Index

_

__del__() (phenotypic.abc_.BaseOperation method), [1], [2] (phenotypic.abc_.GridCorrector method), [1], [2] (phenotypic.abc_.GridFinder method), [1], [2] (phenotypic.abc_.GridMeasureFeatures method), [1], [2] (phenotypic.abc_.GridObjectDetector method), [1], [2] (phenotypic.abc_.GridObjectRefiner method), [1], [2] (phenotypic.abc_.GridOperation method), [1], [2] (phenotypic.abc_.ImageCorrector method), [1], [2] (phenotypic.abc_.ImageEnhancer method), [1], [2] (phenotypic.abc_.ImageOperation method), [1], [2] (phenotypic.abc_.MeasureFeatures method), [1], [2] (phenotypic.abc_.ObjectDetector method), [1], [2] (phenotypic.abc_.ObjectRefiner method), [1], [2] (phenotypic.abc_.PrefabPipeline method), [1], [2] (phenotypic.abc_.ThresholdDetector method), [1], [2] (phenotypic.correction.GridAligner method), [1], [2] (phenotypic.detect.CannyDetector method), [1], [2] (phenotypic.detect.IsodataDetector method), [1], [2] (phenotypic.detect.LiDetector method), [1], [2] (phenotypic.detect.MeanDetector method), [1], [2] (phenotypic.detect.MinimumDetector method), [1], [2] (phenotypic.detect.OtsuDetector method), [1], [2] (phenotypic.detect.RoundPeaksDetector method), [1], [2] (phenotypic.detect.TriangleDetector method), [1], [2] (phenotypic.detect.WatershedDetector method), [1], [2] (phenotypic.detect.YenDetector method), [1], [2] (phenotypic.enhance.BilateralDenoise method), [1], [2] (phenotypic.enhance.BM3DDenoiser method), [1], [2] (phenotypic.enhance.CLAHE method), [1], [2] (phenotypic.enhance.ContrastStretching method), [1], [2] (phenotypic.enhance.GaussianBlur method), [1], [2] (phenotypic.enhance.GaussianSubtract method), [1], [2] (phenotypic.enhance.LaplaceEnhancer method), [1], [2] (phenotypic.enhance.MedianFilter method), [1], [2] (phenotypic.enhance.RankMedianEnhancer method), [1], [2] (phenotypic.enhance.RollingBallRemoveBG method), [1], [2] (phenotypic.enhance.SobelFilter method), [1], [2] (phenotypic.enhance.UnsharpMask method), [1], [2] (phenotypic.enhance.WhiteTophatEnhancer method), [1], [2] (phenotypic.grid.AutoGridFinder method), [1], [2] (phenotypic.grid.ManualGridFinder method), [1], [2] (phenotypic.ImagePipeline method) (phenotypic.measure.MeasureBounds method), [1], [2] (phenotypic.measure.MeasureColor method), [1], [2] (phenotypic.measure.MeasureGridLinRegStats method), [1], [2] (phenotypic.measure.MeasureGridSpread method), [1], [2] (phenotypic.measure.MeasureIntensity method), [1], [2] (phenotypic.measure.MeasureShape method), [1], [2] (phenotypic.measure.MeasureSize method), [1], [2] (phenotypic.measure.MeasureTexture method), [1], [2] (phenotypic.prefab.GridSectionPipeline method), [1], [2] (phenotypic.prefab.HeavyOtsuPipeline method), [1], [2] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1], [2] (phenotypic.prefab.HeavyWatershedPipeline method), [1], [2] (phenotypic.prefab.RoundPeaksPipeline method), [1], [2] (phenotypic.refine.BorderObjectRemover method), [1], [2] (phenotypic.refine.CenterDeviationReducer method), [1], [2] (phenotypic.refine.GridOversizedObjectRemover method), [1], [2] (phenotypic.refine.LowCircularityRemover method), [1], [2] (phenotypic.refine.MaskFill method), [1], [2] (phenotypic.refine.MaskOpener method), [1], [2] (phenotypic.refine.MinResidualErrorReducer method), [1], [2] (phenotypic.refine.ResidualOutlierRemover method), [1], [2] (phenotypic.refine.Skeletonize method), [1], [2] (phenotypic.refine.SmallObjectRemover method), [1], [2] (phenotypic.refine.Thinning method), [1], [2] (phenotypic.refine.WhiteTophatModifier method), [1], [2] __eq__() (phenotypic.GridImage method) (phenotypic.Image method) __format__() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2] __getitem__() (phenotypic.GridImage method) (phenotypic.Image method) __getstate__() (phenotypic.abc_.GridCorrector method), [1], [2] (phenotypic.abc_.GridObjectDetector method), [1], [2] (phenotypic.abc_.GridObjectRefiner method), [1], [2] (phenotypic.abc_.GridOperation method), [1], [2] (phenotypic.abc_.ImageCorrector method), [1], [2] (phenotypic.abc_.ImageEnhancer method), [1], [2] (phenotypic.abc_.ImageOperation method), [1], [2] (phenotypic.abc_.ObjectDetector method), [1], [2] (phenotypic.abc_.ObjectRefiner method), [1], [2] (phenotypic.abc_.PrefabPipeline method), [1], [2] (phenotypic.abc_.ThresholdDetector method), [1], [2] (phenotypic.correction.GridAligner method), [1], [2] (phenotypic.detect.CannyDetector method), [1], [2] (phenotypic.detect.IsodataDetector method), [1], [2] (phenotypic.detect.LiDetector method), [1], [2] (phenotypic.detect.MeanDetector method), [1], [2] (phenotypic.detect.MinimumDetector method), [1], [2] (phenotypic.detect.OtsuDetector method), [1], [2] (phenotypic.detect.RoundPeaksDetector method), [1], [2] (phenotypic.detect.TriangleDetector method), [1], [2] (phenotypic.detect.WatershedDetector method), [1], [2] (phenotypic.detect.YenDetector method), [1], [2] (phenotypic.enhance.BilateralDenoise method), [1], [2] (phenotypic.enhance.BM3DDenoiser method), [1], [2] (phenotypic.enhance.CLAHE method), [1], [2] (phenotypic.enhance.ContrastStretching method), [1], [2] (phenotypic.enhance.GaussianBlur method), [1], [2] (phenotypic.enhance.GaussianSubtract method), [1], [2] (phenotypic.enhance.LaplaceEnhancer method), [1], [2] (phenotypic.enhance.MedianFilter method), [1], [2] (phenotypic.enhance.RankMedianEnhancer method), [1], [2] (phenotypic.enhance.RollingBallRemoveBG method), [1], [2] (phenotypic.enhance.SobelFilter method), [1], [2] (phenotypic.enhance.UnsharpMask method), [1], [2] (phenotypic.enhance.WhiteTophatEnhancer method), [1], [2] (phenotypic.ImagePipeline method) (phenotypic.prefab.GridSectionPipeline method), [1], [2] (phenotypic.prefab.HeavyOtsuPipeline method), [1], [2] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1], [2] (phenotypic.prefab.HeavyWatershedPipeline method), [1], [2] (phenotypic.prefab.RoundPeaksPipeline method), [1], [2] (phenotypic.refine.BorderObjectRemover method), [1], [2] (phenotypic.refine.CenterDeviationReducer method), [1], [2] (phenotypic.refine.GridOversizedObjectRemover method), [1], [2] (phenotypic.refine.LowCircularityRemover method), [1], [2] (phenotypic.refine.MaskFill method), [1], [2] (phenotypic.refine.MaskOpener method), [1], [2] (phenotypic.refine.MinResidualErrorReducer method), [1], [2] (phenotypic.refine.ResidualOutlierRemover method), [1], [2] (phenotypic.refine.Skeletonize method), [1], [2] (phenotypic.refine.SmallObjectRemover method), [1], [2] (phenotypic.refine.Thinning method), [1], [2] (phenotypic.refine.WhiteTophatModifier method), [1], [2]

