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) __del__() (phenotypic.abc_.BaseOperation 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_.ImageEnhancer method) (phenotypic.abc_.ImageOperation method) (phenotypic.abc_.MeasureFeatures method) (phenotypic.abc_.ObjectDetector method) (phenotypic.abc_.ObjectRefiner method) (phenotypic.abc_.PostMeasurement method) (phenotypic.abc_.PrefabPipeline method) (phenotypic.abc_.ThresholdDetector method) (phenotypic.correction.BayesShrinkCorrector method) (phenotypic.correction.ColorCorrector method) (phenotypic.correction.GridAligner method) (phenotypic.correction.ImageCropper method) (phenotypic.correction.ImagePadder method) (phenotypic.correction.StableDenoise 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.ManualDetector method) (phenotypic.detect.ManualGridDetector 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.WatershedDetector method) (phenotypic.detect.YenDetector method) (phenotypic.enhance.AnscombeForward method) (phenotypic.enhance.AnscombeInverse method) (phenotypic.enhance.BayesShrinkEnhancer method) (phenotypic.enhance.BilateralDenoise method) (phenotypic.enhance.BM3DDenoiser method) (phenotypic.enhance.CLAHE method) (phenotypic.enhance.CoherenceEnhancingDiffusion method) (phenotypic.enhance.ContrastStretching method) (phenotypic.enhance.FrangiVesselness method) (phenotypic.enhance.GaussianBlur method) (phenotypic.enhance.GrayOpening method) (phenotypic.enhance.HessianFilter method) (phenotypic.enhance.HomomorphicFilter method) (phenotypic.enhance.ImageInverter method) (phenotypic.enhance.LaplaceEnhancer method) (phenotypic.enhance.MedianFilter method) (phenotypic.enhance.MeijeringRidgeFilter method) (phenotypic.enhance.MultiscaleLoGEnhancer method) (phenotypic.enhance.NonLocalMeansDenoiser method) (phenotypic.enhance.OpeningSubtractBg method) (phenotypic.enhance.PhaseCongruencyEnhancer method) (phenotypic.enhance.RankMedianEnhancer method) (phenotypic.enhance.SatoRidgeFilter method) (phenotypic.enhance.SetDetectMode method) (phenotypic.enhance.SobelFilter method) (phenotypic.enhance.SubtractGaussian method) (phenotypic.enhance.SubtractRollingBall method) (phenotypic.enhance.SubtractWhiteTophat method) (phenotypic.enhance.UnsharpMask method) (phenotypic.enhance.VisuShrinkEnhancer method) (phenotypic.enhance.WhiteTophatEnhance method) (phenotypic.grid.AutoGridFinder method) (phenotypic.grid.ManualGridFinder method) (phenotypic.measure.MeasureBounds method) (phenotypic.measure.MeasureColor method) (phenotypic.measure.MeasureGridLinRegStats method) (phenotypic.measure.MeasureGridSpatial method) (phenotypic.measure.MeasureGridSpread method) (phenotypic.measure.MeasureIntensity method) (phenotypic.measure.MeasureShape method) (phenotypic.measure.MeasureSize method) (phenotypic.measure.MeasureSymmetricZones method) (phenotypic.measure.MeasureTexture method) (phenotypic.post.AppendString method) (phenotypic.post.ExpandMetadata method) (phenotypic.post.MergeMetadata method) (phenotypic.post.PrependString 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.AsymmetricSpurTrimmer method) (phenotypic.refine.BorderObjectRemover method) (phenotypic.refine.CenterDeviationReducer method) (phenotypic.refine.GMMCoreExtractor method) (phenotypic.refine.GridAlignmentRefiner method) (phenotypic.refine.GridOversizedObjectRemover method) (phenotypic.refine.GridSectionLargest method) (phenotypic.refine.LowCircularityRemover method) (phenotypic.refine.MaskCloser method) (phenotypic.refine.MaskDilator method) (phenotypic.refine.MaskEroder method) (phenotypic.refine.MaskFill method) (phenotypic.refine.MaskGradient method) (phenotypic.refine.MaskOpener method) (phenotypic.refine.NearestNeighborMerger method) (phenotypic.refine.ReduceMultipleGridObjects method) (phenotypic.refine.ResidualOutlierRemover method) (phenotypic.refine.SeparateObjects method) (phenotypic.refine.SineAlignmentRefiner method) (phenotypic.refine.Skeletonize method) (phenotypic.refine.SmallObjectRemover method) (phenotypic.refine.SmallToLargeMerger method) (phenotypic.refine.Thinning method) (phenotypic.refine.TransitiveDistanceMerger method) (phenotypic.refine.WhiteTophat method) __delitem__() (phenotypic._core._image_parts.accessors._metadata_accessor.MetadataAccessor method) __dir__() (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) __eq__() (phenotypic.Image method) __format__() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) __getattr__() (in module phenotypic.gui) (in module phenotypic.gui.components) (in module phenotypic.gui.sweep) (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._grid_accessor.GridAccessor 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) __getstate__() (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_.ImageEnhancer method) (phenotypic.abc_.ImageOperation method) (phenotypic.abc_.ObjectDetector method) (phenotypic.abc_.ObjectRefiner method) (phenotypic.abc_.PrefabPipeline method) (phenotypic.abc_.ThresholdDetector method) (phenotypic.correction.BayesShrinkCorrector method) (phenotypic.correction.ColorCorrector method) (phenotypic.correction.GridAligner method) (phenotypic.correction.ImageCropper method) (phenotypic.correction.ImagePadder method) (phenotypic.correction.StableDenoise 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.ManualDetector method) (phenotypic.detect.ManualGridDetector 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.WatershedDetector method) (phenotypic.detect.YenDetector method) (phenotypic.enhance.AnscombeForward method) (phenotypic.enhance.AnscombeInverse method) (phenotypic.enhance.BayesShrinkEnhancer method) (phenotypic.enhance.BilateralDenoise method) (phenotypic.enhance.BM3DDenoiser method) (phenotypic.enhance.CLAHE method) (phenotypic.enhance.CoherenceEnhancingDiffusion method) (phenotypic.enhance.ContrastStretching method) (phenotypic.enhance.FrangiVesselness method) (phenotypic.enhance.GaussianBlur method) (phenotypic.enhance.GrayOpening method) (phenotypic.enhance.HessianFilter method) (phenotypic.enhance.HomomorphicFilter method) (phenotypic.enhance.ImageInverter method) (phenotypic.enhance.LaplaceEnhancer method) (phenotypic.enhance.MedianFilter method) (phenotypic.enhance.MeijeringRidgeFilter method) (phenotypic.enhance.MultiscaleLoGEnhancer method) (phenotypic.enhance.NonLocalMeansDenoiser method) (phenotypic.enhance.OpeningSubtractBg method) (phenotypic.enhance.PhaseCongruencyEnhancer method) (phenotypic.enhance.RankMedianEnhancer method) (phenotypic.enhance.SatoRidgeFilter method) (phenotypic.enhance.SetDetectMode method) (phenotypic.enhance.SobelFilter method) (phenotypic.enhance.SubtractGaussian method) (phenotypic.enhance.SubtractRollingBall method) (phenotypic.enhance.SubtractWhiteTophat method) (phenotypic.enhance.UnsharpMask method) (phenotypic.enhance.VisuShrinkEnhancer method) (phenotypic.enhance.WhiteTophatEnhance 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.AsymmetricSpurTrimmer method) (phenotypic.refine.BorderObjectRemover method) (phenotypic.refine.CenterDeviationReducer method) (phenotypic.refine.GMMCoreExtractor method) (phenotypic.refine.GridAlignmentRefiner method) (phenotypic.refine.GridOversizedObjectRemover method) (phenotypic.refine.GridSectionLargest method) (phenotypic.refine.LowCircularityRemover method) (phenotypic.refine.MaskCloser method) (phenotypic.refine.MaskDilator method) (phenotypic.refine.MaskEroder method) (phenotypic.refine.MaskFill method) (phenotypic.refine.MaskGradient method) (phenotypic.refine.MaskOpener method) (phenotypic.refine.NearestNeighborMerger method) (phenotypic.refine.ReduceMultipleGridObjects method) (phenotypic.refine.ResidualOutlierRemover method) (phenotypic.refine.SeparateObjects method) (phenotypic.refine.SineAlignmentRefiner method) (phenotypic.refine.Skeletonize method) (phenotypic.refine.SmallObjectRemover method) (phenotypic.refine.SmallToLargeMerger method) (phenotypic.refine.Thinning method) (phenotypic.refine.TransitiveDistanceMerger method) (phenotypic.refine.WhiteTophat method) (phenotypic.tools_.LazyWidgetMixin method) (phenotypic.tools_.mixin.LazyWidgetMixin method) __hash__() (phenotypic.Image method) __iand__() (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask method) __init__() (phenotypic._core._image_parts.accessors._color_accessor.ColorAccessor method) (phenotypic._core._image_parts.accessors._metadata_accessor.MetadataAccessor method) (phenotypic._core._image_parts.accessors._objects_accessor.ObjectsAccessor method) (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) (phenotypic.abc_.PrefabPipeline method) (phenotypic.analysis.EdgeCorrector method) (phenotypic.analysis.LinearSoftplusModel method) (phenotypic.analysis.LogGrowthModel method) (phenotypic.analysis.TukeyOutlierRemover method) (phenotypic.correction.BayesShrinkCorrector method) (phenotypic.correction.ColorCorrector method) (phenotypic.correction.ImageCropper method) (phenotypic.correction.ImagePadder method) (phenotypic.correction.StableDenoise method) (phenotypic.correction.VisuShrinkCorrector method) (phenotypic.detect.CannyDetector method) (phenotypic.detect.InoculumDetector method) (phenotypic.detect.RoundPeaksDetector method) (phenotypic.detect.SinePeakDetector method) (phenotypic.enhance.AnscombeForward method) (phenotypic.enhance.AnscombeInverse method) (phenotypic.enhance.BayesShrinkEnhancer method) (phenotypic.enhance.BilateralDenoise method) (phenotypic.enhance.BM3DDenoiser method) (phenotypic.enhance.CLAHE method) (phenotypic.enhance.CoherenceEnhancingDiffusion method) (phenotypic.enhance.ContrastStretching method) (phenotypic.enhance.FrangiVesselness method) (phenotypic.enhance.GaussianBlur method) (phenotypic.enhance.GrayOpening method) (phenotypic.enhance.HessianFilter method) (phenotypic.enhance.HomomorphicFilter method) (phenotypic.enhance.ImageInverter method) (phenotypic.enhance.LaplaceEnhancer method) (phenotypic.enhance.MedianFilter method) (phenotypic.enhance.MeijeringRidgeFilter method) (phenotypic.enhance.MultiscaleLoGEnhancer method) (phenotypic.enhance.NonLocalMeansDenoiser method) (phenotypic.enhance.PhaseCongruencyEnhancer method) (phenotypic.enhance.RankMedianEnhancer method) (phenotypic.enhance.SatoRidgeFilter method) (phenotypic.enhance.SubtractGaussian method) (phenotypic.enhance.SubtractRollingBall method) (phenotypic.enhance.SubtractWhiteTophat method) (phenotypic.enhance.UnsharpMask method) (phenotypic.enhance.VisuShrinkEnhancer method) (phenotypic.grid.ManualGridFinder method) (phenotypic.GridImage method) (phenotypic.Image method) (phenotypic.ImagePipeline method) (phenotypic.measure.MeasureTexture method) (phenotypic.prefab.GridSectionPipeline method) (phenotypic.prefab.HeavyOtsuPipeline method) (phenotypic.prefab.HeavyRoundPeaksPipeline method) (phenotypic.prefab.HeavyWatershedPipeline method) (phenotypic.refine.BorderObjectRemover method) (phenotypic.refine.GMMCoreExtractor method) (phenotypic.refine.GridAlignmentRefiner method) (phenotypic.refine.LowCircularityRemover method) (phenotypic.refine.MaskCloser method) (phenotypic.refine.MaskDilator method) (phenotypic.refine.MaskEroder method) (phenotypic.refine.MaskFill method) (phenotypic.refine.MaskGradient method) (phenotypic.refine.MaskOpener method) (phenotypic.refine.NearestNeighborMerger method) (phenotypic.refine.ResidualOutlierRemover method) (phenotypic.refine.SeparateObjects method) (phenotypic.refine.SineAlignmentRefiner method) (phenotypic.refine.Skeletonize method) (phenotypic.refine.SmallObjectRemover method) (phenotypic.refine.SmallToLargeMerger method) (phenotypic.refine.Thinning method) (phenotypic.refine.TransitiveDistanceMerger method) (phenotypic.refine.WhiteTophat method) (phenotypic.tools_.HDF method) (phenotypic.tools_.hdf_.HDF 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) __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) __new_member__() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) __or__() (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask method) __repr__() (phenotypic.Image 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.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE 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) _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) _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 A_STAR_COEFF_VARIANCE (phenotypic.tools_.measurement_info_.ColorLab attribute) a_star_headers() (phenotypic.tools_.measurement_info_.ColorLab class method) A_STAR_MAXIMUM (phenotypic.tools_.measurement_info_.ColorLab attribute) A_STAR_MEAN (phenotypic.tools_.measurement_info_.ColorLab attribute) A_STAR_MEDIAN (phenotypic.tools_.measurement_info_.ColorLab attribute) A_STAR_MINIMUM (phenotypic.tools_.measurement_info_.ColorLab attribute) A_STAR_Q1 (phenotypic.tools_.measurement_info_.ColorLab attribute) A_STAR_Q3 (phenotypic.tools_.measurement_info_.ColorLab attribute) A_STAR_STDDEV (phenotypic.tools_.measurement_info_.ColorLab attribute) ABOVE_DISTANCE (phenotypic.tools_.measurement_info_.GRID_SPATIAL attribute) ABOVE_NEIGHBOR_OBJ_LABEL (phenotypic.tools_.measurement_info_.GRID_SPATIAL attribute) ACCEPTED_FILE_EXTENSIONS (phenotypic.tools_.constants_.IO attribute) accessor add_plotly_gridlines() (phenotypic._core._image_parts.accessors._detect_mat_accessor.DetectMatAccessor static method) (phenotypic._core._image_parts.accessors._grayscale_accessor.Grayscale static method) (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap static method) (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask static method) (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor static method) (phenotypic._core._image_parts.accessors._rgb_accessor.ImageRGB static method) add_plotly_obj_labels() (phenotypic._core._image_parts.accessors._detect_mat_accessor.DetectMatAccessor static method) (phenotypic._core._image_parts.accessors._grayscale_accessor.Grayscale static method) (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap static method) (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask static method) (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor static method) (phenotypic._core._image_parts.accessors._rgb_accessor.ImageRGB static method) add_plotly_section_boxes() (phenotypic._core._image_parts.accessors._detect_mat_accessor.DetectMatAccessor static method) (phenotypic._core._image_parts.accessors._grayscale_accessor.Grayscale