic.analysis.MADOutlierRemover class method) (phenotypic.analysis.MaxModifiedZScore class method) (phenotypic.analysis.RelativeMAD class method) (phenotypic.analysis.ReplicateAgreement class method) (phenotypic.analysis.TukeyOutlierFraction class method) (phenotypic.analysis.TukeyOutlierRemover class method) (phenotypic.correction.BayesShrinkCorrector class method) (phenotypic.correction.CaptureMetadata class method) (phenotypic.correction.ColorCheckerProfile class method) (phenotypic.correction.ColorCorrector class method) (phenotypic.correction.ColorDenoise class method) (phenotypic.correction.DenoiseBlockMatch class method) (phenotypic.correction.GridAligner class method) (phenotypic.correction.ImageCropper class method) (phenotypic.correction.ImagePadder class method) (phenotypic.correction.VisuShrinkCorrector class method) (phenotypic.detect.CannyDetector class method) (phenotypic.detect.ChanVeseDetector class method) (phenotypic.detect.CompositeDetector class method) (phenotypic.detect.FilamentousFungiDetector class method) (phenotypic.detect.HysteresisDetector class method) (phenotypic.detect.InoculumDetector class method) (phenotypic.detect.IsodataDetector class method) (phenotypic.detect.LiDetector class method) (phenotypic.detect.MadHysteresisDetector class method) (phenotypic.detect.ManualGridPointDetector class method) (phenotypic.detect.ManualPointDetector class method) (phenotypic.detect.MeanDetector class method) (phenotypic.detect.MinimumDetector class method) (phenotypic.detect.OtsuDetector class method) (phenotypic.detect.RankOtsuDetector class method) (phenotypic.detect.RoundPeaksDetector class method) (phenotypic.detect.SecondaryOtsuDetector class method) (phenotypic.detect.SinePeakDetector class method) (phenotypic.detect.TriangleDetector class method) (phenotypic.detect.UserThreshold class method) (phenotypic.detect.WatershedDetector class method) (phenotypic.detect.YenDetector class method) (phenotypic.enhance.BayesShrinkEnhancer class method) (phenotypic.enhance.CompositeEnhance class method) (phenotypic.enhance.ContrastStretching class method) (phenotypic.enhance.EnhanceBlockMatch class method) (phenotypic.enhance.EnhanceLocalContrast class method) (phenotypic.enhance.FlattenIllumination class method) (phenotypic.enhance.FocusBlobLoG class method) (phenotypic.enhance.FocusEdgeFrangi class method) (phenotypic.enhance.FocusEdgeHessian class method) (phenotypic.enhance.FocusEdgeLaplace class method) (phenotypic.enhance.FocusEdgeMeijering class method) (phenotypic.enhance.FocusEdgePhase class method) (phenotypic.enhance.FocusEdgeSato class method) (phenotypic.enhance.FocusEdgeSobel class method) (phenotypic.enhance.GaussianBlur class method) (phenotypic.enhance.GrayOpening class method) (phenotypic.enhance.ImageInverter class method) (phenotypic.enhance.LocalEdgeDenoise class method) (phenotypic.enhance.MedianFilter class method) (phenotypic.enhance.NonLocalMeansDenoiser class method) (phenotypic.enhance.RankMedianEnhancer class method) (phenotypic.enhance.SetDetectMode class method) (phenotypic.enhance.SharpenEdgeGauss class method) (phenotypic.enhance.StructureSmoothing class method) (phenotypic.enhance.SubtractGaussian class method) (phenotypic.enhance.SubtractOpening class method) (phenotypic.enhance.SubtractRollingBall class method) (phenotypic.enhance.SubtractWhiteTophat class method) (phenotypic.enhance.VisuShrinkEnhancer class method) (phenotypic.enhance.WhiteTophatEnhance class