__init__() (phenotypic.abc_.PrefabPipeline method), [1], [2] (phenotypic.analysis.EdgeCorrector method), [1], [2] (phenotypic.analysis.LogGrowthModel method), [1], [2] (phenotypic.analysis.TukeyOutlierRemover method), [1], [2] (phenotypic.detect.CannyDetector method), [1], [2] (phenotypic.detect.RoundPeaksDetector method), [1], [2] (phenotypic.enhance.BilateralDenoise method), [1], [2] (phenotypic.enhance.BM3DDenoiser method), [1], [2] (phenotypic.enhance.CLAHE method), [1], [2] (phenotypic.enhance.ContrastStretching method), [1], [2] (phenotypic.enhance.GaussianBlur method), [1], [2] (phenotypic.enhance.GaussianSubtract method), [1], [2] (phenotypic.enhance.LaplaceEnhancer method), [1], [2] (phenotypic.enhance.MedianFilter method), [1], [2] (phenotypic.enhance.RankMedianEnhancer method), [1], [2] (phenotypic.enhance.RollingBallRemoveBG method), [1], [2] (phenotypic.enhance.UnsharpMask method), [1], [2] (phenotypic.enhance.WhiteTophatEnhancer method), [1], [2] (phenotypic.grid.AutoGridFinder method), [1], [2] (phenotypic.grid.ManualGridFinder method), [1], [2] (phenotypic.GridImage method) (phenotypic.Image method) (phenotypic.ImagePipeline method) (phenotypic.measure.MeasureTexture method), [1], [2] (phenotypic.prefab.GridSectionPipeline method), [1], [2] (phenotypic.prefab.HeavyOtsuPipeline method), [1], [2] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1], [2] (phenotypic.prefab.HeavyWatershedPipeline method), [1], [2] (phenotypic.refine.BorderObjectRemover method), [1], [2] (phenotypic.refine.LowCircularityRemover method), [1], [2] (phenotypic.refine.MaskFill method), [1], [2] (phenotypic.refine.MaskOpener method), [1], [2] (phenotypic.refine.ResidualOutlierRemover method), [1], [2] (phenotypic.refine.Skeletonize method), [1], [2] (phenotypic.refine.SmallObjectRemover method), [1], [2] (phenotypic.refine.Thinning method), [1], [2] (phenotypic.refine.WhiteTophatModifier method), [1], [2] (phenotypic.tools.HDF method), [1], [2] (phenotypic.tools.hdf_.HDF method) __setitem__() (phenotypic.GridImage method) (phenotypic.Image method) _apply_to_single_image() (phenotypic.abc_.ImageOperation method), [1], [2] _logger (phenotypic.abc_.BaseOperation attribute), [1], [2] _make_footprint() (phenotypic.abc_.ImageEnhancer method), [1], [2] (phenotypic.abc_.ObjectRefiner method), [1], [2] _operate() (phenotypic.abc_.ImageEnhancer method), [1], [2] (phenotypic.abc_.ImageOperation method), [1], [2] (phenotypic.abc_.ObjectDetector method), [1], [2] (phenotypic.abc_.ObjectRefiner method), [1], [2] _tracemalloc_started (phenotypic.abc_.BaseOperation attribute), [1], [2]

A

ACCEPTED_FILE_EXTENSIONS (phenotypic.tools.constants_.IO attribute), [1], [2] aligner_axis (phenotypic.prefab.GridSectionPipeline attribute), [1], [2] aligner_mode (phenotypic.prefab.GridSectionPipeline attribute), [1], [2] alpha (phenotypic.analysis.LogGrowthModel attribute), [1], [2] AMBIGUOUS_FORMATS (phenotypic.tools.constants_.IMAGE_MODE attribute), [1], [2] amount (phenotypic.enhance.UnsharpMask attribute), [1], [2] analyze() (phenotypic.analysis.abc_.ModelFitter method) (phenotypic.analysis.abc_.SetAnalyzer method) (phenotypic.analysis.EdgeCorrector method), [1], [2] (phenotypic.analysis.LogGrowthModel method), [1], [2] (phenotypic.analysis.TukeyOutlierRemover method), [1], [2] append_rst_to_doc() (phenotypic.abc_.MeasurementInfo class method), [1], [2] (phenotypic.tools.constants_.BBOX class method), [1], [2] (phenotypic.tools.constants_.GRID class method), [1], [2] (phenotypic.tools.constants_.METADATA class method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS class method), [1], [2] apply() (phenotypic.abc_.GridCorrector method), [1], [2] (phenotypic.abc_.GridObjectDetector method), [1], [2] (phenotypic.abc_.GridObjectRefiner method), [1], [2] (phenotypic.abc_.GridOperation method), [1], [2] (phenotypic.abc_.ImageCorrector method), [1], [2] (phenotypic.abc_.ImageEnhancer method), [1], [2], [3], [4], [5] (phenotypic.abc_.ImageOperation method), [1], [2], [3], [4], [5] (phenotypic.abc_.ObjectDetector method), [1], [2], [3], [4], [5] (phenotypic.abc_.ObjectRefiner method), [1], [2], [3], [4], [5] (phenotypic.abc_.PrefabPipeline method), [1], [2] (phenotypic.abc_.ThresholdDetector method), [1], [2] (phenotypic.correction.GridAligner method), [1], [2] (phenotypic.detect.CannyDetector method), [1], [2] (phenotypic.detect.IsodataDetector method), [1], [2], [3], [4], [5] (phenotypic.detect.LiDetector method), [1], [2], [3], [4], [5] (phenotypic.detect.MeanDetector method), [1], [2], [3], [4], [5] (phenotypic.detect.MinimumDetector method), [1], [2], [3], [4], [5] (phenotypic.detect.OtsuDetector method), [1], [2], [3], [4], [5] (phenotypic.detect.RoundPeaksDetector method), [1], [2] (phenotypic.detect.TriangleDetector method), [1], [2], [3], [4], [5] (phenotypic.detect.WatershedDetector method), [1], [2] (phenotypic.detect.YenDetector method), [1], [2], [3], [4], [5] (phenotypic.enhance.BilateralDenoise method), [1], [2] (phenotypic.enhance.BM3DDenoiser method), [1], [2] (phenotypic.enhance.CLAHE method), [1], [2] (phenotypic.enhance.ContrastStretching method), [1], [2] (phenotypic.enhance.GaussianBlur method), [1], [2] (phenotypic.enhance.GaussianSubtract method), [1], [2] (phenotypic.enhance.LaplaceEnhancer method), [1], [2] (phenotypic.enhance.MedianFilter method), [1], [2] (phenotypic.enhance.RankMedianEnhancer method), [1], [2] (phenotypic.enhance.RollingBallRemoveBG method), [1], [2] (phenotypic.enhance.SobelFilter method), [1], [2] (phenotypic.enhance.UnsharpMask method), [1], [2] (phenotypic.enhance.WhiteTophatEnhancer method), [1], [2] (phenotypic.ImagePipeline method) (phenotypic.prefab.GridSectionPipeline method), [1], [2] (phenotypic.prefab.HeavyOtsuPipeline method), [1], [2] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1], [2] (phenotypic.prefab.HeavyWatershedPipeline method), [1], [2] (phenotypic.prefab.RoundPeaksPipeline method), [1], [2] (phenotypic.refine.BorderObjectRemover method), [1], [2] (phenotypic.refine.CenterDeviationReducer method), [1], [2] (phenotypic.refine.GridOversizedObjectRemover method), [1], [2] (phenotypic.refine.LowCircularityRemover method), [1], [2] (phenotypic.refine.MaskFill method), [1], [2] (phenotypic.refine.MaskOpener method), [1], [2] (phenotypic.refine.MinResidualErrorReducer method), [1], [2] (phenotypic.refine.ResidualOutlierRemover method), [1], [2] (phenotypic.refine.Skeletonize method), [1], [2] (phenotypic.refine.SmallObjectRemover method), [1], [2] (phenotypic.refine.Thinning method), [1], [2] (phenotypic.refine.WhiteTophatModifier method), [1], [2] (phenotypic.util.GridApply method), [1], [2]