static method) (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap static method) (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask static method) (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor static method) (phenotypic._core._image_parts.accessors._rgb_accessor.ImageRGB static method) all() (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) all_headers() (phenotypic.tools_.measurement_info_.ColorComposition class method) alpha (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL attribute) AMBIGUOUS_FORMATS (phenotypic.tools_.constants_.IMAGE_MODE attribute) AnalysisPluginRegistry (class in phenotypic.tools_.register) analyze() (phenotypic.analysis.abc_.ModelFitter method) (phenotypic.analysis.abc_.SetAnalyzer method) (phenotypic.analysis.EdgeCorrector method) (phenotypic.analysis.LinearSoftplusModel method) (phenotypic.analysis.LogGrowthModel method) (phenotypic.analysis.TukeyOutlierRemover method) ANGULAR_SECOND_MOMENT (phenotypic.tools_.measurement_info_.TEXTURE attribute) AnscombeForward (class in phenotypic.enhance) AnscombeInverse (class in phenotypic.enhance) append_rst_to_doc() (phenotypic.abc_.MeasurementInfo class method) (phenotypic.tools_.constants_.ConstantLabels class method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS class method) (phenotypic.tools_.constants_.METADATA class method) (phenotypic.tools_.constants_.PIPE_STATUS class method) (phenotypic.tools_.measurement_info_.BBOX class method) (phenotypic.tools_.measurement_info_.ColorComposition class method) (phenotypic.tools_.measurement_info_.ColorHSV class method) (phenotypic.tools_.measurement_info_.ColorLab class method) (phenotypic.tools_.measurement_info_.Colorxy class method) (phenotypic.tools_.measurement_info_.ColorXYZ class method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION class method) (phenotypic.tools_.measurement_info_.GRID class method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS class method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL class method) (phenotypic.tools_.measurement_info_.GRID_SPREAD class method) (phenotypic.tools_.measurement_info_.INTENSITY class method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL class method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL class method) (phenotypic.tools_.measurement_info_.MODEL_METRICS class method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION class method) (phenotypic.tools_.measurement_info_.SHAPE class method) (phenotypic.tools_.measurement_info_.SIZE class method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS class method) (phenotypic.tools_.measurement_info_.TEXTURE class method) AppendString (class in phenotypic.post) apply() (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_.ImageEnhancer method), [1] (phenotypic.abc_.ImageOperation method), [1] (phenotypic.abc_.ObjectDetector method), [1] (phenotypic.abc_.ObjectRefiner method), [1] (phenotypic.abc_.PostMeasurement method) (phenotypic.abc_.PrefabPipeline method) (phenotypic.abc_.ThresholdDetector method) (phenotypic.correction.BayesShrinkCorrector method) (phenotypic.correction.ColorCorrector method) (phenotypic.correction.GridAligner method) (phenotypic.correction.ImageCropper method) (phenotypic.correction.ImagePadder method) (phenotypic.correction.StableDenoise 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.ManualDetector method) (phenotypic.detect.ManualGridDetector 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.WatershedDetector method) (phenotypic.detect.YenDetector method) (phenotypic.enhance.AnscombeForward method) (phenotypic.enhance.AnscombeInverse method) (phenotypic.enhance.BayesShrinkEnhancer method) (phenotypic.enhance.BilateralDenoise method) (phenotypic.enhance.BM3DDenoiser method) (phenotypic.enhance.CLAHE method) (phenotypic.enhance.CoherenceEnhancingDiffusion method) (phenotypic.enhance.ContrastStretching method) (phenotypic.enhance.FrangiVesselness method) (phenotypic.enhance.GaussianBlur method) (phenotypic.enhance.GrayOpening method) (phenotypic.enhance.HessianFilter method) (phenotypic.enhance.HomomorphicFilter method) (phenotypic.enhance.ImageInverter method) (phenotypic.enhance.LaplaceEnhancer method) (phenotypic.enhance.MedianFilter method) (phenotypic.enhance.MeijeringRidgeFilter method) (phenotypic.enhance.MultiscaleLoGEnhancer method) (phenotypic.enhance.NonLocalMeansDenoiser method) (phenotypic.enhance.OpeningSubtractBg method) (phenotypic.enhance.PhaseCongruencyEnhancer method) (phenotypic.enhance.RankMedianEnhancer method) (phenotypic.enhance.SatoRidgeFilter method) (phenotypic.enhance.SetDetectMode method) (phenotypic.enhance.SobelFilter method) (phenotypic.enhance.SubtractGaussian method) (phenotypic.enhance.SubtractRollingBall method) (phenotypic.enhance.SubtractWhiteTophat method) (phenotypic.enhance.UnsharpMask method) (phenotypic.enhance.VisuShrinkEnhancer method) (phenotypic.enhance.WhiteTophatEnhance method) (phenotypic.grid.GridApply method) (phenotypic.ImagePipeline method) (phenotypic.post.AppendString method) (phenotypic.post.ExpandMetadata method) (phenotypic.post.MergeMetadata method) (phenotypic.post.PrependString 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.AsymmetricSpurTrimmer method) (phenotypic.refine.BorderObjectRemover method) (phenotypic.refine.CenterDeviationReducer method) (phenotypic.refine.GMMCoreExtractor method) (phenotypic.refine.GridAlignmentRefiner method) (phenotypic.refine.GridOversizedObjectRemover method) (phenotypic.refine.GridSectionLargest method) (phenotypic.refine.LowCircularityRemover method) (phenotypic.refine.MaskCloser method) (phenotypic.refine.MaskDilator method) (phenotypic.refine.MaskEroder method) (phenotypic.refine.MaskFill method) (phenotypic.refine.MaskGradient method) (phenotypic.refine.MaskOpener method) (phenotypic.refine.NearestNeighborMerger method) (phenotypic.refine.ReduceMultipleGridObjects method) (phenotypic.refine.ResidualOutlierRemover method) (phenotypic.refine.SeparateObjects method) (phenotypic.refine.SineAlignmentRefiner method) (phenotypic.refine.Skeletonize method) (phenotypic.refine.SmallObjectRemover method) (phenotypic.refine.SmallToLargeMerger method) (phenotypic.refine.Thinning method) (phenotypic.refine.TransitiveDistanceMerger method) (phenotypic.refine.WhiteTophat 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_border_penalty() (in module phenotypic.tools_.branch_pathfinding) apply_distance_gap_penalty() (in module phenotypic.tools_.branch_pathfinding) apply_filter_cascade() (in module phenotypic.tools_.branch_pathfinding) 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_structure_mask() (in module phenotypic.tools_.branch_pathfinding) 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) AREA (phenotypic.tools_.measurement_info_.SHAPE attribute) (phenotypic.tools_.measurement_info_.SIZE attribute) args (phenotypic.tools_.exceptions_.ArrayKeyValueShapeMismatchError attribute) (phenotypic.tools_.exceptions_.DataIntegrityError attribute) (phenotypic.tools_.exceptions_.EmptyImageError attribute) (phenotypic.tools_.exceptions_.GrayscaleOutOfRangeError attribute) (phenotypic.tools_.exceptions_.GridImageInputError attribute) (phenotypic.tools_.exceptions_.IllegalAssignmentError attribute) (phenotypic.tools_.exceptions_.IllegalElementAssignmentError attribute) (phenotypic.tools_.exceptions_.ImageOperationError attribute) (phenotypic.tools_.exceptions_.ImmutableComponentError attribute) (phenotypic.tools_.exceptions_.InputShapeMismatchError attribute) (phenotypic.tools_.exceptions_.InterfaceError attribute) (phenotypic.tools_.exceptions_.InvalidHsvSchemaError attribute) (phenotypic.tools_.exceptions_.InvalidMapValueError attribute) (phenotypic.tools_.exceptions_.InvalidMaskScalarValueError attribute) (phenotypic.tools_.exceptions_.InvalidMaskValueError attribute) (phenotypic.tools_.exceptions_.InvalidShapeError attribute) (phenotypic.tools_.exceptions_.MetadataKeySpacesError attribute) (phenotypic.tools_.exceptions_.MetadataKeyValueError attribute) (phenotypic.tools_.exceptions_.MetadataValueNonScalarError attribute) (phenotypic.tools_.exceptions_.NoArrayError attribute) (phenotypic.tools_.exceptions_.NoComponentError attribute) (phenotypic.tools_.exceptions_.NoImageDataError attribute) (phenotypic.tools_.exceptions_.NoObjectsError attribute) (phenotypic.tools_.exceptions_.NoOutputError attribute) (phenotypic.tools_.exceptions_.ObjectNotFoundError attribute) (phenotypic.tools_.exceptions_.OperationFailedError attribute) (phenotypic.tools_.exceptions_.OperationIntegrityError attribute) (phenotypic.tools_.exceptions_.OutputValueError attribute) (phenotypic.tools_.exceptions_.PhenoTypicError attribute) (phenotypic.tools_.exceptions_.UnknownError attribute) (phenotypic.tools_.exceptions_.UnsupportedFileTypeError attribute) (phenotypic.tools_.exceptions_.UnsupportedImageFormat attribute) (phenotypic.tools_.exceptions_.UuidAssignmentError attribute) (phenotypic.tools_.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) assemble_composite_cost() (in module phenotypic.tools_.branch_pathfinding) assemble_connected_mask() (in module phenotypic.tools_.branch_pathfinding) assert_swmr_on() (phenotypic.tools_.HDF static method) (phenotypic.tools_.hdf_.HDF static method) assign_fragments_to_colonies() (in module phenotypic.tools_.branch_pathfinding) AsymmetricSpurTrimmer (class in phenotypic.refine) AutoGridFinder (class in phenotypic.grid) available() (phenotypic.tools_.register.AnalysisPluginRegistry class method) (phenotypic.tools_.register.BaseRegistry class method) (phenotypic.tools_.register.DashboardRegistry class method) (phenotypic.tools_.register.PlotterRegistry class method) available_analysis_plugins() (in module phenotypic.tools_.register) available_dashboards() (in module phenotypic.tools_.register) available_plotters() (in module phenotypic.tools_.register) B B_STAR_COEFF_VARIANCE (phenotypic.tools_.measurement_info_.ColorLab attribute) b_star_headers() (phenotypic.tools_.measurement_info_.ColorLab class method) B_STAR_MAXIMUM (phenotypic.tools_.measurement_info_.ColorLab attribute) B_STAR_MEAN (phenotypic.tools_.measurement_info_.ColorLab attribute) B_STAR_MEDIAN (phenotypic.tools_.measurement_info_.ColorLab attribute) B_STAR_MINIMUM (phenotypic.tools_.measurement_info_.ColorLab attribute) B_STAR_Q1 (phenotypic.tools_.measurement_info_.ColorLab attribute) B_STAR_Q3 (phenotypic.tools_.measurement_info_.ColorLab attribute) B_STAR_STDDEV (phenotypic.tools_.measurement_info_.ColorLab attribute) background_estimate (phenotypic.util.BackgroundMetrics attribute) (phenotypic.util.image_metrics.BackgroundMetrics attribute) BackgroundMetrics (class in phenotypic.util) (class in phenotypic.util.image_metrics) backtrack_path() (in module phenotypic.tools_.branch_pathfinding) band_cost_variance (phenotypic.tools_.branch_pathfinding.PathMetrics attribute), [1] band_variance_values (phenotypic.tools_.branch_pathfinding.CalibrationData attribute), [1] BASE (phenotypic.tools_.constants_.IMAGE_TYPES attribute) BaseOperation (class in phenotypic.abc_) BaseRegistry (class in phenotypic.tools_.register) BayesShrinkCorrector (class in phenotypic.correction) BayesShrinkEnhancer (class in phenotypic.enhance) BBOX (class in phenotypic.tools_.measurement_info_) BBOX_AREA (phenotypic.tools_.measurement_info_.SHAPE attribute) benchmark (phenotypic.prefab.HeavyRoundPeaksPipeline 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) beta (phenotypic.analysis.LinearSoftplusModel attribute) (phenotypic.analysis.LogGrowthModel attribute) (phenotypic.detect.FilamentousFungiDetector attribute) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL attribute) BETA (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL attribute) BGR (phenotypic.tools_.constants_.IMAGE_MODE attribute) BGRA (phenotypic.tools_.constants_.IMAGE_MODE attribute) BilateralDenoise (class in phenotypic.enhance) BIT_DEPTH (phenotypic.tools_.constants_.METADATA attribute) bit_depth (phenotypic.util.image_metrics.ImageMetricsCalculator attribute) (phenotypic.util.image_metrics.ImageMetricsCalculator property) (phenotypic.util.ImageMetricsCalculator attribute) (phenotypic.util.ImageMetricsCalculator property) BLACK_PCT (phenotypic.tools_.measurement_info_.ColorComposition attribute) BLUE_PCT (phenotypic.tools_.measurement_info_.ColorComposition attribute) 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) BM3DDenoiser (class in phenotypic.enhance) border_remover_size (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) BorderObjectRemover (class in phenotypic.refine) boundary_displacement() (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) BRIGHTNESS_COEFF_VARIANCE (phenotypic.tools_.measurement_info_.ColorHSV attribute) brightness_headers() (phenotypic.tools_.measurement_info_.ColorHSV class method) BRIGHTNESS_MAXIMUM (phenotypic.tools_.measurement_info_.ColorHSV attribute) BRIGHTNESS_MEAN (phenotypic.tools_.measurement_info_.ColorHSV attribute) BRIGHTNESS_MEDIAN (phenotypic.tools_.measurement_info_.ColorHSV attribute) BRIGHTNESS_MINIMUM (phenotypic.tools_.measurement_info_.ColorHSV attribute) BRIGHTNESS_Q1 (phenotypic.tools_.measurement_info_.ColorHSV attribute) BRIGHTNESS_Q3 (phenotypic.tools_.measurement_info_.ColorHSV attribute) BRIGHTNESS_STDDEV (phenotypic.tools_.measurement_info_.ColorHSV attribute) BROWN_PCT (phenotypic.tools_.measurement_info_.ColorComposition attribute) build_layer_resolution_index() (in module phenotypic.gui.sweep) by_image (phenotypic.gui.sweep.SweepOutputData attribute) by_pipeline (phenotypic.gui.sweep.SweepOutputData attribute) C calculate_optimal_array_chunks() (in module phenotypic.tools_.slurm) calibrate_screening_threshold() (in module phenotypic.tools_.branch_pathfinding) calibrate_thresholds() (in module phenotypic.tools_.branch_pathfinding) CalibrationData (class in phenotypic.tools_.branch_pathfinding) CannyDetector (class in phenotypic.detect) capitalize() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) casefold() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) CATEGORY (phenotypic.abc_.MeasurementInfo attribute) (phenotypic.abc_.MeasurementInfo property) (phenotypic.tools_.constants_.ConstantLabels property) (phenotypic.tools_.constants_.GAMMA_ENCODINGS property) (phenotypic.tools_.constants_.METADATA property) (phenotypic.tools_.constants_.PIPE_STATUS