method) (phenotypic.grid.AutoGridFinder class method) (phenotypic.grid.CenteredAutoGridFinder class method) (phenotypic.grid.GridApply class method) (phenotypic.grid.ManualGridFinder class method) (phenotypic.measure.MeasureBounds class method) (phenotypic.measure.MeasureColor class method) (phenotypic.measure.MeasureGridLinRegStats class method) (phenotypic.measure.MeasureGridSpread class method) (phenotypic.measure.MeasureIntensity class method) (phenotypic.measure.MeasureNeighborDist class method) (phenotypic.measure.MeasureOrientationZones class method) (phenotypic.measure.MeasureShape class method) (phenotypic.measure.MeasureSize class method) (phenotypic.measure.MeasureSymmetricZones class method) (phenotypic.measure.MeasureTexture class method) (phenotypic.prefab.FilamentousFungiPipeline class method) (phenotypic.prefab.GridSectionPipeline class method) (phenotypic.prefab.HeavyOtsuPipeline class method) (phenotypic.prefab.HeavyRoundPeaksPipeline class method) (phenotypic.prefab.HeavyWatershedPipeline class method) (phenotypic.prefab.RoundPeaksPipeline class method) (phenotypic.prefab.SpImagerPipeline class method) (phenotypic.refine.ExtractColonyCore class method) (phenotypic.refine.GridAlignmentRefiner class method) (phenotypic.refine.GridOversizedObjectRemover class method) (phenotypic.refine.KeepNearestCenter class method) (phenotypic.refine.KeepSectionLargest class method) (phenotypic.refine.ManualRefine class method) (phenotypic.refine.MaskClosing class method) (phenotypic.refine.MaskDilation class method) (phenotypic.refine.MaskErosion class method) (phenotypic.refine.MaskFill class method) (phenotypic.refine.MaskGradient class method) (phenotypic.refine.MaskOpening class method) (phenotypic.refine.MaskWhiteTophat class method) (phenotypic.refine.MergeFragmentChains class method) (phenotypic.refine.NearestNeighborMerger class method) (phenotypic.refine.ReduceSectionsByLine class method) (phenotypic.refine.RefineBySineFit class method) (phenotypic.refine.RemoveBorderObjects class method) (phenotypic.refine.RemoveByFeature class method) (phenotypic.refine.RemoveGridOutliers class method) (phenotypic.refine.RemoveLowCircularity class method) (phenotypic.refine.SeparateObjects class method) (phenotypic.refine.Skeletonize class method) (phenotypic.refine.SmallObjectRemover class method) (phenotypic.refine.SmallToLargeMerger class method) (phenotypic.refine.Thinning class method) (phenotypic.refine.TrimAsymmetry class method) (phenotypic.tune.Budget class method) (phenotypic.tune.Categorical class method) (phenotypic.tune.EvaluationResult class method) (phenotypic.tune.Evaluator class method) (phenotypic.tune.Excluded class method) (phenotypic.tune.Fixed class method) (phenotypic.tune.FloatRange class method) (phenotypic.tune.HeldOutConfig class method) (phenotypic.tune.ImportanceReport class method) (phenotypic.tune.InferredSearchSpace class method) (phenotypic.tune.IntRange class method) (phenotypic.tune.Knob class method) (phenotypic.tune.score.CompositeScorer class method) (phenotypic.tune.score.GroundTruthMasks class method) (phenotypic.tune.score.QCScorer class method) (phenotypic.tune.score.ReferenceFreeScorer class method) (phenotypic.tune.score.Scorer class method) (phenotypic.tune.score.SupervisedScorer class method) (phenotypic.tune.SearchSpace class method) (phenotypic.tune.strategy.GridConfig class method) (phenotypic.tune.strategy.OptunaConfig class method) (phenotypic.tune.strategy.RandomConfig