apply_and_measure() (phenotypic.abc_.PrefabPipeline method), [1], [2] (phenotypic.ImagePipeline method) (phenotypic.prefab.GridSectionPipeline method), [1], [2] (phenotypic.prefab.HeavyOtsuPipeline method), [1], [2] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1], [2] (phenotypic.prefab.HeavyWatershedPipeline method), [1], [2] (phenotypic.prefab.RoundPeaksPipeline method), [1], [2] args (phenotypic.tools.exceptions_.ArrayKeyValueShapeMismatchError attribute), [1], [2] (phenotypic.tools.exceptions_.DataIntegrityError attribute), [1], [2] (phenotypic.tools.exceptions_.EmptyImageError attribute), [1], [2] (phenotypic.tools.exceptions_.GridImageInputError attribute), [1], [2] (phenotypic.tools.exceptions_.IllegalAssignmentError attribute), [1], [2] (phenotypic.tools.exceptions_.IllegalElementAssignmentError attribute), [1], [2] (phenotypic.tools.exceptions_.ImageOperationError attribute), [1], [2] (phenotypic.tools.exceptions_.ImmutableComponentError attribute), [1], [2] (phenotypic.tools.exceptions_.InputShapeMismatchError attribute), [1], [2] (phenotypic.tools.exceptions_.InterfaceError attribute), [1], [2] (phenotypic.tools.exceptions_.InvalidHsvSchemaError attribute), [1], [2] (phenotypic.tools.exceptions_.InvalidMapValueError attribute), [1], [2] (phenotypic.tools.exceptions_.InvalidMaskScalarValueError attribute), [1], [2] (phenotypic.tools.exceptions_.InvalidMaskValueError attribute), [1], [2] (phenotypic.tools.exceptions_.InvalidShapeError attribute), [1], [2] (phenotypic.tools.exceptions_.MetadataKeySpacesError attribute), [1], [2] (phenotypic.tools.exceptions_.MetadataKeyValueError attribute), [1], [2] (phenotypic.tools.exceptions_.MetadataValueNonScalarError attribute), [1], [2] (phenotypic.tools.exceptions_.NoArrayError attribute), [1], [2] (phenotypic.tools.exceptions_.NoComponentError attribute), [1], [2] (phenotypic.tools.exceptions_.NoImageDataError attribute), [1], [2] (phenotypic.tools.exceptions_.NoObjectsError attribute), [1], [2] (phenotypic.tools.exceptions_.NoOutputError attribute), [1], [2] (phenotypic.tools.exceptions_.ObjectNotFoundError attribute), [1], [2] (phenotypic.tools.exceptions_.OperationFailedError attribute), [1], [2] (phenotypic.tools.exceptions_.OperationIntegrityError attribute), [1], [2] (phenotypic.tools.exceptions_.OutputValueError attribute), [1], [2] (phenotypic.tools.exceptions_.PhenoTypicError attribute), [1], [2] (phenotypic.tools.exceptions_.UnknownError attribute), [1], [2] (phenotypic.tools.exceptions_.UnsupportedFileTypeError attribute), [1], [2] (phenotypic.tools.exceptions_.UnsupportedImageFormat attribute), [1], [2] (phenotypic.tools.exceptions_.UuidAssignmentError attribute), [1], [2] (phenotypic.tools.exceptions_.UUIDReassignmentError attribute), [1], [2] ArrayKeyValueShapeMismatchError, [1], [2] assert_swmr_on() (phenotypic.tools.HDF static method), [1], [2] (phenotypic.tools.hdf_.HDF static method) AutoGridFinder (class in phenotypic.grid), [1], [2] axis (phenotypic.refine.ResidualOutlierRemover attribute), [1], [2]

B

BASE (phenotypic.tools.constants_.IMAGE_TYPES attribute), [1], [2] BaseOperation (class in phenotypic.abc_), [1], [2] BBOX (class in phenotypic.tools.constants_), [1], [2] benchmark (phenotypic.ImagePipeline attribute) (phenotypic.prefab.GridSectionPipeline attribute), [1], [2] (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1], [2] benchmark_results() (phenotypic.abc_.PrefabPipeline method), [1], [2] (phenotypic.ImagePipeline method) (phenotypic.prefab.GridSectionPipeline method), [1], [2] (phenotypic.prefab.HeavyOtsuPipeline method), [1], [2] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1], [2] (phenotypic.prefab.HeavyWatershedPipeline method), [1], [2] (phenotypic.prefab.RoundPeaksPipeline method), [1], [2]

BGR (phenotypic.tools.constants_.IMAGE_MODE attribute), [1], [2] BGRA (phenotypic.tools.constants_.IMAGE_MODE attribute), [1], [2] BilateralDenoise (class in phenotypic.enhance), [1], [2] bit_depth (phenotypic.GridImage property) (phenotypic.Image property) BIT_DEPTH (phenotypic.tools.constants_.METADATA attribute), [1], [2] bm3d_sigma (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1], [2] bm3d_stage_arg (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1], [2] BM3DDenoiser (class in phenotypic.enhance), [1], [2] border_remover_size (phenotypic.prefab.GridSectionPipeline attribute), [1], [2] (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1], [2] border_size (phenotypic.refine.BorderObjectRemover attribute), [1], [2] BorderObjectRemover (class in phenotypic.refine), [1], [2]

C

CannyDetector (class in phenotypic.detect), [1], [2] capitalize() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2] casefold() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2] CATEGORY (phenotypic.abc_.MeasurementInfo property), [1], [2] (phenotypic.tools.constants_.BBOX property), [1], [2] (phenotypic.tools.constants_.GRID property), [1], [2] (phenotypic.tools.constants_.METADATA property), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS property), [1], [2] category() (phenotypic.abc_.MeasurementInfo class method), [1], [2] (phenotypic.tools.constants_.BBOX class method), [1], [2] (phenotypic.tools.constants_.GRID class method), [1], [2] (phenotypic.tools.constants_.METADATA class method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS class method), [1], [2] center() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2] CENTER_CC (phenotypic.tools.constants_.BBOX attribute), [1], [2] CENTER_RR (phenotypic.tools.constants_.BBOX attribute), [1], [2] CenterDeviationReducer (class in phenotypic.refine), [1], [2] CHANNELS_DEFAULT (phenotypic.tools.constants_.IMAGE_MODE attribute), [1], [2] circularity_cutoff (phenotypic.prefab.GridSectionPipeline attribute), [1], [2] CLAHE (class in phenotypic.enhance), [1], [2] clahe_clip_limit (phenotypic.prefab.GridSectionPipeline attribute), [1], [2] clahe_kernel_size (phenotypic.prefab.GridSectionPipeline attribute), [1], [2] (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1], [2]

clear() (phenotypic.GridImage method) (phenotypic.Image method) clip_limit (phenotypic.enhance.CLAHE attribute), [1], [2] close_handle() (phenotypic.tools.HDF static method), [1], [2] (phenotypic.tools.hdf_.HDF static method) col_edges (phenotypic.grid.ManualGridFinder attribute), [1], [2] COL_INTERVAL_END (phenotypic.tools.constants_.GRID attribute), [1], [2] COL_INTERVAL_START (phenotypic.tools.constants_.GRID attribute), [1], [2] COL_LINREG_B (phenotypic.tools.constants_.GRID_LINREG_STATS_EXTRACTOR attribute), [1], [2] COL_LINREG_M (phenotypic.tools.constants_.GRID_LINREG_STATS_EXTRACTOR attribute), [1], [2] COL_NUM (phenotypic.tools.constants_.GRID attribute), [1], [2] color (phenotypic.GridImage property) (phenotypic.Image property), [1] color_chroma_min (phenotypic.prefab.GridSectionPipeline attribute), [1], [2] color_include_XYZ (phenotypic.prefab.GridSectionPipeline attribute), [1], [2] color_white_chroma_max (phenotypic.prefab.GridSectionPipeline attribute), [1], [2] compactness (phenotypic.detect.WatershedDetector attribute), [1], [2] connectivity (phenotypic.detect.CannyDetector attribute), [1], [2] (phenotypic.detect.WatershedDetector attribute), [1], [2] ContrastStretching (class in phenotypic.enhance), [1], [2] copy() (phenotypic.GridImage method) (phenotypic.Image method) count() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2] CROP (phenotypic.tools.constants_.IMAGE_TYPES attribute), [1], [2] cutoff (phenotypic.refine.LowCircularityRemover attribute), [1], [2] cutoff_multiplier (phenotypic.refine.ResidualOutlierRemover attribute), [1], [2] cval (phenotypic.enhance.BilateralDenoise attribute), [1], [2] (phenotypic.enhance.GaussianBlur attribute), [1], [2] (phenotypic.enhance.GaussianSubtract attribute), [1], [2] (phenotypic.enhance.MedianFilter attribute), [1], [2], [3], [4], [5]