property) (phenotypic.tools_.measurement_info_.BBOX property) (phenotypic.tools_.measurement_info_.ColorComposition property) (phenotypic.tools_.measurement_info_.ColorHSV property) (phenotypic.tools_.measurement_info_.ColorLab property) (phenotypic.tools_.measurement_info_.Colorxy property) (phenotypic.tools_.measurement_info_.ColorXYZ property) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION property) (phenotypic.tools_.measurement_info_.GRID property) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS property) (phenotypic.tools_.measurement_info_.GRID_SPATIAL property) (phenotypic.tools_.measurement_info_.GRID_SPREAD property) (phenotypic.tools_.measurement_info_.INTENSITY property) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL property) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL property) (phenotypic.tools_.measurement_info_.MODEL_METRICS property) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION property) (phenotypic.tools_.measurement_info_.SHAPE property) (phenotypic.tools_.measurement_info_.SIZE property) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS property) (phenotypic.tools_.measurement_info_.TEXTURE property) category() (phenotypic.abc_.MeasurementInfo class method) (phenotypic.tools_.constants_.ConstantLabels class method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS class method) (phenotypic.tools_.constants_.METADATA class method) (phenotypic.tools_.constants_.PIPE_STATUS class method) (phenotypic.tools_.measurement_info_.BBOX class method) (phenotypic.tools_.measurement_info_.ColorComposition class method) (phenotypic.tools_.measurement_info_.ColorHSV class method) (phenotypic.tools_.measurement_info_.ColorLab class method) (phenotypic.tools_.measurement_info_.Colorxy class method) (phenotypic.tools_.measurement_info_.ColorXYZ class method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION class method) (phenotypic.tools_.measurement_info_.GRID class method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS class method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL class method) (phenotypic.tools_.measurement_info_.GRID_SPREAD class method) (phenotypic.tools_.measurement_info_.INTENSITY class method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL class method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL class method) (phenotypic.tools_.measurement_info_.MODEL_METRICS class method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION class method) (phenotypic.tools_.measurement_info_.SHAPE class method) (phenotypic.tools_.measurement_info_.SIZE class method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS class method) (phenotypic.tools_.measurement_info_.TEXTURE class method) center() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) CENTER_CC (phenotypic.tools_.measurement_info_.BBOX attribute) CENTER_RR (phenotypic.tools_.measurement_info_.BBOX attribute) CenterDeviationReducer (class in phenotypic.refine) CHANNELS_DEFAULT (phenotypic.tools_.constants_.IMAGE_MODE attribute) ChanVeseDetector (class in phenotypic.detect) CHROMA_EST_MEAN (phenotypic.tools_.measurement_info_.ColorLab attribute) CHROMA_EST_MEDIAN (phenotypic.tools_.measurement_info_.ColorLab attribute) cieX_headers() (phenotypic.tools_.measurement_info_.ColorXYZ class method) cieY_headers() (phenotypic.tools_.measurement_info_.ColorXYZ class method) cieZ_headers() (phenotypic.tools_.measurement_info_.ColorXYZ class method) CIRCULARITY (phenotypic.tools_.measurement_info_.SHAPE attribute) CLAHE (class in phenotypic.enhance) clahe_clip_limit (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) clahe_kernel_size (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) clear() (phenotypic.util.BackgroundMetrics method) (phenotypic.util.ContrastMetrics method) (phenotypic.util.image_metrics.BackgroundMetrics method) (phenotypic.util.image_metrics.ContrastMetrics method) (phenotypic.util.image_metrics.NoiseMetrics method) (phenotypic.util.image_metrics.QualityScores method) (phenotypic.util.image_metrics.StructureMetrics method) (phenotypic.util.NoiseMetrics method) (phenotypic.util.QualityScores method) (phenotypic.util.StructureMetrics method) ClipControlMixin (class in phenotypic.tools_) (class in phenotypic.tools_.mixin) close_handle() (phenotypic.tools_.HDF static method) (phenotypic.tools_.hdf_.HDF static method) COEFFICIENT_VARIANCE_INTENSITY (phenotypic.tools_.measurement_info_.INTENSITY attribute) Coherence (phenotypic.util.image_metrics.QualityScores attribute) (phenotypic.util.QualityScores attribute) coherence_map (phenotypic.util.image_metrics.StructureMetrics attribute) (phenotypic.util.StructureMetrics attribute) CoherenceEnhancingDiffusion (class in phenotypic.enhance) col_edges (phenotypic.grid.ManualGridFinder attribute) COL_INTERVAL_END (phenotypic.tools_.measurement_info_.GRID attribute) COL_INTERVAL_START (phenotypic.tools_.measurement_info_.GRID attribute) COL_LINREG_B (phenotypic.tools_.constants_.GRID_LINREG_STATS_EXTRACTOR attribute) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS attribute) COL_LINREG_M (phenotypic.tools_.constants_.GRID_LINREG_STATS_EXTRACTOR attribute) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS attribute) COL_MAJOR_IDX (phenotypic.tools_.measurement_info_.GRID attribute) COL_NUM (phenotypic.tools_.measurement_info_.GRID attribute) colony colony_centroids (phenotypic.tools_.branch_pathfinding.DijkstraResult attribute), [1] colony_id (phenotypic.tools_.branch_pathfinding.DijkstraResult attribute), [1] (phenotypic.tools_.branch_pathfinding.FragmentAssignment attribute), [1] (phenotypic.tools_.branch_pathfinding.FragmentPath attribute), [1] color (phenotypic.Image property), [1] 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) ColorComposition (class in phenotypic.tools_.measurement_info_) ColorCorrector (class in phenotypic.correction) ColorHSV (class in phenotypic.tools_.measurement_info_) ColorLab (class in phenotypic.tools_.measurement_info_) Colorxy (class in phenotypic.tools_.measurement_info_) ColorXYZ (class in phenotypic.tools_.measurement_info_) COMPACTNESS (phenotypic.tools_.measurement_info_.SHAPE attribute) CompositeDetector (class in phenotypic.detect) compute() (phenotypic.abc_.DetectionMode method) compute_all() (phenotypic.util.image_metrics.ImageMetricsCalculator method) (phenotypic.util.ImageMetricsCalculator method) compute_anisotropy() (in module phenotypic.tools_.branch_pathfinding) compute_background_metrics() (phenotypic.util.image_metrics.ImageMetricsCalculator method) (phenotypic.util.ImageMetricsCalculator method) compute_contrast_metrics() (phenotypic.util.image_metrics.ImageMetricsCalculator method) (phenotypic.util.ImageMetricsCalculator method) compute_local_contrast() (phenotypic.util.image_metrics.ImageMetricsCalculator method) (phenotypic.util.ImageMetricsCalculator method) compute_local_mad_map() (in module phenotypic.tools_.branch_pathfinding) compute_local_variance() (phenotypic.util.image_metrics.ImageMetricsCalculator method) (phenotypic.util.ImageMetricsCalculator method) compute_min_cost_envelope() (in module phenotypic.tools_.branch_pathfinding) compute_noise_metrics() (phenotypic.util.image_metrics.ImageMetricsCalculator method) (phenotypic.util.ImageMetricsCalculator method) compute_orientation_coherence() (in module phenotypic.tools_.branch_pathfinding) compute_path_metrics() (in module phenotypic.tools_.branch_pathfinding) compute_psd() (phenotypic.util.image_metrics.ImageMetricsCalculator method) (phenotypic.util.ImageMetricsCalculator method) compute_quality_scores() (phenotypic.util.image_metrics.ImageMetricsCalculator method) (phenotypic.util.ImageMetricsCalculator method) compute_structure_metrics() (phenotypic.util.image_metrics.ImageMetricsCalculator method) (phenotypic.util.ImageMetricsCalculator method) config_group (phenotypic.gui.sweep.PipelineConfig attribute) connectivity_correct_labels() (in module phenotypic.tools_.branch_pathfinding) ConstantLabels (class in phenotypic.tools_.constants_) CONTRAST (phenotypic.tools_.measurement_info_.TEXTURE attribute) Contrast (phenotypic.util.image_metrics.QualityScores attribute) (phenotypic.util.QualityScores attribute) ContrastMetrics (class in phenotypic.util) (class in phenotypic.util.image_metrics) ContrastStretching (class in phenotypic.enhance) CONVEX_AREA (phenotypic.tools_.measurement_info_.SHAPE attribute) CONVEX_DENSITY (phenotypic.tools_.measurement_info_.INTENSITY attribute) coords (phenotypic.tools_.branch_pathfinding.FragmentPath attribute), [1] copy() (phenotypic._core._image_parts.accessors._detect_mat_accessor.DetectMatAccessor method) (phenotypic._core._image_parts.accessors._grayscale_accessor.Grayscale method) (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap method) (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask method) (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) (phenotypic._core._image_parts.accessors._rgb_accessor.ImageRGB method) (phenotypic.GridImage method) (phenotypic.Image method) (phenotypic.util.BackgroundMetrics method) (phenotypic.util.ContrastMetrics method) (phenotypic.util.image_metrics.BackgroundMetrics method) (phenotypic.util.image_metrics.ContrastMetrics method) (phenotypic.util.image_metrics.NoiseMetrics method) (phenotypic.util.image_metrics.QualityScores method) (phenotypic.util.image_metrics.StructureMetrics method) (phenotypic.util.NoiseMetrics method) (phenotypic.util.QualityScores method) (phenotypic.util.StructureMetrics method) CORE_AREA (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS attribute) CORE_END_RADIUS (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS attribute) CORE_RADIUS (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION attribute) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS attribute) CORRECTED_CAP (phenotypic.tools_.measurement_info_.EDGE_CORRECTION attribute) correction_matrix (phenotypic.correction.ColorCheckerProfile attribute) (phenotypic.correction.ColorCheckerProfile property) (phenotypic.correction.ColorCorrector attribute) CORRELATION (phenotypic.tools_.measurement_info_.TEXTURE attribute) correlation_length (phenotypic.util.image_metrics.NoiseMetrics attribute) (phenotypic.util.NoiseMetrics attribute) cost_distance (phenotypic.tools_.branch_pathfinding.DijkstraResult attribute), [1] cost_profile (phenotypic.tools_.branch_pathfinding.FragmentPath attribute), [1] count() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) CROP (phenotypic.tools_.constants_.IMAGE_TYPES attribute) cval (phenotypic.enhance.MedianFilter attribute) CYAN_PCT (phenotypic.tools_.measurement_info_.ColorComposition attribute) D 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.analysis.abc_.ModelFitter method) (phenotypic.analysis.abc_.SetAnalyzer method) (phenotypic.analysis.EdgeCorrector method) (phenotypic.analysis.LinearSoftplusModel method) (phenotypic.analysis.LogGrowthModel method) (phenotypic.analysis.TukeyOutlierRemover method) dashboard() (phenotypic.correction.ColorCheckerProfile method) (phenotypic.correction.ColorCorrector method) DashboardRegistry (class in phenotypic.tools_.register) DataIntegrityError DEFAULT_SCHEMA (phenotypic.tools_.constants_.IMAGE_MODE attribute) degree (phenotypic.correction.ColorCorrector attribute) delta (phenotypic.detect.FilamentousFungiDetector attribute) DENSE_AREA (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS attribute) DENSE_END_RADIUS (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS attribute) DENSITY (phenotypic.tools_.measurement_info_.INTENSITY attribute) desc (phenotypic.abc_.MeasurementInfo attribute) (phenotypic.abc_.PrefabPipeline 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) detect_mat (phenotypic.gui.sweep.ResolvedLayerSources attribute) (phenotypic.Image property) detect_sweep_dir() (phenotypic.gui.sweep.SweepOutputScanner static 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) (phenotypic.correction.ColorCheckerProfile property) diagnostics() (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) DIFFERENCE_ENTROPY (phenotypic.tools_.measurement_info_.TEXTURE attribute) DIFFERENCE_VARIANCE (phenotypic.tools_.measurement_info_.TEXTURE attribute) DijkstraResult (class in phenotypic.tools_.branch_pathfinding) display_or_return() (in module phenotypic.tools_.panel_) DIST_WEIGHTED_CENTER_CC (phenotypic.tools_.measurement_info_.BBOX attribute) DIST_WEIGHTED_CENTER_RR (phenotypic.tools_.measurement_info_.BBOX 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) (phenotypic.util.image_metrics.ContrastMetrics attribute) E ECCENTRICITY (phenotypic.tools_.measurement_info_.SHAPE attribute) EDGE_CORRECTION (class in phenotypic.tools_.measurement_info_) EdgeCorrector (class in phenotypic.analysis) EmptyImageError encode() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) endswith() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) ensure_panel_extension() (in module phenotypic.tools_.panel_) ENTROPY (phenotypic.tools_.measurement_info_.TEXTURE attribute) error_exit() (in module phenotypic.phenotypicCLI) estimate_concurrent_capacity() (in module phenotypic.tools_.slurm) euclidean_voronoi_assign() (in module phenotypic.tools_.branch_pathfinding) ExpandMetadata (class in phenotypic.post) expandtabs() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) EXT (phenotypic.tools_.HDF attribute), [1] (phenotypic.tools_.hdf_.HDF attribute), [1] EXTENT (phenotypic.tools_.measurement_info_.SHAPE attribute) extract_calibration_branches() (in module phenotypic.tools_.branch_pathfinding) extract_fragment_paths() (in module phenotypic.tools_.branch_pathfinding) F FIGSIZE (phenotypic.settings_.MPL attribute) FilamentousFungiDetector (class in phenotypic.detect) FilamentousFungiPipeline (class in phenotypic.prefab) filepath (phenotypic.tools_.HDF attribute), [1] (phenotypic.tools_.hdf_.HDF attribute), [1] filter_paths() (in module phenotypic.tools_.branch_pathfinding) FilterResult (class in phenotypic.tools_.branch_pathfinding) FilterThresholds (class in phenotypic.tools_.branch_pathfinding) find() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) fit() (phenotypic.correction.ColorCheckerProfile method) Fixed (class in phenotypic.sweep) FootprintMixin (class in phenotypic.abc_) (class in phenotypic.tools_) (class in phenotypic.tools_.mixin) foreground() (phenotypic._core._image_parts.accessors._detect_mat_accessor.DetectMatAccessor