class method) (phenotypic.tune.strategy.StrategyConfig class method) (phenotypic.tune.Trial class method) (phenotypic.tune.TuningSpec class method) upper() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method) upper_percentile (phenotypic.enhance.ContrastStretching attribute) use_badge (phenotypic.abc_.MeasurementInfo property) (phenotypic.sdk_.constants_.ConstantLabels property) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS property) (phenotypic.sdk_.constants_.PIPE_STATUS property) use_gat (phenotypic.correction.BayesShrinkCorrector attribute) (phenotypic.correction.ColorDenoise attribute) (phenotypic.correction.VisuShrinkCorrector attribute) (phenotypic.enhance.BayesShrinkEnhancer attribute) (phenotypic.enhance.EnhanceBlockMatch attribute) (phenotypic.enhance.LocalEdgeDenoise attribute) (phenotypic.enhance.NonLocalMeansDenoiser attribute) (phenotypic.enhance.VisuShrinkEnhancer attribute) use_label (phenotypic.abc_.MeasurementInfo property) (phenotypic.sdk_.constants_.ConstantLabels property) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS property) (phenotypic.sdk_.constants_.PIPE_STATUS property) use_quantiles (phenotypic.detect.CannyDetector attribute) UserThreshold (class in phenotypic.detect) UuidAssignmentError UUIDReassignmentError V 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) (phenotypic.abc_.BaseOperation class method) (phenotypic.abc_.ContrastAdjustment class method) (phenotypic.abc_.FocusBlob class method) (phenotypic.abc_.FocusEdge class method) (phenotypic.abc_.GpuDetector class method) (phenotypic.abc_.GridCorrector class method) (phenotypic.abc_.GridFinder class method) (phenotypic.abc_.GridMeasureFeatures class method) (phenotypic.abc_.GridObjectDetector class method) (phenotypic.abc_.GridObjectRefiner class method) (phenotypic.abc_.GridOperation class method) (phenotypic.abc_.ImageCorrector class method) (phenotypic.abc_.ImageDenoiser class method) (phenotypic.abc_.ImageEnhancer class method) (phenotypic.abc_.ImageOperation class method) (phenotypic.abc_.MeasureFeatures class method) (phenotypic.abc_.MorphologicalFiltering class method) (phenotypic.abc_.ObjectDetector class method) (phenotypic.abc_.ObjectRefiner class method) (phenotypic.abc_.PostMeasurement class method) (phenotypic.abc_.PrefabPipeline class method) (phenotypic.abc_.Smoothing class method) (phenotypic.abc_.ThresholdDetector class method) (phenotypic.analysis.EdgeCorrector class method) (phenotypic.analysis.ErrorCutoffFinder class method) (phenotypic.analysis.ExpectedVsDetectedCount class method) (phenotypic.analysis.GridOccupancy class method) (phenotypic.analysis.ICC class method) (phenotypic.analysis.LinearCapAndLagModel class method) (phenotypic.analysis.LinearLagModel class method) (phenotypic.analysis.LogGrowthModel class method) (phenotypic.analysis.MADOutlierRemover class method) (phenotypic.analysis.MaxModifiedZScore class method) (phenotypic.analysis.RelativeMAD class method) (phenotypic.analysis.ReplicateAgreement class method) (phenotypic.analysis.TukeyOutlierFraction class method) (phenotypic.analysis.TukeyOutlierRemover class method) (phenotypic.correction.BayesShrinkCorrector class method) (phenotypic.correction.CaptureMetadata class method) (phenotypic.correction.ColorCheckerProfile class method) (phenotypic.correction.ColorCorrector class method) (phenotypic.correction.ColorDenoise class method) (phenotypic.correction.DenoiseBlockMatch class method) (phenotypic.correction.GridAligner