D

DataIntegrityError, [1], [2] DEFAULT_SCHEMA (phenotypic.tools.constants_.IMAGE_MODE attribute), [1], [2] detector_expf (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1], [2] detector_fast_resize (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1], [2] detector_fixed_square (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1], [2] detector_remove_noise (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1], [2] detector_subtract_background (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1], [2] detector_thresh_method (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1], [2] dispose_widgets() (phenotypic.abc_.GridCorrector method), [1], [2] (phenotypic.abc_.GridObjectDetector method), [1], [2] (phenotypic.abc_.GridObjectRefiner method), [1], [2] (phenotypic.abc_.GridOperation method), [1], [2] (phenotypic.abc_.ImageCorrector method), [1], [2] (phenotypic.abc_.ImageEnhancer method), [1], [2] (phenotypic.abc_.ImageOperation method), [1], [2] (phenotypic.abc_.ObjectDetector method), [1], [2] (phenotypic.abc_.ObjectRefiner method), [1], [2] (phenotypic.abc_.PrefabPipeline method), [1], [2] (phenotypic.abc_.ThresholdDetector method), [1], [2] (phenotypic.correction.GridAligner method), [1], [2] (phenotypic.detect.CannyDetector method), [1], [2] (phenotypic.detect.IsodataDetector method), [1], [2] (phenotypic.detect.LiDetector method), [1], [2] (phenotypic.detect.MeanDetector method), [1], [2] (phenotypic.detect.MinimumDetector method), [1], [2] (phenotypic.detect.OtsuDetector method), [1], [2] (phenotypic.detect.RoundPeaksDetector method), [1], [2] (phenotypic.detect.TriangleDetector method), [1], [2] (phenotypic.detect.WatershedDetector method), [1], [2] (phenotypic.detect.YenDetector method), [1], [2] (phenotypic.enhance.BilateralDenoise method), [1], [2] (phenotypic.enhance.BM3DDenoiser method), [1], [2] (phenotypic.enhance.CLAHE method), [1], [2] (phenotypic.enhance.ContrastStretching method), [1], [2] (phenotypic.enhance.GaussianBlur method), [1], [2] (phenotypic.enhance.GaussianSubtract method), [1], [2] (phenotypic.enhance.LaplaceEnhancer method), [1], [2] (phenotypic.enhance.MedianFilter method), [1], [2] (phenotypic.enhance.RankMedianEnhancer method), [1], [2] (phenotypic.enhance.RollingBallRemoveBG method), [1], [2] (phenotypic.enhance.SobelFilter method), [1], [2] (phenotypic.enhance.UnsharpMask method), [1], [2] (phenotypic.enhance.WhiteTophatEnhancer method), [1], [2] (phenotypic.ImagePipeline method) (phenotypic.prefab.GridSectionPipeline method), [1], [2] (phenotypic.prefab.HeavyOtsuPipeline method), [1], [2] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1], [2] (phenotypic.prefab.HeavyWatershedPipeline method), [1], [2] (phenotypic.prefab.RoundPeaksPipeline method), [1], [2] (phenotypic.refine.BorderObjectRemover method), [1], [2] (phenotypic.refine.CenterDeviationReducer method), [1], [2] (phenotypic.refine.GridOversizedObjectRemover method), [1], [2] (phenotypic.refine.LowCircularityRemover method), [1], [2] (phenotypic.refine.MaskFill method), [1], [2] (phenotypic.refine.MaskOpener method), [1], [2] (phenotypic.refine.MinResidualErrorReducer method), [1], [2] (phenotypic.refine.ResidualOutlierRemover method), [1], [2] (phenotypic.refine.Skeletonize method), [1], [2] (phenotypic.refine.SmallObjectRemover method), [1], [2] (phenotypic.refine.Thinning method), [1], [2] (phenotypic.refine.WhiteTophatModifier method), [1], [2]

E

edge_refinement (phenotypic.detect.RoundPeaksDetector attribute), [1], [2] EdgeCorrector (class in phenotypic.analysis), [1], [2] EmptyImageError, [1], [2] encode() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2] endswith() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2]

enh_gray (phenotypic.GridImage property) (phenotypic.Image property), [1] expandtabs() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2] EXT (phenotypic.tools.HDF attribute), [1], [2], [3], [4], [5] (phenotypic.tools.hdf_.HDF attribute), [1]

F

FIGSIZE (phenotypic.tools.constants_.MPL attribute), [1], [2] filepath (phenotypic.tools.HDF attribute), [1], [2], [3], [4], [5] (phenotypic.tools.hdf_.HDF attribute), [1] find() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2] footprint (phenotypic.detect.WatershedDetector attribute), [1], [2] (phenotypic.refine.MaskOpener attribute), [1], [2] footprint_radius (phenotypic.detect.RoundPeaksDetector attribute), [1], [2] (phenotypic.refine.WhiteTophatModifier attribute), [1], [2] footprint_shape (phenotypic.refine.WhiteTophatModifier attribute), [1], [2] format() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2]

format_map() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2] from_json() (phenotypic.abc_.PrefabPipeline class method), [1], [2] (phenotypic.ImagePipeline class method) (phenotypic.prefab.GridSectionPipeline class method), [1], [2] (phenotypic.prefab.HeavyOtsuPipeline class method), [1], [2] (phenotypic.prefab.HeavyRoundPeaksPipeline class method), [1], [2] (phenotypic.prefab.HeavyWatershedPipeline class method), [1], [2] (phenotypic.prefab.RoundPeaksPipeline class method), [1], [2]

G

gaussian_mode (phenotypic.prefab.GridSectionPipeline attribute), [1], [2] gaussian_sigma (phenotypic.prefab.GridSectionPipeline attribute), [1], [2] gaussian_truncate (phenotypic.prefab.GridSectionPipeline attribute), [1], [2] GaussianBlur (class in phenotypic.enhance), [1], [2] GaussianSubtract (class in phenotypic.enhance), [1], [2] geometric_median() (in module phenotypic.util), [1], [2] get_col_edges() (phenotypic.abc_.GridFinder method), [1], [2] (phenotypic.grid.AutoGridFinder method), [1], [2] (phenotypic.grid.ManualGridFinder method), [1], [2] get_data_group() (phenotypic.tools.HDF method), [1], [2] (phenotypic.tools.hdf_.HDF method) get_group() (phenotypic.tools.HDF static method), [1], [2] (phenotypic.tools.hdf_.HDF static method) get_headers() (phenotypic.abc_.MeasurementInfo class method), [1], [2] (phenotypic.tools.constants_.BBOX class method), [1], [2] (phenotypic.tools.constants_.GRID class method), [1], [2] (phenotypic.tools.constants_.METADATA class method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS class method), [1], [2] get_home() (phenotypic.tools.HDF method), [1], [2] (phenotypic.tools.hdf_.HDF method) get_image_group() (phenotypic.tools.HDF method), [1], [2] (phenotypic.tools.hdf_.HDF method) get_image_measurement_subgroup() (phenotypic.tools.HDF method), [1], [2] (phenotypic.tools.hdf_.HDF method) get_labels() (phenotypic.abc_.MeasurementInfo class method), [1], [2] (phenotypic.tools.constants_.BBOX class method), [1], [2] (phenotypic.tools.constants_.GRID class method), [1], [2] (phenotypic.tools.constants_.METADATA class method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS class method), [1], [2] get_protected_metadata_subgroup() (phenotypic.tools.HDF method), [1], [2] (phenotypic.tools.hdf_.HDF method) get_public_metadata_subgroup() (phenotypic.tools.HDF method), [1], [2] (phenotypic.tools.hdf_.HDF method)

get_root_group() (phenotypic.tools.HDF method), [1], [2] (phenotypic.tools.hdf_.HDF method) get_row_edges() (phenotypic.abc_.GridFinder method), [1], [2] (phenotypic.grid.AutoGridFinder method), [1], [2] (phenotypic.grid.ManualGridFinder method), [1], [2] get_status_subgroup() (phenotypic.tools.HDF method), [1], [2] (phenotypic.tools.hdf_.HDF method) get_uncompressed_sizes_for_group() (phenotypic.tools.HDF static method), [1], [2] (phenotypic.tools.hdf_.HDF static method) gray (phenotypic.GridImage property) (phenotypic.Image property), [1] GRAYSCALE (phenotypic.tools.constants_.IMAGE_MODE attribute), [1], [2] GRAYSCALE_SINGLE_CHANNEL (phenotypic.tools.constants_.IMAGE_MODE attribute), [1], [2] GRID (class in phenotypic.tools.constants_), [1], [2] grid (phenotypic.GridImage property), [1] GRID (phenotypic.tools.constants_.IMAGE_TYPES attribute), [1], [2] grid_apply_reset_enh_matrix (phenotypic.prefab.GridSectionPipeline attribute), [1], [2] grid_finder (phenotypic.GridImage attribute) (phenotypic.GridImage property) GRID_LINREG_STATS_EXTRACTOR (class in phenotypic.tools.constants_), [1], [2] GRID_SECTION (phenotypic.tools.constants_.IMAGE_TYPES attribute), [1], [2] GridAligner (class in phenotypic.correction), [1], [2] GridApply (class in phenotypic.util), [1], [2] GridCorrector (class in phenotypic.abc_), [1], [2] GridFinder (class in phenotypic.abc_), [1], [2] GridImage (class in phenotypic) GridImageInputError, [1], [2] GridMeasureFeatures (class in phenotypic.abc_), [1], [2] GridObjectDetector (class in phenotypic.abc_), [1], [2] GridObjectRefiner (class in phenotypic.abc_), [1], [2] GridOperation (class in phenotypic.abc_), [1], [2] GridOversizedObjectRemover (class in phenotypic.refine), [1], [2] GridSectionPipeline (class in phenotypic.prefab), [1], [2] groupby (phenotypic.analysis.TukeyOutlierRemover attribute), [1], [2]