method) (phenotypic._core._image_parts.accessors._grayscale_accessor.Grayscale method) (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap method) (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask method) (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) (phenotypic._core._image_parts.accessors._rgb_accessor.ImageRGB method) format() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) format_map() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) format_sbatch_directives() (in module phenotypic.tools_.slurm) fragment_id (phenotypic.tools_.branch_pathfinding.FragmentAssignment attribute), [1] (phenotypic.tools_.branch_pathfinding.FragmentPath attribute), [1] FragmentAssignment (class in phenotypic.tools_.branch_pathfinding) FragmentPath (class in phenotypic.tools_.branch_pathfinding) FrangiVesselness (class in phenotypic.enhance) from_dict() (phenotypic.correction.ColorCheckerProfile class method) from_json() (phenotypic.abc_.PrefabPipeline class method) (phenotypic.ImagePipeline 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) fromkeys() (phenotypic.util.BackgroundMetrics method) (phenotypic.util.ContrastMetrics method) (phenotypic.util.image_metrics.BackgroundMetrics method) (phenotypic.util.image_metrics.ContrastMetrics method) (phenotypic.util.image_metrics.NoiseMetrics method) (phenotypic.util.image_metrics.QualityScores method) (phenotypic.util.image_metrics.StructureMetrics method) (phenotypic.util.NoiseMetrics method) (phenotypic.util.QualityScores method) (phenotypic.util.StructureMetrics method) G gamma (phenotypic.detect.FilamentousFungiDetector attribute) GAMMA_ENCODINGS (class in phenotypic.tools_.constants_) gauss_n_iter (phenotypic.detect.FilamentousFungiDetector attribute) GaussianBlur (class in phenotypic.enhance) generate_dispatcher_chain() (in module phenotypic.tools_.slurm) generate_dispatcher_script() (in module phenotypic.tools_.slurm) generate_interpretation() (phenotypic.util.image_metrics.ImageMetricsCalculator static method) (phenotypic.util.ImageMetricsCalculator static method) generate_recommendations() (phenotypic.util.image_metrics.ImageMetricsCalculator static method) (phenotypic.util.ImageMetricsCalculator static method) generate_sweep_manifest() (in module phenotypic.sweep) geometric_median() (in module phenotypic.util) get() (phenotypic._core._image_parts.accessors._metadata_accessor.MetadataAccessor method) (phenotypic.tools_.register.AnalysisPluginRegistry class method) (phenotypic.tools_.register.BaseRegistry class method) (phenotypic.tools_.register.DashboardRegistry class method) (phenotypic.tools_.register.PlotterRegistry class method) (phenotypic.util.BackgroundMetrics method) (phenotypic.util.ContrastMetrics method) (phenotypic.util.image_metrics.BackgroundMetrics method) (phenotypic.util.image_metrics.ContrastMetrics method) (phenotypic.util.image_metrics.NoiseMetrics method) (phenotypic.util.image_metrics.QualityScores method) (phenotypic.util.image_metrics.StructureMetrics method) (phenotypic.util.NoiseMetrics method) (phenotypic.util.QualityScores method) (phenotypic.util.StructureMetrics method) get_analysis_plugin() (in module phenotypic.tools_.register) get_centroid_alignment_info() (phenotypic._core._image_parts.accessors._grid_accessor.GridAccessor method) get_col_edges() (phenotypic._core._image_parts.accessors._grid_accessor.GridAccessor method) (phenotypic.abc_.GridFinder method) (phenotypic.grid.AutoGridFinder method) (phenotypic.grid.ManualGridFinder method) get_col_map() (phenotypic._core._image_parts.accessors._grid_accessor.GridAccessor method) get_dashboard() (in module phenotypic.tools_.register) get_data_group() (phenotypic.tools_.HDF method) (phenotypic.tools_.hdf_.HDF method) get_group() (phenotypic.tools_.HDF static method) (phenotypic.tools_.hdf_.HDF static method) get_headers() (phenotypic.abc_.MeasurementInfo class method) (phenotypic.tools_.constants_.ConstantLabels class method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS class method) (phenotypic.tools_.constants_.METADATA class method) (phenotypic.tools_.constants_.PIPE_STATUS class method) (phenotypic.tools_.measurement_info_.BBOX class method) (phenotypic.tools_.measurement_info_.ColorComposition class method) (phenotypic.tools_.measurement_info_.ColorHSV class method) (phenotypic.tools_.measurement_info_.ColorLab class method) (phenotypic.tools_.measurement_info_.Colorxy class method) (phenotypic.tools_.measurement_info_.ColorXYZ class method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION class method) (phenotypic.tools_.measurement_info_.GRID class method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS class method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL class method) (phenotypic.tools_.measurement_info_.GRID_SPREAD class method) (phenotypic.tools_.measurement_info_.INTENSITY class method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL class method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL class method) (phenotypic.tools_.measurement_info_.MODEL_METRICS class method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION class method) (phenotypic.tools_.measurement_info_.SHAPE class method) (phenotypic.tools_.measurement_info_.SIZE class method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS class method) (phenotypic.tools_.measurement_info_.TEXTURE class method) get_home() (phenotypic.tools_.HDF method) (phenotypic.tools_.hdf_.HDF method) get_image_group() (phenotypic.tools_.HDF method) (phenotypic.tools_.hdf_.HDF method) get_image_measurement_subgroup() (phenotypic.tools_.HDF method) (phenotypic.tools_.hdf_.HDF method) get_info_by_section() (phenotypic._core._image_parts.accessors._grid_accessor.GridAccessor method) get_label_idx() (phenotypic._core._image_parts.accessors._objects_accessor.ObjectsAccessor method) get_labels() (phenotypic.abc_.MeasurementInfo class method) (phenotypic.tools_.constants_.ConstantLabels class method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS class method) (phenotypic.tools_.constants_.METADATA class method) (phenotypic.tools_.constants_.PIPE_STATUS class method) (phenotypic.tools_.measurement_info_.BBOX class method) (phenotypic.tools_.measurement_info_.ColorComposition class method) (phenotypic.tools_.measurement_info_.ColorHSV class method) (phenotypic.tools_.measurement_info_.ColorLab class method) (phenotypic.tools_.measurement_info_.Colorxy class method) (phenotypic.tools_.measurement_info_.ColorXYZ class method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION class method) (phenotypic.tools_.measurement_info_.GRID class method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS class method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL class method) (phenotypic.tools_.measurement_info_.GRID_SPREAD class method) (phenotypic.tools_.measurement_info_.INTENSITY class method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL class method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL class method) (phenotypic.tools_.measurement_info_.MODEL_METRICS class method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION class method) (phenotypic.tools_.measurement_info_.SHAPE class method) (phenotypic.tools_.measurement_info_.SIZE class method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS class method) (phenotypic.tools_.measurement_info_.TEXTURE 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_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.tools_.register) get_protected_metadata_subgroup() (phenotypic.tools_.HDF method) (phenotypic.tools_.hdf_.HDF method) get_public_metadata_subgroup() (phenotypic.tools_.HDF method) (phenotypic.tools_.hdf_.HDF method) get_root_group() (phenotypic.tools_.HDF method) (phenotypic.tools_.hdf_.HDF method) get_row_edges() (phenotypic._core._image_parts.accessors._grid_accessor.GridAccessor method) (phenotypic.abc_.GridFinder method) (phenotypic.grid.AutoGridFinder method) (phenotypic.grid.ManualGridFinder method) get_row_map() (phenotypic._core._image_parts.accessors._grid_accessor.GridAccessor method) get_section_counts() (phenotypic._core._image_parts.accessors._grid_accessor.GridAccessor method) get_section_map() (phenotypic._core._image_parts.accessors._grid_accessor.GridAccessor method) get_slurm_array_limit() (in module phenotypic.tools_.slurm) get_slurm_max_submit_jobs() (in module phenotypic.tools_.slurm) get_status_subgroup() (phenotypic.tools_.HDF method) (phenotypic.tools_.hdf_.HDF method) get_uncompressed_sizes_for_group() (phenotypic.tools_.HDF static method) (phenotypic.tools_.hdf_.HDF static method) GMMCoreExtractor (class in phenotypic.refine) GpuDetector (class in phenotypic.abc_) gray (phenotypic.gui.sweep.ResolvedLayerSources attribute) (phenotypic.Image property) gray_band_snr (phenotypic.tools_.branch_pathfinding.PathMetrics attribute), [1] GRAY_PCT (phenotypic.tools_.measurement_info_.ColorComposition attribute) gray_snr_values (phenotypic.tools_.branch_pathfinding.CalibrationData attribute), [1] GrayOpening (class in phenotypic.enhance) Grayscale (class in phenotypic._core._image_parts.accessors._grayscale_accessor) GRAYSCALE (phenotypic.tools_.constants_.IMAGE_MODE attribute) GRAYSCALE_SINGLE_CHANNEL (phenotypic.tools_.constants_.IMAGE_MODE attribute) GrayscaleOutOfRangeError GREEN_PCT (phenotypic.tools_.measurement_info_.ColorComposition attribute) GRID (class in phenotypic.tools_.measurement_info_) grid (phenotypic.GridImage property) GRID (phenotypic.tools_.constants_.IMAGE_TYPES attribute) grid section grid_aligner_axis (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) grid_aligner_mode (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) GRID_LINREG_STATS (class in phenotypic.tools_.measurement_info_) GRID_LINREG_STATS_EXTRACTOR (class in phenotypic.tools_.constants_) GRID_SECTION (phenotypic.tools_.constants_.IMAGE_TYPES attribute) GRID_SPATIAL (class in phenotypic.tools_.measurement_info_) GRID_SPREAD (class in phenotypic.tools_.measurement_info_) GridAccessor (class in phenotypic._core._image_parts.accessors._grid_accessor) GridAligner (class in phenotypic.correction) GridAlignmentRefiner (class in phenotypic.refine) GridApply (class in phenotypic.grid) GridCorrector (class in phenotypic.abc_) GridFinder (class in phenotypic.abc_) GridImage GridImageInputError GridInferenceMixin (class in phenotypic.tools_) (class in phenotypic.tools_.mixin) GridMeasureFeatures (class in phenotypic.abc_) GridObjectDetector (class in phenotypic.abc_) GridObjectRefiner (class in phenotypic.abc_) GridOperation (class in phenotypic.abc_) GridOversizedObjectRemover (class in phenotypic.refine) GridSectionLargest (class in phenotypic.refine) GridSectionPipeline (class in phenotypic.prefab) groupby (phenotypic.analysis.TukeyOutlierRemover attribute) GROWTH_RATE (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL attribute) H h5_path (phenotypic.gui.sweep.IntermediateStep attribute) HDF (class in phenotypic.tools_) (class in phenotypic.tools_.hdf_) hdf5_files (phenotypic.gui.sweep.SweepOutputData attribute) HeavyOtsuPipeline (class in phenotypic.prefab) HeavyRoundPeaksPipeline (class in phenotypic.prefab) HeavyWatershedPipeline (class in phenotypic.prefab) HessianFilter (class in phenotypic.enhance) 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.tools_.HDF attribute), [1] (phenotypic.tools_.hdf_.HDF attribute), [1] HomomorphicFilter (class in phenotypic.enhance) hsv (phenotypic._core._image_parts.accessors._color_accessor.ColorAccessor property) HSV (phenotypic.tools_.constants_.IMAGE_MODE attribute) HUE_COEFF_VARIANCE (phenotypic.tools_.measurement_info_.ColorHSV attribute) hue_headers() (phenotypic.tools_.measurement_info_.ColorHSV class method) HUE_MAXIMUM (phenotypic.tools_.measurement_info_.ColorHSV attribute) HUE_MEAN (phenotypic.tools_.measurement_info_.ColorHSV attribute) HUE_MEDIAN (phenotypic.tools_.measurement_info_.ColorHSV attribute) HUE_MINIMUM (phenotypic.tools_.measurement_info_.ColorHSV attribute) HUE_Q1 (phenotypic.tools_.measurement_info_.ColorHSV attribute) HUE_Q3 (phenotypic.tools_.measurement_info_.ColorHSV attribute) HUE_STDDEV (phenotypic.tools_.measurement_info_.ColorHSV attribute) hyphae HysteresisDetector (class in phenotypic.detect) I IllegalAssignmentError IllegalElementAssignmentError iloc() (phenotypic._core._image_parts.accessors._objects_accessor.ObjectsAccessor method) Image (in module phenotypic.tools_.funcs_) IMAGE_MEASUREMENT_IMAGE_SUBGROUP_KEY (phenotypic.tools_.constants_.IO attribute) IMAGE_MEASUREMENT_SUBGROUP_KEY (phenotypic.tools_.HDF attribute), [1] (phenotypic.tools_.hdf_.HDF attribute), [1] IMAGE_MODE (class in phenotypic.tools_.constants_) IMAGE_NAME (phenotypic.tools_.constants_.METADATA attribute) IMAGE_SET_DATA_POSIX (phenotypic.tools_.HDF attribute), [1] (phenotypic.tools_.hdf_.HDF attribute), [1] IMAGE_SET_HDF5_PARENT_GROUP (phenotypic.tools_.constants_.IO attribute) IMAGE_SET_ROOT_POSIX (phenotypic.tools_.HDF attribute), [1] (phenotypic.tools_.hdf_.HDF attribute), [1] IMAGE_STATUS_SUBGROUP_KEY (phenotypic.tools_.constants_.IO attribute) (phenotypic.tools_.HDF attribute), [1] (phenotypic.tools_.hdf_.HDF attribute), [1] image_stem (phenotypic.gui.sweep.SweepHDF5File attribute) image_stems (phenotypic.gui.sweep.SweepOutputData attribute) IMAGE_TYPE (phenotypic.tools_.constants_.METADATA attribute) IMAGE_TYPES (class in phenotypic.tools_.constants_) ImageCorrector (class in phenotypic.abc_) ImageCropper (class in phenotypic.correction) ImageEnhancer (class in phenotypic.abc_) ImageInverter (class in phenotypic.enhance) ImageMetricsCalculator (class in phenotypic.util) (class in phenotypic.util.image_metrics) ImageOperation (class in phenotypic.abc_) ImageOperationError ImagePadder (class in phenotypic.correction) ImagePipeline ImageRGB (class in phenotypic._core._image_parts.accessors._rgb_accessor) IMC1 (phenotypic.tools_.measurement_info_.TEXTURE attribute) IMC2 (phenotypic.tools_.measurement_info_.TEXTURE attribute) IMFORMAT (phenotypic.tools_.constants_.METADATA attribute) ImmutableComponentError 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) in_ipython() (in module phenotypic.tools_.panel_) in_jupyter() (in module phenotypic.tools_.panel_) index (phenotypic.gui.sweep.IntermediateStep attribute) index() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) info() (phenotypic._core._image_parts.accessors._grid_accessor.GridAccessor