class method) (phenotypic.correction.ImageCropper class method) (phenotypic.correction.ImagePadder class method) (phenotypic.correction.VisuShrinkCorrector class method) (phenotypic.detect.CannyDetector class method) (phenotypic.detect.ChanVeseDetector class method) (phenotypic.detect.CompositeDetector class method) (phenotypic.detect.FilamentousFungiDetector class method) (phenotypic.detect.HysteresisDetector class method) (phenotypic.detect.InoculumDetector class method) (phenotypic.detect.IsodataDetector class method) (phenotypic.detect.LiDetector class method) (phenotypic.detect.MadHysteresisDetector class method) (phenotypic.detect.ManualGridPointDetector class method) (phenotypic.detect.ManualPointDetector class method) (phenotypic.detect.MeanDetector class method) (phenotypic.detect.MinimumDetector class method) (phenotypic.detect.OtsuDetector class method) (phenotypic.detect.RankOtsuDetector class method) (phenotypic.detect.RoundPeaksDetector class method) (phenotypic.detect.SecondaryOtsuDetector class method) (phenotypic.detect.SinePeakDetector class method) (phenotypic.detect.TriangleDetector class method) (phenotypic.detect.UserThreshold class method) (phenotypic.detect.WatershedDetector class method) (phenotypic.detect.YenDetector class method) (phenotypic.enhance.BayesShrinkEnhancer class method) (phenotypic.enhance.CompositeEnhance class method) (phenotypic.enhance.ContrastStretching class method) (phenotypic.enhance.EnhanceBlockMatch class method) (phenotypic.enhance.EnhanceLocalContrast class method) (phenotypic.enhance.FlattenIllumination class method) (phenotypic.enhance.FocusBlobLoG class method) (phenotypic.enhance.FocusEdgeFrangi class method) (phenotypic.enhance.FocusEdgeHessian class method) (phenotypic.enhance.FocusEdgeLaplace class method) (phenotypic.enhance.FocusEdgeMeijering class method) (phenotypic.enhance.FocusEdgePhase class method) (phenotypic.enhance.FocusEdgeSato class method) (phenotypic.enhance.FocusEdgeSobel class method) (phenotypic.enhance.GaussianBlur class method) (phenotypic.enhance.GrayOpening class method) (phenotypic.enhance.ImageInverter class method) (phenotypic.enhance.LocalEdgeDenoise class method) (phenotypic.enhance.MedianFilter class method) (phenotypic.enhance.NonLocalMeansDenoiser class method) (phenotypic.enhance.RankMedianEnhancer class method) (phenotypic.enhance.SetDetectMode class method) (phenotypic.enhance.SharpenEdgeGauss class method) (phenotypic.enhance.StructureSmoothing class method) (phenotypic.enhance.SubtractGaussian class method) (phenotypic.enhance.SubtractOpening class method) (phenotypic.enhance.SubtractRollingBall class method) (phenotypic.enhance.SubtractWhiteTophat class method) (phenotypic.enhance.VisuShrinkEnhancer class method) (phenotypic.enhance.WhiteTophatEnhance class method) (phenotypic.grid.AutoGridFinder class method) (phenotypic.grid.CenteredAutoGridFinder class method) (phenotypic.grid.GridApply class method) (phenotypic.grid.ManualGridFinder class method) (phenotypic.measure.MeasureBounds class method) (phenotypic.measure.MeasureColor class method) (phenotypic.measure.MeasureGridLinRegStats class method) (phenotypic.measure.MeasureGridSpread class method) (phenotypic.measure.MeasureIntensity class method) (phenotypic.measure.MeasureNeighborDist class method) (phenotypic.measure.MeasureOrientationZones class method) (phenotypic.measure.MeasureShape class method) (phenotypic.measure.MeasureSize class