H

HDF (class in phenotypic.tools), [1], [2] (class in phenotypic.tools.hdf_) HeavyOtsuPipeline (class in phenotypic.prefab), [1], [2] HeavyRoundPeaksPipeline (class in phenotypic.prefab), [1], [2]

HeavyWatershedPipeline (class in phenotypic.prefab), [1], [2] high_threshold (phenotypic.detect.CannyDetector attribute), [1], [2] home_posix (phenotypic.tools.HDF attribute), [1], [2], [3], [4], [5] (phenotypic.tools.hdf_.HDF attribute), [1] HSV (phenotypic.tools.constants_.IMAGE_MODE attribute), [1], [2]

I

ignore_zeros (phenotypic.detect.WatershedDetector attribute), [1], [2] IllegalAssignmentError, [1], [2] IllegalElementAssignmentError, [1], [2] Image (class in phenotypic) (in module phenotypic.tools.funcs_) IMAGE_MEASUREMENT_IMAGE_SUBGROUP_KEY (phenotypic.tools.constants_.IO attribute), [1], [2] IMAGE_MEASUREMENT_SUBGROUP_KEY (phenotypic.tools.HDF attribute), [1], [2], [3], [4], [5] (phenotypic.tools.hdf_.HDF attribute), [1] IMAGE_MODE (class in phenotypic.tools.constants_), [1], [2] IMAGE_NAME (phenotypic.tools.constants_.METADATA attribute), [1], [2] IMAGE_SET_DATA_POSIX (phenotypic.tools.HDF attribute), [1], [2], [3], [4], [5] (phenotypic.tools.hdf_.HDF attribute), [1] IMAGE_SET_HDF5_PARENT_GROUP (phenotypic.tools.constants_.IO attribute), [1], [2] IMAGE_SET_ROOT_POSIX (phenotypic.tools.HDF attribute), [1], [2], [3], [4], [5] (phenotypic.tools.hdf_.HDF attribute), [1] IMAGE_STATUS_SUBGROUP_KEY (phenotypic.tools.constants_.IO attribute), [1], [2] (phenotypic.tools.HDF attribute), [1], [2], [3], [4], [5] (phenotypic.tools.hdf_.HDF attribute), [1] IMAGE_TYPE (phenotypic.tools.constants_.METADATA attribute), [1], [2] IMAGE_TYPES (class in phenotypic.tools.constants_), [1], [2] ImageCorrector (class in phenotypic.abc_), [1], [2] ImageEnhancer (class in phenotypic.abc_), [1], [2] ImageOperation (class in phenotypic.abc_), [1], [2] ImageOperationError, [1], [2] ImagePipeline (class in phenotypic) IMFORMAT (phenotypic.tools.constants_.METADATA attribute), [1], [2] ImmutableComponentError, [1], [2] imread() (phenotypic.GridImage class method) (phenotypic.Image class method) index() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2] info() (phenotypic.GridImage method) (phenotypic.Image method) InputShapeMismatchError, [1], [2] InterfaceError, [1], [2] InvalidHsvSchemaError, [1], [2] InvalidMapValueError, [1], [2] InvalidMaskScalarValueError, [1], [2] InvalidMaskValueError, [1], [2] InvalidShapeError, [1], [2] invert_edges (phenotypic.detect.CannyDetector attribute), [1], [2] IO (class in phenotypic.tools.constants_), [1], [2] is_ambiguous() (phenotypic.tools.constants_.IMAGE_MODE method), [1], [2] is_array() (phenotypic.tools.constants_.IMAGE_MODE method), [1], [2] is_binary_mask() (in module phenotypic.tools), [1], [2] (in module phenotypic.tools.funcs_) is_matrix() (phenotypic.tools.constants_.IMAGE_MODE method), [1], [2] is_none() (phenotypic.tools.constants_.IMAGE_MODE method), [1], [2] is_static_method() (in module phenotypic.tools.funcs_) isalnum() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2]

isalpha() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2] isascii() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2] isdecimal() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2] isdigit() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2] isempty() (phenotypic.GridImage method) (phenotypic.Image method) isidentifier() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2] islower() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2] isnumeric() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2] IsodataDetector (class in phenotypic.detect), [1], [2] isprintable() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2] isspace() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2] istitle() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2] isupper() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2]

J

join() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2]

JPEG_FILE_EXTENSIONS (phenotypic.tools.constants_.IO attribute), [1], [2]

K

k (phenotypic.analysis.TukeyOutlierRemover attribute), [1], [2] kernel (phenotypic.enhance.RollingBallRemoveBG attribute), [1], [2]

kernel_size (phenotypic.enhance.CLAHE attribute), [1], [2] Kmax_label (phenotypic.analysis.LogGrowthModel attribute), [1], [2]

L

LABEL (phenotypic.tools.constants_.OBJECT attribute), [1], [2] lam (phenotypic.analysis.LogGrowthModel attribute), [1], [2] LaplaceEnhancer (class in phenotypic.enhance), [1], [2] LiDetector (class in phenotypic.detect), [1], [2] LINEAR_RGB (phenotypic.tools.constants_.IMAGE_MODE attribute), [1], [2] ljust() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2] load_colony() (in module phenotypic.data), [1], [2] load_early_colony() (in module phenotypic.data), [1], [2] load_faint_early_colony() (in module phenotypic.data), [1], [2] load_frame() (phenotypic.tools.HDF static method), [1], [2] (phenotypic.tools.hdf_.HDF static method) load_hdf5() (phenotypic.GridImage class method) (phenotypic.Image class method) load_pickle() (phenotypic.GridImage class method) (phenotypic.Image class method) load_plate_12hr() (in module phenotypic.data), [1], [2] load_plate_72hr() (in module phenotypic.data), [1], [2]

load_plate_series() (in module phenotypic.data), [1], [2] load_series() (phenotypic.tools.HDF static method), [1], [2] (phenotypic.tools.hdf_.HDF static method) load_smear_plate_12hr() (in module phenotypic.data), [1], [2] load_smear_plate_24hr() (in module phenotypic.data), [1], [2] load_synthetic_colony() (in module phenotypic.data), [1], [2] load_synthetic_detection_image() (in module phenotypic.data), [1], [2] LogGrowthModel (class in phenotypic.analysis), [1], [2] loss (phenotypic.analysis.LogGrowthModel attribute), [1], [2] low_threshold (phenotypic.detect.CannyDetector attribute), [1], [2] LowCircularityRemover (class in phenotypic.refine), [1], [2] lower() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2] lstrip() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2]