method) (phenotypic._core._image_parts.accessors._objects_accessor.ObjectsAccessor method) inoc_size_label (phenotypic.analysis.LinearSoftplusModel attribute) inoculum InoculumDetector (class in phenotypic.detect) InputShapeMismatchError insert_metadata() (phenotypic._core._image_parts.accessors._metadata_accessor.MetadataAccessor method) inspect() (phenotypic.grid.AutoGridFinder method) (phenotypic.measure.MeasureSymmetricZones method) INTEGRATED_INTENSITY (phenotypic.tools_.measurement_info_.INTENSITY attribute) (phenotypic.tools_.measurement_info_.SIZE attribute) INTENSITY (class in phenotypic.tools_.measurement_info_) INTENSITY_WEIGHTED_CENTER_CC (phenotypic.tools_.measurement_info_.BBOX attribute) INTENSITY_WEIGHTED_CENTER_RR (phenotypic.tools_.measurement_info_.BBOX attribute) InterfaceError intermediates (phenotypic.gui.sweep.SweepOutputData attribute) IntermediateStep (class in phenotypic.gui.sweep) InvalidHsvSchemaError InvalidMapValueError InvalidMaskScalarValueError InvalidMaskValueError InvalidShapeError INVERSE_DIFFERENCE_MOMENT (phenotypic.tools_.measurement_info_.TEXTURE attribute) IO (class in phenotypic.tools_.constants_) IQR_INTENSITY (phenotypic.tools_.measurement_info_.INTENSITY attribute) is_ambiguous() (phenotypic.tools_.constants_.IMAGE_MODE method) is_array() (phenotypic.tools_.constants_.IMAGE_MODE method) is_base (phenotypic.gui.sweep.IntermediateStep attribute) is_binary_mask() (in module phenotypic.tools_) (in module phenotypic.tools_.funcs_) is_bridge (phenotypic.tools_.branch_pathfinding.FragmentAssignment attribute), [1] is_fitted (phenotypic.correction.ColorCheckerProfile attribute) (phenotypic.correction.ColorCheckerProfile property) is_matrix() (phenotypic.tools_.constants_.IMAGE_MODE method) is_none() (phenotypic.tools_.constants_.IMAGE_MODE method) is_static_method() (in module phenotypic.tools_.funcs_) isalnum() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) isalpha() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) isascii() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) isdecimal() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) isdigit() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE 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.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) islower() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) isnumeric() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) IsodataDetector (class in phenotypic.detect) isprintable() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) isspace() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) istitle() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) isupper() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) items() (phenotypic._core._image_parts.accessors._metadata_accessor.MetadataAccessor method) (phenotypic.util.BackgroundMetrics method) (phenotypic.util.ContrastMetrics method) (phenotypic.util.image_metrics.BackgroundMetrics method) (phenotypic.util.image_metrics.ContrastMetrics method) (phenotypic.util.image_metrics.NoiseMetrics method) (phenotypic.util.image_metrics.QualityScores method) (phenotypic.util.image_metrics.StructureMetrics method) (phenotypic.util.NoiseMetrics method) (phenotypic.util.QualityScores method) (phenotypic.util.StructureMetrics method) J join() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) JPEG_FILE_EXTENSIONS (phenotypic.tools_.constants_.IO attribute) K k (phenotypic.analysis.TukeyOutlierRemover attribute) K_FIT (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL attribute) k_iqr (phenotypic.tools_.branch_pathfinding.FilterThresholds attribute), [1] K_MAX (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL attribute) keys() (phenotypic._core._image_parts.accessors._metadata_accessor.MetadataAccessor method) (phenotypic.util.BackgroundMetrics method) (phenotypic.util.ContrastMetrics method) (phenotypic.util.image_metrics.BackgroundMetrics method) (phenotypic.util.image_metrics.ContrastMetrics method) (phenotypic.util.image_metrics.NoiseMetrics method) (phenotypic.util.image_metrics.QualityScores method) (phenotypic.util.image_metrics.StructureMetrics method) (phenotypic.util.NoiseMetrics method) (phenotypic.util.QualityScores method) (phenotypic.util.StructureMetrics method) Kmax_label (phenotypic.analysis.LogGrowthModel attribute) L L_STAR_COEFF_VARIANCE (phenotypic.tools_.measurement_info_.ColorLab attribute) l_star_headers() (phenotypic.tools_.measurement_info_.ColorLab class method) L_STAR_MAXIMUM (phenotypic.tools_.measurement_info_.ColorLab attribute) L_STAR_MEAN (phenotypic.tools_.measurement_info_.ColorLab attribute) L_STAR_MEDIAN (phenotypic.tools_.measurement_info_.ColorLab attribute) L_STAR_MINIMUM (phenotypic.tools_.measurement_info_.ColorLab attribute) L_STAR_Q1 (phenotypic.tools_.measurement_info_.ColorLab attribute) L_STAR_Q3 (phenotypic.tools_.measurement_info_.ColorLab attribute) L_STAR_STDDEV (phenotypic.tools_.measurement_info_.ColorLab attribute) Lab (phenotypic._core._image_parts.accessors._color_accessor.ColorAccessor property) label (phenotypic.abc_.MeasurementInfo attribute) LABEL (phenotypic.tools_.constants_.OBJECT attribute) 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) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL attribute) LAM (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL attribute) LaplaceEnhancer (class in phenotypic.enhance) layers (phenotypic.gui.sweep.IntermediateStep attribute) LazyWidgetMixin (class in phenotypic.tools_) (class in phenotypic.tools_.mixin) LEFT_DISTANCE (phenotypic.tools_.measurement_info_.GRID_SPATIAL attribute) LEFT_NEIGHBOR_OBJ_LABEL (phenotypic.tools_.measurement_info_.GRID_SPATIAL attribute) LiDetector (class in phenotypic.detect) LINEAR (phenotypic.tools_.constants_.GAMMA_ENCODINGS attribute) LINEAR_RGB (phenotypic.tools_.constants_.IMAGE_MODE attribute) LINEAR_SOFTPLUS_MODEL (class in phenotypic.tools_.measurement_info_) LinearSoftplusModel (class in phenotypic.analysis) ljust() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE 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.tools_.HDF static method) (phenotypic.tools_.hdf_.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_pipeline_names_from_manifest() (in module phenotypic.sweep) load_plate_12hr() (in module phenotypic.data) load_plate_72hr() (in module phenotypic.data) load_plate_series() (in module phenotypic.data) load_series() (phenotypic.tools_.HDF static method) (phenotypic.tools_.hdf_.HDF static method) load_single_pipeline_from_manifest() (in module phenotypic.sweep) load_smear_plate_12hr() (in module phenotypic.data) load_smear_plate_24hr() (in module phenotypic.data) load_sweep_manifest() (in module phenotypic.sweep) load_synth_yeast_plate() (in module phenotypic.data) load_synthetic_colony() (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) LOG_GROWTH_MODEL (class in phenotypic.tools_.measurement_info_) LogGrowthModel (class in phenotypic.analysis) loss (phenotypic.analysis.abc_.ModelFitter attribute) LOSS (phenotypic.tools_.measurement_info_.MODEL_METRICS attribute) LowCircularityRemover (class in phenotypic.refine) lower() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) lstrip() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) M MadHysteresisDetector (class in phenotypic.detect) MAE (phenotypic.tools_.measurement_info_.MODEL_METRICS attribute) MAJOR_AXIS_LENGTH (phenotypic.tools_.measurement_info_.SHAPE attribute) majority_fraction (phenotypic.tools_.branch_pathfinding.FragmentAssignment attribute), [1] 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.tools_.constants_.ConstantLabels static method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS static method) (phenotypic.tools_.constants_.METADATA static method) (phenotypic.tools_.constants_.PIPE_STATUS static method) (phenotypic.tools_.measurement_info_.BBOX static method) (phenotypic.tools_.measurement_info_.ColorComposition static method) (phenotypic.tools_.measurement_info_.ColorHSV static method) (phenotypic.tools_.measurement_info_.ColorLab static method) (phenotypic.tools_.measurement_info_.Colorxy static method) (phenotypic.tools_.measurement_info_.ColorXYZ static method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION static method) (phenotypic.tools_.measurement_info_.GRID static method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS static method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL static method) (phenotypic.tools_.measurement_info_.GRID_SPREAD static method) (phenotypic.tools_.measurement_info_.INTENSITY static method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL static method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL static method) (phenotypic.tools_.measurement_info_.MODEL_METRICS static method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION static method) (phenotypic.tools_.measurement_info_.SHAPE static method) (phenotypic.tools_.measurement_info_.SIZE static method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS static method) (phenotypic.tools_.measurement_info_.TEXTURE static method) manifest_raw (phenotypic.gui.sweep.SweepOutputData attribute) ManualDetector (class in phenotypic.detect) ManualGridDetector (class in phenotypic.detect) ManualGridFinder (class in phenotypic.grid) ManualPointDetector (class in phenotypic.detect) 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) MaskCloser (class in phenotypic.refine) MaskDilator (class in phenotypic.refine) MaskEroder (class in phenotypic.refine) MaskFill (class in phenotypic.refine) MaskGradient (class in phenotypic.refine) MaskOpener (class in phenotypic.refine) MATRIX_FORMATS (phenotypic.tools_.constants_.IMAGE_MODE attribute) MAX_BRANCH_LENGTH (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION attribute) MAX_CC (phenotypic.tools_.measurement_info_.BBOX attribute) MAX_EXPANSION (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS attribute) MAX_FERET_DIAMETER (phenotypic.tools_.measurement_info_.SHAPE attribute) max_intensity (phenotypic.util.image_metrics.ImageMetricsCalculator property) (phenotypic.util.ImageMetricsCalculator property) MAX_RADIUS (phenotypic.tools_.measurement_info_.SHAPE attribute) MAX_RR (phenotypic.tools_.measurement_info_.BBOX attribute) max_window_cost (phenotypic.tools_.branch_pathfinding.PathMetrics attribute), [1] max_window_cost_values (phenotypic.tools_.branch_pathfinding.CalibrationData attribute), [1] MAXIMUM_INTENSITY (phenotypic.tools_.measurement_info_.INTENSITY attribute) mean_coherence (phenotypic.util.image_metrics.StructureMetrics attribute) (phenotypic.util.StructureMetrics attribute) mean_cost (phenotypic.tools_.branch_pathfinding.FragmentAssignment attribute), [1] MEAN_EXPANSION (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS attribute) mean_gradient (phenotypic.util.BackgroundMetrics attribute) (phenotypic.util.image_metrics.BackgroundMetrics attribute) MEAN_INTENSITY (phenotypic.tools_.measurement_info_.INTENSITY attribute) MEAN_RADIUS (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION attribute) (phenotypic.tools_.measurement_info_.SHAPE attribute) MeanDetector (class in phenotypic.detect) measure() (phenotypic.abc_.GridFinder method) (phenotypic.abc_.GridMeasureFeatures method) (phenotypic.abc_.MeasureFeatures method) (phenotypic.abc_.PrefabPipeline method) (phenotypic.grid.AutoGridFinder method) (phenotypic.grid.ManualGridFinder method) (phenotypic.ImagePipeline method) (phenotypic.measure.MeasureBounds method) (phenotypic.measure.MeasureColor method) (phenotypic.measure.MeasureGridLinRegStats method) (phenotypic.measure.MeasureGridSpatial method) (phenotypic.measure.MeasureGridSpread method) (phenotypic.measure.MeasureIntensity 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) MeasureBounds (class in phenotypic.measure) MeasureColor (class in phenotypic.measure) MEASURED (phenotypic.tools_.constants_.PIPE_STATUS attribute) MeasureFeatures (class in phenotypic.abc_) MeasureGridLinRegStats (class in phenotypic.measure) MeasureGridSpatial (class in phenotypic.measure) MeasureGridSpread (class in phenotypic.measure) MeasureIntensity (class in phenotypic.measure) MeasurementInfo (class in phenotypic.abc_) measurements (phenotypic.gui.sweep.PipelineConfig attribute) MeasureShape (class in phenotypic.measure) MeasureSize (class in phenotypic.measure) MeasureSymmetricZones (class in phenotypic.measure) MeasureTexture (class in phenotypic.measure) median_cost_values (phenotypic.tools_.branch_pathfinding.CalibrationData attribute), [1] median_cval (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) MEDIAN_INTENSITY (phenotypic.tools_.measurement_info_.INTENSITY attribute) median_mode (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) median_radius (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) MEDIAN_RADIUS (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION attribute) (phenotypic.tools_.measurement_info_.SHAPE attribute) median_raw_cost (phenotypic.tools_.branch_pathfinding.PathMetrics attribute), [1] median_shape (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) MedianFilter (class in phenotypic.enhance) MeijeringRidgeFilter (class in phenotypic.enhance) MergeMetadata (class in phenotypic.post) METADATA (class in phenotypic.tools_.constants_) metadata (phenotypic.Image property) MetadataAccessor (class in phenotypic._core._image_parts.accessors._metadata_accessor) MetadataKeySpacesError MetadataKeyValueError MetadataValueNonScalarError metrics (phenotypic.tools_.branch_pathfinding.FilterResult attribute), [1] michelson (phenotypic.util.ContrastMetrics attribute) (phenotypic.util.image_metrics.ContrastMetrics attribute) MIN_CC (phenotypic.tools_.measurement_info_.BBOX attribute) MIN_FERET_DIAMETER (phenotypic.tools_.measurement_info_.SHAPE attribute) MIN_RR (phenotypic.tools_.measurement_info_.BBOX attribute) MINIMUM_INTENSITY (phenotypic.tools_.measurement_info_.INTENSITY attribute) MinimumDetector (class in phenotypic.detect) MINOR_AXIS_LENGTH (phenotypic.tools_.measurement_info_.SHAPE attribute) mode (phenotypic.enhance.MedianFilter attribute) (phenotypic.tools_.HDF attribute), [1] (phenotypic.tools_.hdf_.HDF attribute), [1] model_func() (phenotypic.analysis.abc_.ModelFitter static method) (phenotypic.analysis.LinearSoftplusModel static