method) (phenotypic.measure.MeasureSymmetricZones class method) (phenotypic.measure.MeasureTexture class method) (phenotypic.prefab.FilamentousFungiPipeline class method) (phenotypic.prefab.GridSectionPipeline class method) (phenotypic.prefab.HeavyOtsuPipeline class method) (phenotypic.prefab.HeavyRoundPeaksPipeline class method) (phenotypic.prefab.HeavyWatershedPipeline class method) (phenotypic.prefab.RoundPeaksPipeline class method) (phenotypic.prefab.SpImagerPipeline class method) (phenotypic.refine.ExtractColonyCore class method) (phenotypic.refine.GridAlignmentRefiner class method) (phenotypic.refine.GridOversizedObjectRemover class method) (phenotypic.refine.KeepNearestCenter class method) (phenotypic.refine.KeepSectionLargest class method) (phenotypic.refine.ManualRefine class method) (phenotypic.refine.MaskClosing class method) (phenotypic.refine.MaskDilation class method) (phenotypic.refine.MaskErosion class method) (phenotypic.refine.MaskFill class method) (phenotypic.refine.MaskGradient class method) (phenotypic.refine.MaskOpening class method) (phenotypic.refine.MaskWhiteTophat class method) (phenotypic.refine.MergeFragmentChains class method) (phenotypic.refine.NearestNeighborMerger class method) (phenotypic.refine.ReduceSectionsByLine class method) (phenotypic.refine.RefineBySineFit class method) (phenotypic.refine.RemoveBorderObjects class method) (phenotypic.refine.RemoveByFeature class method) (phenotypic.refine.RemoveGridOutliers class method) (phenotypic.refine.RemoveLowCircularity class method) (phenotypic.refine.SeparateObjects class method) (phenotypic.refine.Skeletonize class method) (phenotypic.refine.SmallObjectRemover class method) (phenotypic.refine.SmallToLargeMerger class method) (phenotypic.refine.Thinning class method) (phenotypic.refine.TrimAsymmetry class method) (phenotypic.tune.Budget class method) (phenotypic.tune.Categorical class method) (phenotypic.tune.EvaluationResult class method) (phenotypic.tune.Evaluator class method) (phenotypic.tune.Excluded class method) (phenotypic.tune.Fixed class method) (phenotypic.tune.FloatRange class method) (phenotypic.tune.HeldOutConfig class method) (phenotypic.tune.ImportanceReport class method) (phenotypic.tune.InferredSearchSpace class method) (phenotypic.tune.IntRange class method) (phenotypic.tune.Knob class method) (phenotypic.tune.score.CompositeScorer class method) (phenotypic.tune.score.GroundTruthMasks class method) (phenotypic.tune.score.QCScorer class method) (phenotypic.tune.score.ReferenceFreeScorer class method) (phenotypic.tune.score.Scorer class method) (phenotypic.tune.score.SupervisedScorer class method) (phenotypic.tune.SearchSpace class method) (phenotypic.tune.strategy.GridConfig class method) (phenotypic.tune.strategy.OptunaConfig class method) (phenotypic.tune.strategy.RandomConfig class method) (phenotypic.tune.strategy.StrategyConfig class method) (phenotypic.tune.Trial class method) (phenotypic.tune.TuningSpec class method) validate_array_chunk() (in module phenotypic.sdk_.slurm) validate_obj_count (phenotypic.detect.InoculumDetector attribute) value (phenotypic.refine.RemoveByFeature attribute) (phenotypic.tune.Fixed attribute) values() (phenotypic._core._image_parts.accessors._metadata_accessor.MetadataAccessor method) (phenotypic.tune.FloatRange method) (phenotypic.tune.IntRange method) (phenotypic.util.BackgroundMetrics method) (phenotypic.util.ContrastMetrics method) (phenotypic.util.NoiseMetrics method) (phenotypic.util.QualityScores