M

make_synthetic_colony() (in module phenotypic.data), [1], [2] make_synthetic_plate() (in module phenotypic.data), [1], [2] maketrans() (phenotypic.abc_.MeasurementInfo static method), [1], [2] (phenotypic.tools.constants_.BBOX static method), [1], [2] (phenotypic.tools.constants_.GRID static method), [1], [2] (phenotypic.tools.constants_.METADATA static method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS static method), [1], [2] ManualGridFinder (class in phenotypic.grid), [1], [2] mask_opener_footprint (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1], [2] MaskFill (class in phenotypic.refine), [1], [2] MaskOpener (class in phenotypic.refine), [1], [2] MATRIX_FORMATS (phenotypic.tools.constants_.IMAGE_MODE attribute), [1], [2] MAX_CC (phenotypic.tools.constants_.BBOX attribute), [1], [2] max_coeff_variance (phenotypic.refine.ResidualOutlierRemover attribute), [1], [2] max_iter (phenotypic.grid.AutoGridFinder attribute), [1], [2] max_num_iter (phenotypic.refine.Thinning attribute), [1], [2] MAX_RR (phenotypic.tools.constants_.BBOX attribute), [1], [2] MeanDetector (class in phenotypic.detect), [1], [2] measure() (phenotypic.abc_.GridFinder method), [1], [2] (phenotypic.abc_.GridMeasureFeatures method), [1], [2] (phenotypic.abc_.MeasureFeatures method), [1], [2] (phenotypic.abc_.PrefabPipeline method), [1], [2] (phenotypic.grid.AutoGridFinder method), [1], [2] (phenotypic.grid.ManualGridFinder method), [1], [2] (phenotypic.ImagePipeline method) (phenotypic.measure.MeasureBounds method), [1], [2] (phenotypic.measure.MeasureColor method), [1], [2] (phenotypic.measure.MeasureGridLinRegStats method), [1], [2] (phenotypic.measure.MeasureGridSpread method), [1], [2] (phenotypic.measure.MeasureIntensity method), [1], [2] (phenotypic.measure.MeasureShape method), [1], [2] (phenotypic.measure.MeasureSize method), [1], [2] (phenotypic.measure.MeasureTexture method), [1], [2] (phenotypic.prefab.GridSectionPipeline method), [1], [2] (phenotypic.prefab.HeavyOtsuPipeline method), [1], [2] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1], [2] (phenotypic.prefab.HeavyWatershedPipeline method), [1], [2] (phenotypic.prefab.RoundPeaksPipeline method), [1], [2] MeasureBounds (class in phenotypic.measure), [1], [2] MeasureColor (class in phenotypic.measure), [1], [2] MEASURED (phenotypic.tools.constants_.PIPE_STATUS attribute), [1], [2] MeasureFeatures (class in phenotypic.abc_), [1], [2] MeasureGridLinRegStats (class in phenotypic.measure), [1], [2] MeasureGridSpread (class in phenotypic.measure), [1], [2] MeasureIntensity (class in phenotypic.measure), [1], [2] MeasurementInfo (class in phenotypic.abc_), [1], [2] MeasureShape (class in phenotypic.measure), [1], [2] MeasureSize (class in phenotypic.measure), [1], [2] MeasureTexture (class in phenotypic.measure), [1], [2] median_cval (phenotypic.prefab.GridSectionPipeline attribute), [1], [2]

median_mode (phenotypic.prefab.GridSectionPipeline attribute), [1], [2] median_radius (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1], [2] median_shape (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1], [2] MedianFilter (class in phenotypic.enhance), [1], [2] METADATA (class in phenotypic.tools.constants_), [1], [2] metadata (phenotypic.GridImage property) (phenotypic.Image property) MetadataKeySpacesError, [1], [2] MetadataKeyValueError, [1], [2] MetadataValueNonScalarError, [1], [2] method (phenotypic.refine.Skeletonize attribute), [1], [2] MIN_CC (phenotypic.tools.constants_.BBOX attribute), [1], [2] min_peak_distance (phenotypic.detect.RoundPeaksDetector attribute), [1], [2] MIN_RR (phenotypic.tools.constants_.BBOX attribute), [1], [2] min_size (phenotypic.detect.CannyDetector attribute), [1], [2] (phenotypic.detect.WatershedDetector attribute), [1], [2] MinimumDetector (class in phenotypic.detect), [1], [2] MinResidualErrorReducer (class in phenotypic.refine), [1], [2] mode (phenotypic.enhance.BilateralDenoise attribute), [1], [2] (phenotypic.enhance.GaussianBlur attribute), [1], [2] (phenotypic.enhance.GaussianSubtract attribute), [1], [2] (phenotypic.enhance.MedianFilter attribute), [1], [2], [3], [4], [5] (phenotypic.tools.HDF attribute), [1], [2], [3], [4], [5] (phenotypic.tools.hdf_.HDF attribute), [1] model_func() (phenotypic.analysis.abc_.ModelFitter static method) (phenotypic.analysis.LogGrowthModel static method), [1], [2] ModelFitter (class in phenotypic.analysis.abc_) module phenotypic, [1] phenotypic.abc_, [1] phenotypic.analysis, [1] phenotypic.analysis.abc_ phenotypic.core phenotypic.correction, [1] phenotypic.data, [1] phenotypic.detect, [1] phenotypic.enhance, [1] phenotypic.grid, [1] phenotypic.measure, [1] phenotypic.phenotypic_cli phenotypic.prefab, [1] phenotypic.refine, [1] phenotypic.tools, [1] phenotypic.tools.colourspaces_, [1] phenotypic.tools.constants_, [1] phenotypic.tools.exceptions_, [1] phenotypic.tools.funcs_ phenotypic.tools.hdf_ phenotypic.util, [1] MPL (class in phenotypic.tools.constants_), [1], [2] murmur3_array_signature() (in module phenotypic.tools.funcs_)

N

name (phenotypic.GridImage property) (phenotypic.Image property) (phenotypic.tools.exceptions_.DataIntegrityError attribute), [1], [2] (phenotypic.tools.exceptions_.EmptyImageError attribute), [1], [2] (phenotypic.tools.exceptions_.IllegalElementAssignmentError attribute), [1], [2] (phenotypic.tools.exceptions_.ImmutableComponentError attribute), [1], [2] (phenotypic.tools.exceptions_.InvalidHsvSchemaError attribute), [1], [2] (phenotypic.tools.exceptions_.NoArrayError attribute), [1], [2] (phenotypic.tools.exceptions_.NoComponentError attribute), [1], [2] (phenotypic.tools.exceptions_.NoImageDataError attribute), [1], [2] (phenotypic.tools.exceptions_.NoObjectsError attribute), [1], [2] (phenotypic.tools.exceptions_.ObjectNotFoundError attribute), [1], [2] (phenotypic.tools.exceptions_.OperationIntegrityError attribute), [1], [2] (phenotypic.tools.exceptions_.UuidAssignmentError attribute), [1], [2] (phenotypic.tools.exceptions_.UUIDReassignmentError attribute), [1], [2] (phenotypic.tools.HDF attribute), [1], [2], [3], [4], [5] (phenotypic.tools.hdf_.HDF attribute), [1] nansafe (phenotypic.enhance.RollingBallRemoveBG attribute), [1], [2] ncols (phenotypic.grid.AutoGridFinder attribute), [1], [2] (phenotypic.grid.ManualGridFinder attribute), [1], [2] (phenotypic.GridImage attribute) (phenotypic.GridImage property)

NoArrayError, [1], [2] NoComponentError, [1], [2] NoImageDataError, [1], [2] None (phenotypic.abc_.ImageOperation attribute), [1], [2] (phenotypic.abc_.ObjectDetector attribute), [1], [2] NONE (phenotypic.tools.constants_.IMAGE_MODE attribute), [1], [2] NoObjectsError, [1], [2] NoOutputError, [1], [2] normalize_rgb_bitdepth() (in module phenotypic.tools.funcs_) nrows (phenotypic.grid.AutoGridFinder attribute), [1], [2] (phenotypic.grid.ManualGridFinder attribute), [1], [2] (phenotypic.GridImage attribute) (phenotypic.GridImage property) num_objects (phenotypic.GridImage property) (phenotypic.Image property) num_workers (phenotypic.analysis.TukeyOutlierRemover attribute), [1], [2]

O

obj (phenotypic.tools.exceptions_.DataIntegrityError attribute), [1], [2] (phenotypic.tools.exceptions_.EmptyImageError attribute), [1], [2] (phenotypic.tools.exceptions_.IllegalElementAssignmentError attribute), [1], [2] (phenotypic.tools.exceptions_.ImmutableComponentError attribute), [1], [2] (phenotypic.tools.exceptions_.InvalidHsvSchemaError attribute), [1], [2] (phenotypic.tools.exceptions_.NoArrayError attribute), [1], [2] (phenotypic.tools.exceptions_.NoComponentError attribute), [1], [2] (phenotypic.tools.exceptions_.NoImageDataError attribute), [1], [2] (phenotypic.tools.exceptions_.NoObjectsError attribute), [1], [2] (phenotypic.tools.exceptions_.ObjectNotFoundError attribute), [1], [2] (phenotypic.tools.exceptions_.OperationIntegrityError attribute), [1], [2] (phenotypic.tools.exceptions_.UuidAssignmentError attribute), [1], [2] (phenotypic.tools.exceptions_.UUIDReassignmentError attribute), [1], [2] OBJECT (class in phenotypic.tools.constants_), [1], [2] (phenotypic.tools.constants_.IMAGE_TYPES attribute), [1], [2] ObjectDetector (class in phenotypic.abc_), [1], [2] ObjectNotFoundError, [1], [2]