method) (phenotypic.analysis.LogGrowthModel static method) MODEL_METRICS (class in phenotypic.tools_.measurement_info_) ModelFitter (class in phenotypic.analysis.abc_) module phenotypic phenotypic._core phenotypic.abc_ phenotypic.analysis phenotypic.analysis.abc_ phenotypic.correction phenotypic.data phenotypic.detect phenotypic.enhance phenotypic.grid phenotypic.gui phenotypic.gui.components phenotypic.gui.sweep phenotypic.measure phenotypic.nn phenotypic.phenotypicCLI phenotypic.post phenotypic.prefab phenotypic.refine phenotypic.settings_ phenotypic.sweep phenotypic.tools_ phenotypic.tools_.branch_pathfinding phenotypic.tools_.colourspace phenotypic.tools_.constants_ phenotypic.tools_.exceptions_ phenotypic.tools_.funcs_ phenotypic.tools_.generate_report phenotypic.tools_.hdf_ phenotypic.tools_.measurement_info_ phenotypic.tools_.mixin phenotypic.tools_.monitor_slurm_jobs phenotypic.tools_.napari_ phenotypic.tools_.panel_ phenotypic.tools_.register phenotypic.tools_.slurm phenotypic.tools_.slurm_ phenotypic.tools_.submitit_ phenotypic.tools_.typing_ phenotypic.util phenotypic.util.image_metrics morph_progression() (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) MPL (class in phenotypic.settings_) mpl_cmap_to_plotly() (phenotypic._core._image_parts.accessors._detect_mat_accessor.DetectMatAccessor static method) (phenotypic._core._image_parts.accessors._grayscale_accessor.Grayscale static method) (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap static method) (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask static method) (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor static method) (phenotypic._core._image_parts.accessors._rgb_accessor.ImageRGB static method) MSE (phenotypic.tools_.measurement_info_.MODEL_METRICS attribute) MultiscaleLoGEnhancer (class in phenotypic.enhance) murmur3_array_signature() (in module phenotypic.tools_.funcs_) mycelium N N0_FIT (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL attribute) n_iter (phenotypic.enhance.GrayOpening attribute) name (phenotypic.abc_.DetectionMode property) (phenotypic.gui.sweep.PipelineConfig attribute) (phenotypic.tools_.exceptions_.DataIntegrityError attribute) (phenotypic.tools_.exceptions_.EmptyImageError attribute) (phenotypic.tools_.exceptions_.IllegalElementAssignmentError attribute) (phenotypic.tools_.exceptions_.ImmutableComponentError attribute) (phenotypic.tools_.exceptions_.InvalidHsvSchemaError attribute) (phenotypic.tools_.exceptions_.NoArrayError attribute) (phenotypic.tools_.exceptions_.NoComponentError attribute) (phenotypic.tools_.exceptions_.NoImageDataError attribute) (phenotypic.tools_.exceptions_.NoObjectsError attribute) (phenotypic.tools_.exceptions_.ObjectNotFoundError attribute) (phenotypic.tools_.exceptions_.OperationIntegrityError attribute) (phenotypic.tools_.exceptions_.UuidAssignmentError attribute) (phenotypic.tools_.exceptions_.UUIDReassignmentError attribute) (phenotypic.tools_.HDF attribute), [1] (phenotypic.tools_.hdf_.HDF attribute), [1] napari() (phenotypic._core._image_parts.accessors._detect_mat_accessor.DetectMatAccessor method) (phenotypic._core._image_parts.accessors._grayscale_accessor.Grayscale method) (phenotypic._core._image_parts.accessors._grid_accessor.GridAccessor 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.ManualGridDetector method) (phenotypic.detect.ManualPointDetector 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._core._image_parts.accessors._grid_accessor.GridAccessor attribute) (phenotypic._core._image_parts.accessors._grid_accessor.GridAccessor property) (phenotypic.grid.ManualGridFinder 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) NEW_VAL (phenotypic.tools_.measurement_info_.EDGE_CORRECTION attribute) NoArrayError NoComponentError NoImageDataError NoiseMetrics (class in phenotypic.util) (class in phenotypic.util.image_metrics) None (phenotypic.abc_.FootprintMixin attribute) (phenotypic.abc_.ImageOperation attribute) (phenotypic.abc_.ObjectDetector attribute) NONE (phenotypic.tools_.constants_.IMAGE_MODE attribute) None (phenotypic.tools_.FootprintMixin attribute) (phenotypic.tools_.mixin.FootprintMixin attribute) NonLocalMeansDenoiser (class in phenotypic.enhance) nonuniformity_ratio (phenotypic.util.BackgroundMetrics attribute) (phenotypic.util.image_metrics.BackgroundMetrics attribute) NoObjectsError NoOutputError normalize_rgb_bitdepth() (in module phenotypic.tools_.funcs_) normed() (phenotypic._core._image_parts.accessors._rgb_accessor.ImageRGB method) nrows (phenotypic._core._image_parts.accessors._grid_accessor.GridAccessor attribute) (phenotypic._core._image_parts.accessors._grid_accessor.GridAccessor property) (phenotypic.grid.ManualGridFinder attribute) NUM_BRANCHES (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION attribute) num_objects (phenotypic._core._image_parts.accessors._objects_accessor.ObjectsAccessor property) NUM_SAMPLES (phenotypic.tools_.measurement_info_.MODEL_METRICS attribute) num_workers (phenotypic.analysis.TukeyOutlierRemover attribute) O obj (phenotypic.tools_.exceptions_.DataIntegrityError attribute) (phenotypic.tools_.exceptions_.EmptyImageError attribute) (phenotypic.tools_.exceptions_.IllegalElementAssignmentError attribute) (phenotypic.tools_.exceptions_.ImmutableComponentError attribute) (phenotypic.tools_.exceptions_.InvalidHsvSchemaError attribute) (phenotypic.tools_.exceptions_.NoArrayError attribute) (phenotypic.tools_.exceptions_.NoComponentError attribute) (phenotypic.tools_.exceptions_.NoImageDataError attribute) (phenotypic.tools_.exceptions_.NoObjectsError attribute) (phenotypic.tools_.exceptions_.ObjectNotFoundError attribute) (phenotypic.tools_.exceptions_.OperationIntegrityError attribute) (phenotypic.tools_.exceptions_.UuidAssignmentError attribute) (phenotypic.tools_.exceptions_.UUIDReassignmentError attribute) OBJECT (class in phenotypic.tools_.constants_) (phenotypic.tools_.constants_.IMAGE_TYPES attribute) OBJECT_SPREAD (phenotypic.tools_.measurement_info_.GRID_SPREAD attribute) ObjectDetector (class in phenotypic.abc_) 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.gui.sweep.ResolvedLayerSources attribute) (phenotypic.Image property) objmask (phenotypic.Image property) on (phenotypic.analysis.TukeyOutlierRemover attribute) OpeningSubtractBg (class in phenotypic.enhance) operation_name (phenotypic.gui.sweep.IntermediateStep attribute) OperationFailedError OperationIntegrityError operations (phenotypic.gui.sweep.PipelineConfig attribute) optimal_scale (phenotypic.util.image_metrics.StructureMetrics attribute) (phenotypic.util.StructureMetrics attribute) ORANGE_PCT (phenotypic.tools_.measurement_info_.ColorComposition attribute) ORIENTATION (phenotypic.tools_.measurement_info_.SHAPE attribute) OtsuDetector (class in phenotypic.detect) output_illuminant (phenotypic.correction.ColorCorrector attribute) OutputValueError P p1 (phenotypic.util.ContrastMetrics attribute) (phenotypic.util.image_metrics.ContrastMetrics attribute) p99 (phenotypic.util.ContrastMetrics attribute) (phenotypic.util.image_metrics.ContrastMetrics attribute) pair (phenotypic.abc_.MeasurementInfo attribute) PANEL_AVAILABLE (in module phenotypic.tools_.panel_) PANEL_IMPORT_ERROR (in module phenotypic.tools_.panel_) PARENT_IMAGE_NAME (phenotypic.tools_.constants_.METADATA attribute) PARENT_UUID (phenotypic.tools_.constants_.METADATA attribute) parse_job_id() (in module phenotypic.tools_.slurm) partition() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) passed_ids (phenotypic.tools_.branch_pathfinding.FilterResult attribute), [1] (phenotypic.tools_.branch_pathfinding.PrescreenResult attribute), [1] path (phenotypic.gui.sweep.SweepHDF5File attribute) path_length (phenotypic.tools_.branch_pathfinding.FragmentPath attribute), [1] PathMetrics (class in phenotypic.tools_.branch_pathfinding) paths_metrics_dataframe() (in module phenotypic.tools_.branch_pathfinding) pct_energy_band_median (phenotypic.tools_.branch_pathfinding.PathMetrics attribute), [1] pct_energy_median_values (phenotypic.tools_.branch_pathfinding.CalibrationData attribute), [1] pct_n_orient (phenotypic.detect.FilamentousFungiDetector attribute) peak_response (phenotypic.util.image_metrics.StructureMetrics attribute) (phenotypic.util.StructureMetrics attribute) per_filter_rejections (phenotypic.tools_.branch_pathfinding.FilterResult attribute), [1] PERIMETER (phenotypic.tools_.measurement_info_.SHAPE attribute) PhaseCongruencyEnhancer (class in phenotypic.enhance) phenotypic module phenotypic._core module phenotypic.abc_ module phenotypic.analysis module phenotypic.analysis.abc_ module phenotypic.correction module phenotypic.data module phenotypic.detect module phenotypic.enhance module phenotypic.grid module phenotypic.gui module phenotypic.gui.components module phenotypic.gui.sweep module phenotypic.measure module phenotypic.nn module phenotypic.phenotypicCLI module phenotypic.post module phenotypic.prefab module phenotypic.refine module phenotypic.settings_ module phenotypic.sweep module phenotypic.tools_ module phenotypic.tools_.branch_pathfinding module phenotypic.tools_.colourspace module phenotypic.tools_.constants_ module phenotypic.tools_.exceptions_ module phenotypic.tools_.funcs_ module phenotypic.tools_.generate_report module phenotypic.tools_.hdf_ module phenotypic.tools_.measurement_info_ module phenotypic.tools_.mixin module phenotypic.tools_.monitor_slurm_jobs module phenotypic.tools_.napari_ module phenotypic.tools_.panel_ module phenotypic.tools_.register module phenotypic.tools_.slurm module phenotypic.tools_.slurm_ module phenotypic.tools_.submitit_ module phenotypic.tools_.typing_ module phenotypic.util module phenotypic.util.image_metrics module PHENOTYPIC_METADATA_KEY (phenotypic.tools_.constants_.IO attribute) PhenoTypicError PINK_PCT (phenotypic.tools_.measurement_info_.ColorComposition attribute) PIPE_STATUS (class in phenotypic.tools_.constants_) pipeline_configs (phenotypic.gui.sweep.SweepOutputData attribute) pipeline_name (phenotypic.gui.sweep.SweepHDF5File attribute) pipeline_names (phenotypic.gui.sweep.SweepOutputData attribute) PipelineConfig (class in phenotypic.gui.sweep) plot (phenotypic.Image property), [1] plot_cost_distance_heatmap() (in module phenotypic.tools_.branch_pathfinding) plot_paths_over_image() (in module phenotypic.tools_.branch_pathfinding) PlotAccessor (class in phenotypic._core._image_parts.accessors._plot_accessor) PLOTLY_AVAILABLE (in module phenotypic.tools_.panel_) PLOTLY_CONFIG (phenotypic._core._image_parts.accessors._detect_mat_accessor.DetectMatAccessor attribute) (phenotypic._core._image_parts.accessors._grayscale_accessor.Grayscale attribute) (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap attribute) (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask attribute) (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor attribute) (phenotypic._core._image_parts.accessors._rgb_accessor.ImageRGB attribute) plotly_imshow() (phenotypic._core._image_parts.accessors._detect_mat_accessor.DetectMatAccessor static method) (phenotypic._core._image_parts.accessors._grayscale_accessor.Grayscale static method) (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap static method) (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask static method) (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor static method) (phenotypic._core._image_parts.accessors._rgb_accessor.ImageRGB static method) PlotterRegistry (class in phenotypic.tools_.register) PNG_FILE_EXTENSIONS (phenotypic.tools_.constants_.IO attribute) PointPickerWidget (class in phenotypic.tools_.napari_) pop() (phenotypic._core._image_parts.accessors._metadata_accessor.MetadataAccessor method) (phenotypic.util.BackgroundMetrics method) (phenotypic.util.ContrastMetrics method) (phenotypic.util.image_metrics.BackgroundMetrics method) (phenotypic.util.image_metrics.ContrastMetrics method) (phenotypic.util.image_metrics.NoiseMetrics method) (phenotypic.util.image_metrics.QualityScores method) (phenotypic.util.image_metrics.StructureMetrics method) (phenotypic.util.NoiseMetrics method) (phenotypic.util.QualityScores method) (phenotypic.util.StructureMetrics method) popitem() (phenotypic.util.BackgroundMetrics method) (phenotypic.util.ContrastMetrics method) (phenotypic.util.image_metrics.BackgroundMetrics method) (phenotypic.util.image_metrics.ContrastMetrics method) (phenotypic.util.image_metrics.NoiseMetrics method) (phenotypic.util.image_metrics.QualityScores method) (phenotypic.util.image_metrics.StructureMetrics method) (phenotypic.util.NoiseMetrics method) (phenotypic.util.QualityScores method) (phenotypic.util.StructureMetrics method) PostMeasurement (class in phenotypic.abc_) preallocate_frame_layout() (phenotypic.tools_.HDF static method) (phenotypic.tools_.hdf_.HDF static method) preallocate_series_layout() (phenotypic.tools_.HDF static method) (phenotypic.tools_.hdf_.HDF static method) PRED_CC (phenotypic.tools_.constants_.GRID_LINREG_STATS_EXTRACTOR attribute) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS attribute) PRED_RR (phenotypic.tools_.constants_.GRID_LINREG_STATS_EXTRACTOR attribute) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS attribute) predecessor (phenotypic.tools_.branch_pathfinding.DijkstraResult attribute), [1] prefab pipeline PrefabPipeline (class in phenotypic.abc_) PrependString (class in phenotypic.post) prescreen_fragments() (in module phenotypic.tools_.branch_pathfinding) PrescreenResult (class in phenotypic.tools_.branch_pathfinding) Presence (class in phenotypic.sweep) preview_modes() (phenotypic._core._image_parts.accessors._detect_mat_accessor.DetectMatAccessor method) PROCESSED (phenotypic.tools_.constants_.PIPE_STATUS attribute) props (phenotypic._core._image_parts.accessors._objects_accessor.ObjectsAccessor property) PROTECTED_METADATA_SUBGROUP_KEY (phenotypic.tools_.HDF attribute) (phenotypic.tools_.hdf_.HDF attribute) prune_saturated (phenotypic.analysis.LinearSoftplusModel attribute) PUBLIC_METADATA_SUBGROUP_KEY (phenotypic.tools_.HDF attribute) (phenotypic.tools_.hdf_.HDF attribute) PURPLE_PCT (phenotypic.tools_.measurement_info_.ColorComposition attribute) Q Q1_INTENSITY (phenotypic.tools_.measurement_info_.INTENSITY attribute) Q3_INTENSITY (phenotypic.tools_.measurement_info_.INTENSITY attribute) QualityScores (class in phenotypic.util) (class in