method) (phenotypic.util.StructureMetrics method) verbose (phenotypic.abc_.PrefabPipeline attribute) (phenotypic.analysis.LinearCapAndLagModel attribute) (phenotypic.analysis.LinearLagModel attribute) (phenotypic.analysis.LogGrowthModel attribute) (phenotypic.prefab.FilamentousFungiPipeline attribute) (phenotypic.prefab.GridSectionPipeline attribute) (phenotypic.prefab.HeavyOtsuPipeline attribute) (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1] (phenotypic.prefab.HeavyWatershedPipeline attribute) (phenotypic.prefab.RoundPeaksPipeline attribute) (phenotypic.prefab.SpImagerPipeline attribute) verified_parquet (phenotypic.sdk_.BundleLayout property) verified_parquet_path() (in module phenotypic.sdk_) VERSION (phenotypic.sdk_.DashboardManifestKey attribute) (phenotypic.sdk_.ProcessingStateKey attribute) VisuShrinkCorrector (class in phenotypic.correction) VisuShrinkEnhancer (class in phenotypic.enhance) 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] warmup_c (phenotypic.tune.ScreeningConfig attribute) warmup_floor (phenotypic.tune.ScreeningConfig attribute) warn (phenotypic.grid.AutoGridFinder attribute) (phenotypic.grid.CenteredAutoGridFinder attribute) (phenotypic.measure.MeasureTexture attribute) warn_threshold (phenotypic.analysis.ExpectedVsDetectedCount attribute) (phenotypic.analysis.GridOccupancy attribute) (phenotypic.analysis.ICC attribute) (phenotypic.analysis.MaxModifiedZScore attribute) (phenotypic.analysis.RelativeMAD attribute) (phenotypic.analysis.ReplicateAgreement attribute) (phenotypic.analysis.TukeyOutlierFraction attribute) warning (phenotypic.tune.GeneralizationReport attribute) WatershedDetector (class in phenotypic.detect) wavelet (phenotypic.correction.BayesShrinkCorrector attribute) (phenotypic.correction.VisuShrinkCorrector attribute) (phenotypic.enhance.BayesShrinkEnhancer attribute) (phenotypic.enhance.VisuShrinkEnhancer attribute) wavelet_levels (phenotypic.correction.BayesShrinkCorrector attribute) (phenotypic.correction.VisuShrinkCorrector attribute) (phenotypic.enhance.BayesShrinkEnhancer attribute) (phenotypic.enhance.VisuShrinkEnhancer attribute) weights (phenotypic.tune.score.CompositeScorer attribute) well WhiteTophatEnhance (class in phenotypic.enhance) widget() (phenotypic.abc_.BackgroundSubtraction method) (phenotypic.abc_.ContrastAdjustment method) (phenotypic.abc_.FocusBlob method) (phenotypic.abc_.FocusEdge method) (phenotypic.abc_.GpuDetector method) (phenotypic.abc_.GridCorrector method) (phenotypic.abc_.GridObjectDetector method) (phenotypic.abc_.GridObjectRefiner method) (phenotypic.abc_.GridOperation method) (phenotypic.abc_.ImageCorrector method) (phenotypic.abc_.ImageDenoiser method) (phenotypic.abc_.ImageEnhancer method) (phenotypic.abc_.ImageOperation method) (phenotypic.abc_.MorphologicalFiltering method) (phenotypic.abc_.ObjectDetector method) (phenotypic.abc_.ObjectRefiner method) (phenotypic.abc_.PrefabPipeline method) (phenotypic.abc_.Smoothing method) (phenotypic.abc_.ThresholdDetector method) (phenotypic.correction.BayesShrinkCorrector method) (phenotypic.correction.ColorCorrector method) (phenotypic.correction.ColorDenoise method) (phenotypic.correction.DenoiseBlockMatch method) (phenotypic.correction.GridAligner method) (phenotypic.correction.ImageCropper method) (phenotypic.correction.ImagePadder method) (phenotypic.correction.VisuShrinkCorrector method) (phenotypic.detect.CannyDetector method) (phenotypic.detect.ChanVeseDetector