ObjectRefiner (class in phenotypic.abc_), [1], [2] objects (phenotypic.GridImage property) (phenotypic.Image property), [1] objmap (phenotypic.GridImage property) (phenotypic.Image property), [1] objmask (phenotypic.GridImage property) (phenotypic.Image property), [1] on (phenotypic.analysis.TukeyOutlierRemover attribute), [1], [2] OperationFailedError, [1], [2] OperationIntegrityError, [1], [2] origin (phenotypic.refine.MaskFill attribute), [1], [2] otsu_ignore_borders (phenotypic.prefab.GridSectionPipeline attribute), [1], [2] otsu_ignore_zeros (phenotypic.prefab.GridSectionPipeline attribute), [1], [2] OtsuDetector (class in phenotypic.detect), [1], [2] outlier_axis (phenotypic.prefab.GridSectionPipeline attribute), [1], [2] outlier_max_coeff_variance (phenotypic.prefab.GridSectionPipeline attribute), [1], [2] outlier_stddev_multiplier (phenotypic.prefab.GridSectionPipeline attribute), [1], [2] OutputValueError, [1], [2]

P

PARENT_IMAGE_NAME (phenotypic.tools.constants_.METADATA attribute), [1], [2] PARENT_UUID (phenotypic.tools.constants_.METADATA attribute), [1], [2] partition() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2] peak_prominence (phenotypic.detect.RoundPeaksDetector attribute), [1], [2] phenotypic module, [1] phenotypic.abc_ module, [1] phenotypic.analysis module, [1] phenotypic.analysis.abc_ module phenotypic.core module phenotypic.correction module, [1] phenotypic.data module, [1] phenotypic.detect module, [1] phenotypic.enhance module, [1] phenotypic.grid module, [1] phenotypic.measure module, [1] phenotypic.phenotypic_cli module phenotypic.prefab module, [1] phenotypic.refine module, [1]

phenotypic.tools module, [1] phenotypic.tools.colourspaces_ module, [1] phenotypic.tools.constants_ module, [1] phenotypic.tools.exceptions_ module, [1] phenotypic.tools.funcs_ module phenotypic.tools.hdf_ module phenotypic.util module, [1] PHENOTYPIC_METADATA_KEY (phenotypic.tools.constants_.IO attribute), [1], [2] PhenoTypicError, [1], [2] PIPE_STATUS (class in phenotypic.tools.constants_), [1], [2] PNG_FILE_EXTENSIONS (phenotypic.tools.constants_.IO attribute), [1], [2] preallocate_frame_layout() (phenotypic.tools.HDF static method), [1], [2] (phenotypic.tools.hdf_.HDF static method) preallocate_series_layout() (phenotypic.tools.HDF static method), [1], [2] (phenotypic.tools.hdf_.HDF static method) PRED_CC (phenotypic.tools.constants_.GRID_LINREG_STATS_EXTRACTOR attribute), [1], [2] PRED_RR (phenotypic.tools.constants_.GRID_LINREG_STATS_EXTRACTOR attribute), [1], [2] PrefabPipeline (class in phenotypic.abc_), [1], [2] preserve_range (phenotypic.enhance.GaussianSubtract attribute), [1], [2] (phenotypic.enhance.UnsharpMask attribute), [1], [2] process_single_image() (in module phenotypic.phenotypic_cli) PROCESSED (phenotypic.tools.constants_.PIPE_STATUS attribute), [1], [2] props (phenotypic.GridImage property) (phenotypic.Image property) PROTECTED_METADATA_SUBGROUP_KEY (phenotypic.tools.HDF attribute), [1], [2] (phenotypic.tools.hdf_.HDF attribute) PUBLIC_METADATA_SUBGROUP_KEY (phenotypic.tools.HDF attribute), [1], [2] (phenotypic.tools.hdf_.HDF attribute)

R

radius (phenotypic.enhance.MedianFilter attribute), [1], [2] (phenotypic.enhance.RankMedianEnhancer attribute), [1], [2] (phenotypic.enhance.RollingBallRemoveBG attribute), [1], [2] (phenotypic.enhance.UnsharpMask attribute), [1], [2] (phenotypic.enhance.WhiteTophatEnhancer attribute), [1], [2] RankMedianEnhancer (class in phenotypic.enhance), [1], [2] RAW_FILE_EXTENSIONS (phenotypic.tools.constants_.IO attribute), [1], [2] reader() (phenotypic.tools.HDF method), [1], [2] (phenotypic.tools.hdf_.HDF method) relabel (phenotypic.detect.WatershedDetector attribute), [1], [2] remove_noise (phenotypic.detect.RoundPeaksDetector attribute), [1], [2] removeprefix() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2] removesuffix() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2] replace() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2] reset() (phenotypic.GridImage method) (phenotypic.Image method) RESIDUAL_ERR (phenotypic.tools.constants_.GRID_LINREG_STATS_EXTRACTOR attribute), [1], [2] ResidualOutlierRemover (class in phenotypic.refine), [1], [2] results() (phenotypic.analysis.abc_.ModelFitter method) (phenotypic.analysis.abc_.SetAnalyzer method) (phenotypic.analysis.EdgeCorrector method), [1], [2] (phenotypic.analysis.LogGrowthModel method), [1], [2] (phenotypic.analysis.TukeyOutlierRemover method), [1], [2] rfind() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2] rgb (phenotypic.GridImage property) (phenotypic.Image property), [1] RGB (phenotypic.tools.constants_.IMAGE_MODE attribute), [1], [2] RGB_OR_BGR (phenotypic.tools.constants_.IMAGE_MODE attribute), [1], [2]

RGBA (phenotypic.tools.constants_.IMAGE_MODE attribute), [1], [2] RGBA_OR_BGRA (phenotypic.tools.constants_.IMAGE_MODE attribute), [1], [2] rindex() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2] rjust() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2] RollingBallRemoveBG (class in phenotypic.enhance), [1], [2] root_posix (phenotypic.tools.HDF attribute), [1], [2], [3], [4], [5] (phenotypic.tools.hdf_.HDF attribute), [1] rotate() (phenotypic.GridImage method) (phenotypic.Image method) RoundPeaksDetector (class in phenotypic.detect), [1], [2] RoundPeaksPipeline (class in phenotypic.prefab), [1], [2] row_edges (phenotypic.grid.ManualGridFinder attribute), [1], [2] ROW_INTERVAL_END (phenotypic.tools.constants_.GRID attribute), [1], [2] ROW_INTERVAL_START (phenotypic.tools.constants_.GRID attribute), [1], [2] ROW_LINREG_B (phenotypic.tools.constants_.GRID_LINREG_STATS_EXTRACTOR attribute), [1], [2] ROW_LINREG_M (phenotypic.tools.constants_.GRID_LINREG_STATS_EXTRACTOR attribute), [1], [2] ROW_NUM (phenotypic.tools.constants_.GRID attribute), [1], [2] rpartition() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2] rsplit() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2] rst_table() (phenotypic.abc_.MeasurementInfo class method), [1], [2] (phenotypic.tools.constants_.BBOX class method), [1], [2] (phenotypic.tools.constants_.GRID class method), [1], [2] (phenotypic.tools.constants_.METADATA class method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS class method), [1], [2] rstrip() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2]