phenotypic.util.image_metrics) R R2 (phenotypic.tools_.measurement_info_.MODEL_METRICS attribute) R_FIT (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL attribute) RADIAL_EXPANSION (class in phenotypic.tools_.measurement_info_) RankMedianEnhancer (class in phenotypic.enhance) RankOtsuDetector (class in phenotypic.detect) RAW_FILE_EXTENSIONS (phenotypic.tools_.constants_.IO attribute) raw_json (phenotypic.gui.sweep.PipelineConfig attribute) reader() (phenotypic.tools_.HDF method) (phenotypic.tools_.hdf_.HDF method) RED_PCT (phenotypic.tools_.measurement_info_.ColorComposition attribute) ReduceMultipleGridObjects (class in phenotypic.refine) register() (phenotypic.tools_.register.AnalysisPluginRegistry class method) (phenotypic.tools_.register.BaseRegistry class method) (phenotypic.tools_.register.DashboardRegistry class method) (phenotypic.tools_.register.PlotterRegistry class method) register_analysis() (in module phenotypic.tools_.register) register_dashboard() (in module phenotypic.tools_.register) register_detection_mode() (in module phenotypic.abc_) register_plotter() (in module phenotypic.tools_.register) rejected_ids (phenotypic.tools_.branch_pathfinding.FilterResult attribute), [1] (phenotypic.tools_.branch_pathfinding.PrescreenResult attribute), [1] relabel() (phenotypic._core._image_parts.accessors._objects_accessor.ObjectsAccessor method) (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap method) removeprefix() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) removesuffix() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) replace() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) require_panel() (in module phenotypic.tools_.panel_) requires_rgb (phenotypic.abc_.DetectionMode property) 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) RESIDUAL_ERR (phenotypic.tools_.constants_.GRID_LINREG_STATS_EXTRACTOR attribute) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS attribute) ResidualOutlierRemover (class in phenotypic.refine) ResolvedLayerSources (class in phenotypic.gui.sweep) results() (phenotypic.analysis.abc_.ModelFitter method) (phenotypic.analysis.abc_.SetAnalyzer method) (phenotypic.analysis.EdgeCorrector method) (phenotypic.analysis.LinearSoftplusModel method) (phenotypic.analysis.LogGrowthModel method) (phenotypic.analysis.TukeyOutlierRemover method) rfind() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) rgb (phenotypic.gui.sweep.ResolvedLayerSources attribute) (phenotypic.Image property) RGB (phenotypic.tools_.constants_.IMAGE_MODE attribute) RGB_OR_BGR (phenotypic.tools_.constants_.IMAGE_MODE attribute) RGBA (phenotypic.tools_.constants_.IMAGE_MODE attribute) RGBA_OR_BGRA (phenotypic.tools_.constants_.IMAGE_MODE attribute) ridge_method (phenotypic.util.image_metrics.StructureMetrics attribute) (phenotypic.util.StructureMetrics attribute) ridge_responses (phenotypic.util.image_metrics.StructureMetrics attribute) (phenotypic.util.StructureMetrics attribute) RIGHT_DISTANCE (phenotypic.tools_.measurement_info_.GRID_SPATIAL attribute) RIGHT_NEIGHBOR_OBJ_LABEL (phenotypic.tools_.measurement_info_.GRID_SPATIAL attribute) rindex() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) rjust() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) rms_contrast (phenotypic.util.ContrastMetrics attribute) (phenotypic.util.image_metrics.ContrastMetrics attribute) RMSE (phenotypic.tools_.measurement_info_.MODEL_METRICS attribute) ROBUST_MEAN_RADIUS (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION attribute) root_dir (phenotypic.gui.sweep.SweepOutputData attribute) root_posix (phenotypic.tools_.HDF attribute), [1] (phenotypic.tools_.hdf_.HDF attribute), [1] rotate() (phenotypic.Image method) RoundPeaksDetector (class in phenotypic.detect) RoundPeaksPipeline (class in phenotypic.prefab) row_edges (phenotypic.grid.ManualGridFinder attribute) ROW_INTERVAL_END (phenotypic.tools_.measurement_info_.GRID attribute) ROW_INTERVAL_START (phenotypic.tools_.measurement_info_.GRID attribute) ROW_LINREG_B (phenotypic.tools_.constants_.GRID_LINREG_STATS_EXTRACTOR attribute) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS attribute) ROW_LINREG_M (phenotypic.tools_.constants_.GRID_LINREG_STATS_EXTRACTOR attribute) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS attribute) ROW_MAJOR_IDX (phenotypic.tools_.measurement_info_.GRID attribute) ROW_NUM (phenotypic.tools_.measurement_info_.GRID attribute) rpartition() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) rsplit() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) rst_table() (phenotypic.abc_.MeasurementInfo class method) (phenotypic.tools_.constants_.ConstantLabels class method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS class method) (phenotypic.tools_.constants_.METADATA class method) (phenotypic.tools_.constants_.PIPE_STATUS class method) (phenotypic.tools_.measurement_info_.BBOX class method) (phenotypic.tools_.measurement_info_.ColorComposition class method) (phenotypic.tools_.measurement_info_.ColorHSV class method) (phenotypic.tools_.measurement_info_.ColorLab class method) (phenotypic.tools_.measurement_info_.Colorxy class method) (phenotypic.tools_.measurement_info_.ColorXYZ class method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION class method) (phenotypic.tools_.measurement_info_.GRID class method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS class method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL class method) (phenotypic.tools_.measurement_info_.GRID_SPREAD class method) (phenotypic.tools_.measurement_info_.INTENSITY class method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL class method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL class method) (phenotypic.tools_.measurement_info_.MODEL_METRICS class method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION class method) (phenotypic.tools_.measurement_info_.SHAPE class method) (phenotypic.tools_.measurement_info_.SIZE class method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS class method) (phenotypic.tools_.measurement_info_.TEXTURE class method) rstrip() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) run() (phenotypic.tools_.napari_.PointPickerWidget method) run_multisource_dijkstra() (in module phenotypic.tools_.branch_pathfinding) RUNNER_DETECTED (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION attribute) RUNNER_LENGTH (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION attribute) S s0 (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL attribute) safe_writer() (phenotypic.tools_.HDF method) (phenotypic.tools_.hdf_.HDF method) SatoRidgeFilter (class in phenotypic.enhance) saturation_buffer (phenotypic.analysis.LinearSoftplusModel attribute) SATURATION_COEFF_VARIANCE (phenotypic.tools_.measurement_info_.ColorHSV attribute) saturation_headers() (phenotypic.tools_.measurement_info_.ColorHSV class method) SATURATION_MAXIMUM (phenotypic.tools_.measurement_info_.ColorHSV attribute) SATURATION_MEAN (phenotypic.tools_.measurement_info_.ColorHSV attribute) SATURATION_MEDIAN (phenotypic.tools_.measurement_info_.ColorHSV attribute) SATURATION_MINIMUM (phenotypic.tools_.measurement_info_.ColorHSV attribute) SATURATION_Q1 (phenotypic.tools_.measurement_info_.ColorHSV attribute) SATURATION_Q3 (phenotypic.tools_.measurement_info_.ColorHSV attribute) SATURATION_STDDEV (phenotypic.tools_.measurement_info_.ColorHSV attribute) saturation_threshold (phenotypic.analysis.LinearSoftplusModel attribute) save2hdf5() (phenotypic.Image method) save2pickle() (phenotypic.Image method) save_array2hdf5() (phenotypic.tools_.HDF static method) (phenotypic.tools_.hdf_.HDF static method) save_frame_append() (phenotypic.tools_.HDF static method) (phenotypic.tools_.hdf_.HDF static method) save_frame_new() (phenotypic.tools_.HDF static method) (phenotypic.tools_.hdf_.HDF static method) save_frame_update() (phenotypic.tools_.HDF static method) (phenotypic.tools_.hdf_.HDF static method) save_overlay() (phenotypic._core._image_parts.accessors._detect_mat_accessor.DetectMatAccessor method) (phenotypic._core._image_parts.accessors._grayscale_accessor.Grayscale method) (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap method) (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask method) (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) (phenotypic._core._image_parts.accessors._rgb_accessor.ImageRGB method) save_series_append() (phenotypic.tools_.HDF static method) (phenotypic.tools_.hdf_.HDF static method) save_series_new() (phenotypic.tools_.HDF static method) (phenotypic.tools_.hdf_.HDF static method) save_series_update() (phenotypic.tools_.HDF static method) (phenotypic.tools_.hdf_.HDF static method) scales (phenotypic.util.image_metrics.StructureMetrics attribute) (phenotypic.util.StructureMetrics attribute) scan() (phenotypic.gui.sweep.SweepOutputScanner static method) screened_fragment_labels (phenotypic.tools_.branch_pathfinding.PrescreenResult attribute), [1] SecondaryOtsuDetector (class in phenotypic.detect) SeparateObjects (class in phenotypic.refine) set_data_posix (phenotypic.tools_.HDF attribute), [1] (phenotypic.tools_.hdf_.HDF attribute), [1] 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_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) SetAnalyzer (class in phenotypic.analysis.abc_) setdefault() (phenotypic.util.BackgroundMetrics method) (phenotypic.util.ContrastMetrics method) (phenotypic.util.image_metrics.BackgroundMetrics method) (phenotypic.util.image_metrics.ContrastMetrics method) (phenotypic.util.image_metrics.NoiseMetrics method) (phenotypic.util.image_metrics.QualityScores method) (phenotypic.util.image_metrics.StructureMetrics method) (phenotypic.util.NoiseMetrics method) (phenotypic.util.QualityScores method) (phenotypic.util.StructureMetrics method) SetDetectMode (class in phenotypic.enhance) setup_logging() (in module phenotypic.phenotypicCLI) SHAPE (class in phenotypic.tools_.measurement_info_) 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.enhance.GrayOpening attribute) (phenotypic.enhance.MedianFilter attribute) (phenotypic.refine.WhiteTophat attribute) Sharpness (phenotypic.util.image_metrics.QualityScores attribute) (phenotypic.util.QualityScores 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.abc_.ModelFitter method) (phenotypic.analysis.abc_.SetAnalyzer method) (phenotypic.analysis.EdgeCorrector method) (phenotypic.analysis.LinearSoftplusModel method) (phenotypic.analysis.LogGrowthModel method) (phenotypic.analysis.TukeyOutlierRemover method) (phenotypic.Image method) show_column_overlay() (phenotypic._core._image_parts.accessors._grid_accessor.GridAccessor method) show_row_overlay() (phenotypic._core._image_parts.accessors._grid_accessor.GridAccessor method) sigma_mad (phenotypic.util.image_metrics.NoiseMetrics attribute) (phenotypic.util.NoiseMetrics attribute) SineAlignmentRefiner (class in phenotypic.refine) SinePeakDetector (class in phenotypic.detect) SINGLE_IMAGE_HDF5_PARENT_GROUP (phenotypic.tools_.constants_.IO attribute) SINGLE_IMAGE_ROOT_POSIX (phenotypic.tools_.HDF attribute), [1] (phenotypic.tools_.hdf_.HDF attribute), [1] SIZE (class in phenotypic.tools_.measurement_info_) 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_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) small_object_min_size (phenotypic.prefab.HeavyRoundPeaksPipeline attribute) SmallObjectRemover (class in phenotypic.refine) SmallToLargeMerger (class in phenotypic.refine) smax (phenotypic.analysis.LinearSoftplusModel attribute) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL attribute) snr (phenotypic.util.image_metrics.NoiseMetrics attribute) SNR (phenotypic.util.image_metrics.QualityScores attribute) snr (phenotypic.util.NoiseMetrics attribute) SNR (phenotypic.util.QualityScores attribute) SobelFilter (class in phenotypic.enhance) SOLIDITY (phenotypic.tools_.measurement_info_.SHAPE attribute) SPARSE_AREA (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS attribute) SPARSE_END_RADIUS (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS attribute) spatial_size_map() (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) SpImagerPipeline (class in phenotypic.prefab) split() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) splitlines() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) SRGB (phenotypic.tools_.constants_.GAMMA_ENCODINGS attribute) StableDenoise (class in phenotypic.correction) STANDARD_DEVIATION_INTENSITY (phenotypic.tools_.measurement_info_.INTENSITY attribute) startswith() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) STATUS (phenotypic.tools_.measurement_info_.MODEL_METRICS attribute) stderr_label (phenotypic.analysis.LinearSoftplusModel attribute) strict_writer() (phenotypic.tools_.HDF method) (phenotypic.tools_.hdf_.HDF method) strip() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) structural_response_curve() (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) StructureMetrics (class in phenotypic.util) (class in phenotypic.util.image_metrics) submit_drip_feed_start() (in module phenotypic.tools_.slurm) submit_script() (in module phenotypic.tools_.slurm) SubtractGaussian (class in phenotypic.enhance) SubtractRollingBall (class in phenotypic.enhance) SubtractWhiteTophat (class in phenotypic.enhance) SUFFIX (phenotypic.tools_.constants_.METADATA attribute) SUM_AVERAGE (phenotypic.tools_.measurement_info_.TEXTURE attribute) SUM_ENTROPY (phenotypic.tools_.measurement_info_.TEXTURE attribute) SUM_VARIANCE (phenotypic.tools_.measurement_info_.TEXTURE attribute) SUPPORTED_FORMATS (phenotypic.tools_.constants_.IMAGE_MODE attribute) swapcase() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) Sweep (class in phenotypic.sweep) SweepHDF5File (class in phenotypic.gui.sweep) SweepOutputData (class in phenotypic.gui.sweep) SweepOutputScanner (class in phenotypic.gui.sweep) swmr_reader() (phenotypic.tools_.HDF method) (phenotypic.tools_.hdf_.HDF method) swmr_writer() (phenotypic.tools_.HDF method) (phenotypic.tools_.hdf_.HDF method) SYMMETRIC_RADIUS (class in phenotypic.tools_.measurement_info_) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS attribute) T table() (phenotypic._core._image_parts.accessors._metadata_accessor.MetadataAccessor method) tau_band_variance (phenotypic.tools_.branch_pathfinding.FilterThresholds attribute), [1] tau_gray_snr (phenotypic.tools_.branch_pathfinding.FilterThresholds attribute), [1] tau_median_cost (phenotypic.tools_.branch_pathfinding.FilterThresholds attribute), [1] tau_pct_energy_median (phenotypic.tools_.branch_pathfinding.FilterThresholds attribute), [1] tau_window_cost (phenotypic.tools_.branch_pathfinding.FilterThresholds attribute), [1] TEXTURE (class in phenotypic.tools_.measurement_info_) 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) threshold_used (phenotypic.tools_.branch_pathfinding.PrescreenResult attribute), [1] ThresholdDetector (class in phenotypic.abc_) thresholds (phenotypic.tools_.branch_pathfinding.FilterResult attribute), [1] TIFF_EXTENSIONS (phenotypic.tools_.constants_.IO attribute) time_label (phenotypic.analysis.abc_.ModelFitter attribute) timed_execution() (in module phenotypic.tools_) (in module phenotypic.tools_.funcs_) title() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) to_dict() (phenotypic.correction.ColorCheckerProfile method) to_json() (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) total_cost (phenotypic.tools_.branch_pathfinding.FragmentPath attribute), [1] TransitiveDistanceMerger (class in phenotypic.refine) translate() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) TriangleDetector (class in phenotypic.detect) try_thresh() (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) TukeyOutlierRemover (class in phenotypic.analysis) U UNDER_DISTANCE (phenotypic.tools_.measurement_info_.GRID_SPATIAL attribute) UNDER_NEIGHBOR_OBJ_LABEL (phenotypic.tools_.measurement_info_.GRID_SPATIAL attribute) Uniformity (phenotypic.util.image_metrics.QualityScores attribute) (phenotypic.util.QualityScores attribute) UnknownError UnsharpMask (class in phenotypic.enhance) UnsupportedFileTypeError UnsupportedImageFormat update() (phenotypic.util.BackgroundMetrics method) (phenotypic.util.ContrastMetrics method) (phenotypic.util.image_metrics.BackgroundMetrics method) (phenotypic.util.image_metrics.ContrastMetrics method) (phenotypic.util.image_metrics.NoiseMetrics method) (phenotypic.util.image_metrics.QualityScores method) (phenotypic.util.image_metrics.StructureMetrics method) (phenotypic.util.NoiseMetrics method) (phenotypic.util.QualityScores method) (phenotypic.util.StructureMetrics method) upper() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method) UUID (phenotypic.tools_.constants_.METADATA attribute) UuidAssignmentError UUIDReassignmentError V v (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL attribute) v_upper (phenotypic.analysis.LinearSoftplusModel attribute) val_range() (phenotypic._core._image_parts.accessors._detect_mat_accessor.DetectMatAccessor method) (phenotypic._core._image_parts.accessors._grayscale_accessor.Grayscale method) (phenotypic._core._image_parts.accessors._objmap_accessor.ObjectMap method) (phenotypic._core._image_parts.accessors._objmask_accessor.ObjectMask method) (phenotypic._core._image_parts.accessors._plot_accessor.PlotAccessor method) (phenotypic._core._image_parts.accessors._rgb_accessor.ImageRGB method) validate_array_chunk() (in module phenotypic.tools_.slurm) validate_measure_integrity() (in module phenotypic.tools_.funcs_) validate_operation_integrity() (in module phenotypic.tools_.funcs_) values() (phenotypic._core._image_parts.accessors._metadata_accessor.MetadataAccessor method) (phenotypic.util.BackgroundMetrics method) (phenotypic.util.ContrastMetrics method) (phenotypic.util.image_metrics.BackgroundMetrics method) (phenotypic.util.image_metrics.ContrastMetrics method) (phenotypic.util.image_metrics.NoiseMetrics method) (phenotypic.util.image_metrics.QualityScores method) (phenotypic.util.image_metrics.StructureMetrics method) (phenotypic.util.NoiseMetrics method) (phenotypic.util.QualityScores method) (phenotypic.util.StructureMetrics method) VARIANCE (phenotypic.tools_.measurement_info_.TEXTURE attribute) verbose (phenotypic.analysis.abc_.ModelFitter attribute) (phenotypic.prefab.HeavyRoundPeaksPipeline 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 WatershedDetector (class in phenotypic.detect) well WHITE_PCT (phenotypic.tools_.measurement_info_.ColorComposition attribute) WhiteTophat (class in phenotypic.refine) WhiteTophatEnhance (class in phenotypic.enhance) widget() (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_.ImageEnhancer method) (phenotypic.abc_.ImageOperation method) (phenotypic.abc_.ObjectDetector method) (phenotypic.abc_.ObjectRefiner method) (phenotypic.abc_.PrefabPipeline method) (phenotypic.abc_.ThresholdDetector method) (phenotypic.correction.BayesShrinkCorrector method) (phenotypic.correction.ColorCorrector method) (phenotypic.correction.GridAligner method) (phenotypic.correction.ImageCropper method) (phenotypic.correction.ImagePadder method) (phenotypic.correction.StableDenoise 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.ManualDetector method) (phenotypic.detect.ManualGridDetector 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.WatershedDetector method) (phenotypic.detect.YenDetector method) (phenotypic.enhance.AnscombeForward method) (phenotypic.enhance.AnscombeInverse method) (phenotypic.enhance.BayesShrinkEnhancer method) (phenotypic.enhance.BilateralDenoise method) (phenotypic.enhance.BM3DDenoiser method) (phenotypic.enhance.CLAHE method) (phenotypic.enhance.CoherenceEnhancingDiffusion method) (phenotypic.enhance.ContrastStretching method) (phenotypic.enhance.FrangiVesselness method) (phenotypic.enhance.GaussianBlur method) (phenotypic.enhance.GrayOpening method) (phenotypic.enhance.HessianFilter method) (phenotypic.enhance.HomomorphicFilter method) (phenotypic.enhance.ImageInverter method) (phenotypic.enhance.LaplaceEnhancer method) (phenotypic.enhance.MedianFilter method) (phenotypic.enhance.MeijeringRidgeFilter method) (phenotypic.enhance.MultiscaleLoGEnhancer method) (phenotypic.enhance.NonLocalMeansDenoiser method) (phenotypic.enhance.OpeningSubtractBg method) (phenotypic.enhance.PhaseCongruencyEnhancer method) (phenotypic.enhance.RankMedianEnhancer method) (phenotypic.enhance.SatoRidgeFilter method) (phenotypic.enhance.SetDetectMode method) (phenotypic.enhance.SobelFilter method) (phenotypic.enhance.SubtractGaussian method) (phenotypic.enhance.SubtractRollingBall method) (phenotypic.enhance.SubtractWhiteTophat method) (phenotypic.enhance.UnsharpMask method) (phenotypic.enhance.VisuShrinkEnhancer method) (phenotypic.enhance.WhiteTophatEnhance 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.AsymmetricSpurTrimmer method) (phenotypic.refine.BorderObjectRemover method) (phenotypic.refine.CenterDeviationReducer method) (phenotypic.refine.GMMCoreExtractor method) (phenotypic.refine.GridAlignmentRefiner method) (phenotypic.refine.GridOversizedObjectRemover method) (phenotypic.refine.GridSectionLargest method) (phenotypic.refine.LowCircularityRemover method) (phenotypic.refine.MaskCloser method) (phenotypic.refine.MaskDilator method) (phenotypic.refine.MaskEroder method) (phenotypic.refine.MaskFill method) (phenotypic.refine.MaskGradient method) (phenotypic.refine.MaskOpener method) (phenotypic.refine.NearestNeighborMerger method) (phenotypic.refine.ReduceMultipleGridObjects method) (phenotypic.refine.ResidualOutlierRemover method) (phenotypic.refine.SeparateObjects method) (phenotypic.refine.SineAlignmentRefiner method) (phenotypic.refine.Skeletonize method) (phenotypic.refine.SmallObjectRemover method) (phenotypic.refine.SmallToLargeMerger method) (phenotypic.refine.Thinning method) (phenotypic.refine.TransitiveDistanceMerger method) (phenotypic.refine.WhiteTophat method) (phenotypic.tools_.LazyWidgetMixin method) (phenotypic.tools_.mixin.LazyWidgetMixin method) width (phenotypic.enhance.GrayOpening attribute) (phenotypic.enhance.MedianFilter attribute) (phenotypic.refine.WhiteTophat attribute) with_traceback() (phenotypic.tools_.exceptions_.ArrayKeyValueShapeMismatchError method) (phenotypic.tools_.exceptions_.DataIntegrityError method) (phenotypic.tools_.exceptions_.EmptyImageError method) (phenotypic.tools_.exceptions_.GrayscaleOutOfRangeError method) (phenotypic.tools_.exceptions_.GridImageInputError method) (phenotypic.tools_.exceptions_.IllegalAssignmentError method) (phenotypic.tools_.exceptions_.IllegalElementAssignmentError method) (phenotypic.tools_.exceptions_.ImageOperationError method) (phenotypic.tools_.exceptions_.ImmutableComponentError method) (phenotypic.tools_.exceptions_.InputShapeMismatchError method) (phenotypic.tools_.exceptions_.InterfaceError method) (phenotypic.tools_.exceptions_.InvalidHsvSchemaError method) (phenotypic.tools_.exceptions_.InvalidMapValueError method) (phenotypic.tools_.exceptions_.InvalidMaskScalarValueError method) (phenotypic.tools_.exceptions_.InvalidMaskValueError method) (phenotypic.tools_.exceptions_.InvalidShapeError method) (phenotypic.tools_.exceptions_.MetadataKeySpacesError method) (phenotypic.tools_.exceptions_.MetadataKeyValueError method) (phenotypic.tools_.exceptions_.MetadataValueNonScalarError method) (phenotypic.tools_.exceptions_.NoArrayError method) (phenotypic.tools_.exceptions_.NoComponentError method) (phenotypic.tools_.exceptions_.NoImageDataError method) (phenotypic.tools_.exceptions_.NoObjectsError method) (phenotypic.tools_.exceptions_.NoOutputError method) (phenotypic.tools_.exceptions_.ObjectNotFoundError method) (phenotypic.tools_.exceptions_.OperationFailedError method) (phenotypic.tools_.exceptions_.OperationIntegrityError method) (phenotypic.tools_.exceptions_.OutputValueError method) (phenotypic.tools_.exceptions_.PhenoTypicError method) (phenotypic.tools_.exceptions_.UnknownError method) (phenotypic.tools_.exceptions_.UnsupportedFileTypeError method) (phenotypic.tools_.exceptions_.UnsupportedImageFormat method) (phenotypic.tools_.exceptions_.UuidAssignmentError method) (phenotypic.tools_.exceptions_.UUIDReassignmentError method) X x_COEFF_VARIANCE (phenotypic.tools_.measurement_info_.Colorxy attribute) X_COEFF_VARIANCE (phenotypic.tools_.measurement_info_.ColorXYZ attribute) x_headers() (phenotypic.tools_.measurement_info_.Colorxy class method) x_MAXIMUM (phenotypic.tools_.measurement_info_.Colorxy attribute) X_MAXIMUM (phenotypic.tools_.measurement_info_.ColorXYZ attribute) x_MEAN (phenotypic.tools_.measurement_info_.Colorxy attribute) X_MEAN (phenotypic.tools_.measurement_info_.ColorXYZ attribute) x_MEDIAN (phenotypic.tools_.measurement_info_.Colorxy attribute) X_MEDIAN (phenotypic.tools_.measurement_info_.ColorXYZ attribute) x_MINIMUM (phenotypic.tools_.measurement_info_.Colorxy attribute) X_MINIMUM (phenotypic.tools_.measurement_info_.ColorXYZ attribute) x_Q1 (phenotypic.tools_.measurement_info_.Colorxy attribute) X_Q1 (phenotypic.tools_.measurement_info_.ColorXYZ attribute) x_Q3 (phenotypic.tools_.measurement_info_.Colorxy attribute) X_Q3 (phenotypic.tools_.measurement_info_.ColorXYZ attribute) x_STDDEV (phenotypic.tools_.measurement_info_.Colorxy attribute) X_STDDEV (phenotypic.tools_.measurement_info_.ColorXYZ attribute) xy (phenotypic._core._image_parts.accessors._color_accessor.ColorAccessor property) XYZ (phenotypic._core._image_parts.accessors._color_accessor.ColorAccessor property) XYZ_D65 (phenotypic._core._image_parts.accessors._color_accessor.ColorAccessor property) Y y_COEFF_VARIANCE (phenotypic.tools_.measurement_info_.Colorxy attribute) Y_COEFF_VARIANCE (phenotypic.tools_.measurement_info_.ColorXYZ attribute) y_headers() (phenotypic.tools_.measurement_info_.Colorxy class method) y_MAXIMUM (phenotypic.tools_.measurement_info_.Colorxy attribute) Y_MAXIMUM (phenotypic.tools_.measurement_info_.ColorXYZ attribute) y_MEAN (phenotypic.tools_.measurement_info_.Colorxy attribute) Y_MEAN (phenotypic.tools_.measurement_info_.ColorXYZ attribute) y_MEDIAN (phenotypic.tools_.measurement_info_.Colorxy attribute) Y_MEDIAN (phenotypic.tools_.measurement_info_.ColorXYZ attribute) y_MINIMUM (phenotypic.tools_.measurement_info_.Colorxy attribute) Y_MINIMUM (phenotypic.tools_.measurement_info_.ColorXYZ attribute) y_Q1 (phenotypic.tools_.measurement_info_.Colorxy attribute) Y_Q1 (phenotypic.tools_.measurement_info_.ColorXYZ attribute) y_Q3 (phenotypic.tools_.measurement_info_.Colorxy attribute) Y_Q3 (phenotypic.tools_.measurement_info_.ColorXYZ attribute) y_STDDEV (phenotypic.tools_.measurement_info_.Colorxy attribute) Y_STDDEV (phenotypic.tools_.measurement_info_.ColorXYZ attribute) YELLOW_PCT (phenotypic.tools_.measurement_info_.ColorComposition attribute) YenDetector (class in phenotypic.detect) Z Z_COEFF_VARIANCE (phenotypic.tools_.measurement_info_.ColorXYZ attribute) Z_MAXIMUM (phenotypic.tools_.measurement_info_.ColorXYZ attribute) Z_MEAN (phenotypic.tools_.measurement_info_.ColorXYZ attribute) Z_MEDIAN (phenotypic.tools_.measurement_info_.ColorXYZ attribute) Z_MINIMUM (phenotypic.tools_.measurement_info_.ColorXYZ attribute) Z_Q1 (phenotypic.tools_.measurement_info_.ColorXYZ attribute) Z_Q3 (phenotypic.tools_.measurement_info_.ColorXYZ attribute) Z_STDDEV (phenotypic.tools_.measurement_info_.ColorXYZ attribute) zfill() (phenotypic.abc_.MeasurementInfo method) (phenotypic.tools_.constants_.ConstantLabels method) (phenotypic.tools_.constants_.GAMMA_ENCODINGS method) (phenotypic.tools_.constants_.METADATA method) (phenotypic.tools_.constants_.PIPE_STATUS method) (phenotypic.tools_.measurement_info_.BBOX method) (phenotypic.tools_.measurement_info_.ColorComposition method) (phenotypic.tools_.measurement_info_.ColorHSV method) (phenotypic.tools_.measurement_info_.ColorLab method) (phenotypic.tools_.measurement_info_.Colorxy method) (phenotypic.tools_.measurement_info_.ColorXYZ method) (phenotypic.tools_.measurement_info_.EDGE_CORRECTION method) (phenotypic.tools_.measurement_info_.GRID method) (phenotypic.tools_.measurement_info_.GRID_LINREG_STATS method) (phenotypic.tools_.measurement_info_.GRID_SPATIAL method) (phenotypic.tools_.measurement_info_.GRID_SPREAD method) (phenotypic.tools_.measurement_info_.INTENSITY method) (phenotypic.tools_.measurement_info_.LINEAR_SOFTPLUS_MODEL method) (phenotypic.tools_.measurement_info_.LOG_GROWTH_MODEL method) (phenotypic.tools_.measurement_info_.MODEL_METRICS method) (phenotypic.tools_.measurement_info_.RADIAL_EXPANSION method) (phenotypic.tools_.measurement_info_.SHAPE method) (phenotypic.tools_.measurement_info_.SIZE method) (phenotypic.tools_.measurement_info_.SYMMETRIC_RADIUS method) (phenotypic.tools_.measurement_info_.TEXTURE method)