method) (phenotypic.detect.CompositeDetector method) (phenotypic.detect.FilamentousFungiDetector method) (phenotypic.detect.HysteresisDetector method) (phenotypic.detect.InoculumDetector method) (phenotypic.detect.IsodataDetector method) (phenotypic.detect.LiDetector method) (phenotypic.detect.MadHysteresisDetector method) (phenotypic.detect.ManualGridPointDetector method) (phenotypic.detect.ManualPointDetector method) (phenotypic.detect.MeanDetector method) (phenotypic.detect.MinimumDetector method) (phenotypic.detect.OtsuDetector method) (phenotypic.detect.RankOtsuDetector method) (phenotypic.detect.RoundPeaksDetector method) (phenotypic.detect.SecondaryOtsuDetector method) (phenotypic.detect.SinePeakDetector method) (phenotypic.detect.TriangleDetector method) (phenotypic.detect.UserThreshold method) (phenotypic.detect.WatershedDetector method) (phenotypic.detect.YenDetector method) (phenotypic.enhance.BayesShrinkEnhancer method) (phenotypic.enhance.CompositeEnhance method) (phenotypic.enhance.ContrastStretching method) (phenotypic.enhance.EnhanceBlockMatch method) (phenotypic.enhance.EnhanceLocalContrast method) (phenotypic.enhance.FlattenIllumination method) (phenotypic.enhance.FocusBlobLoG method) (phenotypic.enhance.FocusEdgeFrangi method) (phenotypic.enhance.FocusEdgeHessian method) (phenotypic.enhance.FocusEdgeLaplace method) (phenotypic.enhance.FocusEdgeMeijering method) (phenotypic.enhance.FocusEdgePhase method) (phenotypic.enhance.FocusEdgeSato method) (phenotypic.enhance.FocusEdgeSobel method) (phenotypic.enhance.GaussianBlur method) (phenotypic.enhance.GrayOpening method) (phenotypic.enhance.ImageInverter method) (phenotypic.enhance.LocalEdgeDenoise method) (phenotypic.enhance.MedianFilter method) (phenotypic.enhance.NonLocalMeansDenoiser method) (phenotypic.enhance.RankMedianEnhancer method) (phenotypic.enhance.SetDetectMode method) (phenotypic.enhance.SharpenEdgeGauss method) (phenotypic.enhance.StructureSmoothing method) (phenotypic.enhance.SubtractGaussian method) (phenotypic.enhance.SubtractOpening method) (phenotypic.enhance.SubtractRollingBall method) (phenotypic.enhance.SubtractWhiteTophat method) (phenotypic.enhance.VisuShrinkEnhancer method) (phenotypic.enhance.WhiteTophatEnhance method) (phenotypic.grid.GridApply method) (phenotypic.prefab.FilamentousFungiPipeline method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.prefab.RoundPeaksPipeline method) (phenotypic.prefab.SpImagerPipeline method) (phenotypic.refine.ExtractColonyCore method) (phenotypic.refine.GridAlignmentRefiner method) (phenotypic.refine.GridOversizedObjectRemover method) (phenotypic.refine.KeepNearestCenter method) (phenotypic.refine.KeepSectionLargest method) (phenotypic.refine.ManualRefine method) (phenotypic.refine.MaskClosing method) (phenotypic.refine.MaskDilation method) (phenotypic.refine.MaskErosion method) (phenotypic.refine.MaskFill method) (phenotypic.refine.MaskGradient method) (phenotypic.refine.MaskOpening method) (phenotypic.refine.MaskWhiteTophat method) (phenotypic.refine.MergeFragmentChains method) (phenotypic.refine.NearestNeighborMerger method) (phenotypic.refine.ReduceSectionsByLine method) (phenotypic.refine.RefineBySineFit method) (phenotypic.refine.RemoveBorderObjects method) (phenotypic.refine.RemoveByFeature method) (phenotypic.refine.RemoveGridOutliers method) (phenotypic.refine.RemoveLowCircularity method) (phenotypic.refine.SeparateObjects method) (phenotypic.refine.Skeletonize method) (phenotypic.refine.SmallObjectRemover method) (phenotypic.refine.SmallToLargeMerger method) (phenotypic.refine.Thinning method) (phenotypic.refine.TrimAsymmetry method) (phenotypic.sdk_.LazyWidgetMixin method) width (phenotypic.detect.ManualGridPointDetector attribute) (phenotypic.detect.ManualPointDetector attribute) (phenotypic.detect.RankOtsuDetector attribute) (phenotypic.enhance.GrayOpening attribute) (phenotypic.enhance.MedianFilter attribute) (phenotypic.enhance.RankMedianEnhancer attribute) (phenotypic.enhance.SubtractOpening attribute) (phenotypic.enhance.SubtractWhiteTophat attribute) (phenotypic.enhance.WhiteTophatEnhance attribute) (phenotypic.refine.ManualRefine attribute) (phenotypic.refine.MaskClosing attribute) (phenotypic.refine.MaskDilation attribute) (phenotypic.refine.MaskErosion attribute) (phenotypic.refine.MaskGradient attribute) (phenotypic.refine.MaskOpening attribute) (phenotypic.refine.MaskWhiteTophat attribute) win_size (phenotypic.enhance.LocalEdgeDenoise attribute) winner (phenotypic.tune.ScreeningResult attribute) with_traceback() (phenotypic.grid.CenteredAutoGridFinderFallbackWarning method) (phenotypic.sdk_.exceptions_.ArrayKeyValueShapeMismatchError method) (phenotypic.sdk_.exceptions_.DataIntegrityError method) (phenotypic.sdk_.exceptions_.EmptyImageError method) (phenotypic.sdk_.exceptions_.GrayscaleOutOfRangeError method) (phenotypic.sdk_.exceptions_.GridImageInputError method) (phenotypic.sdk_.exceptions_.IllegalAssignmentError method) (phenotypic.sdk_.exceptions_.IllegalElementAssignmentError method) (phenotypic.sdk_.exceptions_.ImageOperationError method) (phenotypic.sdk_.exceptions_.ImmutableComponentError method) (phenotypic.sdk_.exceptions_.InputShapeMismatchError method) (phenotypic.sdk_.exceptions_.InterfaceError method) (phenotypic.sdk_.exceptions_.InvalidHsvSchemaError method) (phenotypic.sdk_.exceptions_.InvalidMapValueError method) (phenotypic.sdk_.exceptions_.InvalidMaskScalarValueError method) (phenotypic.sdk_.exceptions_.InvalidMaskValueError method) (phenotypic.sdk_.exceptions_.InvalidShapeError method) (phenotypic.sdk_.exceptions_.MetadataKeySpacesError method) (phenotypic.sdk_.exceptions_.MetadataKeyValueError method) (phenotypic.sdk_.exceptions_.MetadataValueNonScalarError method) (phenotypic.sdk_.exceptions_.NoArrayError method) (phenotypic.sdk_.exceptions_.NoComponentError method) (phenotypic.sdk_.exceptions_.NoImageDataError method) (phenotypic.sdk_.exceptions_.NoObjectsError method) (phenotypic.sdk_.exceptions_.NoOutputError method) (phenotypic.sdk_.exceptions_.ObjectNotFoundError method) (phenotypic.sdk_.exceptions_.OperationFailedError method) (phenotypic.sdk_.exceptions_.OperationIntegrityError method) (phenotypic.sdk_.exceptions_.OutputValueError method) (phenotypic.sdk_.exceptions_.PhenoTypicError method) (phenotypic.sdk_.exceptions_.UnknownError method) (phenotypic.sdk_.exceptions_.UnsupportedFileTypeError method) (phenotypic.sdk_.exceptions_.UnsupportedImageFormat method) (phenotypic.sdk_.exceptions_.UuidAssignmentError method) (phenotypic.sdk_.exceptions_.UUIDReassignmentError method) within_group_caveat (phenotypic.tune.GeneralizationReport attribute) X 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 YenDetector (class in phenotypic.detect) Z zfill() (phenotypic.abc_.MeasurementInfo method) (phenotypic.sdk_.constants_.ConstantLabels method) (phenotypic.sdk_.constants_.GAMMA_ENCODINGS method) (phenotypic.sdk_.constants_.PIPE_STATUS method)