S

safe_writer() (phenotypic.tools.HDF method), [1], [2] (phenotypic.tools.hdf_.HDF method) save2hdf5() (phenotypic.GridImage method) (phenotypic.Image method) save2pickle() (phenotypic.GridImage method) (phenotypic.Image method) save_array2hdf5() (phenotypic.tools.HDF static method), [1], [2] (phenotypic.tools.hdf_.HDF static method) save_frame_append() (phenotypic.tools.HDF static method), [1], [2] (phenotypic.tools.hdf_.HDF static method) save_frame_new() (phenotypic.tools.HDF static method), [1], [2] (phenotypic.tools.hdf_.HDF static method) save_frame_update() (phenotypic.tools.HDF static method), [1], [2] (phenotypic.tools.hdf_.HDF static method) save_series_append() (phenotypic.tools.HDF static method), [1], [2] (phenotypic.tools.hdf_.HDF static method) save_series_new() (phenotypic.tools.HDF static method), [1], [2] (phenotypic.tools.hdf_.HDF static method) save_series_update() (phenotypic.tools.HDF static method), [1], [2] (phenotypic.tools.hdf_.HDF static method) section_blur_mode (phenotypic.prefab.GridSectionPipeline attribute), [1], [2] section_blur_sigma (phenotypic.prefab.GridSectionPipeline attribute), [1], [2] section_blur_truncate (phenotypic.prefab.GridSectionPipeline attribute), [1], [2] section_contrast_lower_percentile (phenotypic.prefab.GridSectionPipeline attribute), [1], [2] section_contrast_upper_percentile (phenotypic.prefab.GridSectionPipeline attribute), [1], [2] section_median_cval (phenotypic.prefab.GridSectionPipeline attribute), [1], [2] section_median_mode (phenotypic.prefab.GridSectionPipeline attribute), [1], [2] SECTION_NUM (phenotypic.tools.constants_.GRID attribute), [1], [2] section_otsu_ignore_borders (phenotypic.prefab.GridSectionPipeline attribute), [1], [2] section_otsu_ignore_zeros (phenotypic.prefab.GridSectionPipeline attribute), [1], [2] set_data_posix (phenotypic.tools.HDF attribute), [1], [2], [3], [4], [5] (phenotypic.tools.hdf_.HDF attribute), [1] set_image() (phenotypic.GridImage method) (phenotypic.Image method) set_meas() (phenotypic.abc_.PrefabPipeline method), [1], [2] (phenotypic.ImagePipeline method) (phenotypic.prefab.GridSectionPipeline method), [1], [2] (phenotypic.prefab.HeavyOtsuPipeline method), [1], [2] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1], [2] (phenotypic.prefab.HeavyWatershedPipeline method), [1], [2] (phenotypic.prefab.RoundPeaksPipeline method), [1], [2] set_ops() (phenotypic.abc_.PrefabPipeline method), [1], [2] (phenotypic.ImagePipeline method) (phenotypic.prefab.GridSectionPipeline method), [1], [2] (phenotypic.prefab.HeavyOtsuPipeline method), [1], [2] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1], [2] (phenotypic.prefab.HeavyWatershedPipeline method), [1], [2] (phenotypic.prefab.RoundPeaksPipeline method), [1], [2] SetAnalyzer (class in phenotypic.analysis.abc_) shape (phenotypic.enhance.MedianFilter attribute), [1], [2] (phenotypic.enhance.RankMedianEnhancer attribute), [1], [2] (phenotypic.enhance.WhiteTophatEnhancer attribute), [1], [2] (phenotypic.GridImage property) (phenotypic.Image property) shift_x (phenotypic.enhance.RankMedianEnhancer attribute), [1], [2] shift_y (phenotypic.enhance.RankMedianEnhancer attribute), [1], [2] show() (phenotypic.analysis.abc_.ModelFitter method) (phenotypic.analysis.abc_.SetAnalyzer method) (phenotypic.analysis.EdgeCorrector method), [1], [2] (phenotypic.analysis.LogGrowthModel method), [1], [2] (phenotypic.analysis.TukeyOutlierRemover method), [1], [2] (phenotypic.GridImage method) (phenotypic.Image method) show_overlay() (phenotypic.GridImage method) (phenotypic.Image method) sigma (phenotypic.detect.CannyDetector attribute), [1], [2] (phenotypic.enhance.GaussianBlur attribute), [1], [2] (phenotypic.enhance.GaussianSubtract attribute), [1], [2] sigma_color (phenotypic.enhance.BilateralDenoise attribute), [1], [2] sigma_psd (phenotypic.enhance.BM3DDenoiser attribute), [1], [2] sigma_spatial (phenotypic.enhance.BilateralDenoise attribute), [1], [2] SINGLE_IMAGE_HDF5_PARENT_GROUP (phenotypic.tools.constants_.IO attribute), [1], [2] SINGLE_IMAGE_ROOT_POSIX (phenotypic.tools.HDF attribute), [1], [2], [3], [4], [5] (phenotypic.tools.hdf_.HDF attribute), [1] Skeletonize (class in phenotypic.refine), [1], [2] small_object_min_size (phenotypic.prefab.GridSectionPipeline attribute), [1], [2] (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1], [2] small_object_min_size_2 (phenotypic.prefab.GridSectionPipeline attribute), [1], [2] SmallObjectRemover (class in phenotypic.refine), [1], [2] smoothing_sigma (phenotypic.detect.RoundPeaksDetector attribute), [1], [2] SobelFilter (class in phenotypic.enhance), [1], [2] split() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2]

splitlines() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2] stage_arg (phenotypic.enhance.BM3DDenoiser attribute), [1], [2] startswith() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2] strict_writer() (phenotypic.tools.HDF method), [1], [2] (phenotypic.tools.hdf_.HDF method) strip() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2] structure (phenotypic.refine.MaskFill attribute), [1], [2] subtract_background (phenotypic.detect.RoundPeaksDetector attribute), [1], [2] SUFFIX (phenotypic.tools.constants_.METADATA attribute), [1], [2] SUPPORTED_FORMATS (phenotypic.tools.constants_.IMAGE_MODE attribute), [1], [2] swapcase() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2] swmr_reader() (phenotypic.tools.HDF method), [1], [2] (phenotypic.tools.hdf_.HDF method) swmr_writer() (phenotypic.tools.HDF method), [1], [2] (phenotypic.tools.hdf_.HDF method) sync_widgets_from_state() (phenotypic.abc_.GridCorrector method), [1], [2] (phenotypic.abc_.GridObjectDetector method), [1], [2] (phenotypic.abc_.GridObjectRefiner method), [1], [2] (phenotypic.abc_.GridOperation method), [1], [2] (phenotypic.abc_.ImageCorrector method), [1], [2] (phenotypic.abc_.ImageEnhancer method), [1], [2] (phenotypic.abc_.ImageOperation method), [1], [2] (phenotypic.abc_.ObjectDetector method), [1], [2] (phenotypic.abc_.ObjectRefiner method), [1], [2] (phenotypic.abc_.PrefabPipeline method), [1], [2] (phenotypic.abc_.ThresholdDetector method), [1], [2] (phenotypic.correction.GridAligner method), [1], [2] (phenotypic.detect.CannyDetector method), [1], [2] (phenotypic.detect.IsodataDetector method), [1], [2] (phenotypic.detect.LiDetector method), [1], [2] (phenotypic.detect.MeanDetector method), [1], [2] (phenotypic.detect.MinimumDetector method), [1], [2] (phenotypic.detect.OtsuDetector method), [1], [2] (phenotypic.detect.RoundPeaksDetector method), [1], [2] (phenotypic.detect.TriangleDetector method), [1], [2] (phenotypic.detect.WatershedDetector method), [1], [2] (phenotypic.detect.YenDetector method), [1], [2] (phenotypic.enhance.BilateralDenoise method), [1], [2] (phenotypic.enhance.BM3DDenoiser method), [1], [2] (phenotypic.enhance.CLAHE method), [1], [2] (phenotypic.enhance.ContrastStretching method), [1], [2] (phenotypic.enhance.GaussianBlur method), [1], [2] (phenotypic.enhance.GaussianSubtract method), [1], [2] (phenotypic.enhance.LaplaceEnhancer method), [1], [2] (phenotypic.enhance.MedianFilter method), [1], [2] (phenotypic.enhance.RankMedianEnhancer method), [1], [2] (phenotypic.enhance.RollingBallRemoveBG method), [1], [2] (phenotypic.enhance.SobelFilter method), [1], [2] (phenotypic.enhance.UnsharpMask method), [1], [2] (phenotypic.enhance.WhiteTophatEnhancer method), [1], [2] (phenotypic.ImagePipeline method) (phenotypic.prefab.GridSectionPipeline method), [1], [2] (phenotypic.prefab.HeavyOtsuPipeline method), [1], [2] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1], [2] (phenotypic.prefab.HeavyWatershedPipeline method), [1], [2] (phenotypic.prefab.RoundPeaksPipeline method), [1], [2] (phenotypic.refine.BorderObjectRemover method), [1], [2] (phenotypic.refine.CenterDeviationReducer method), [1], [2] (phenotypic.refine.GridOversizedObjectRemover method), [1], [2] (phenotypic.refine.LowCircularityRemover method), [1], [2] (phenotypic.refine.MaskFill method), [1], [2] (phenotypic.refine.MaskOpener method), [1], [2] (phenotypic.refine.MinResidualErrorReducer method), [1], [2] (phenotypic.refine.ResidualOutlierRemover method), [1], [2] (phenotypic.refine.Skeletonize method), [1], [2] (phenotypic.refine.SmallObjectRemover method), [1], [2] (phenotypic.refine.Thinning method), [1], [2] (phenotypic.refine.WhiteTophatModifier method), [1], [2]

T

texture_enhance (phenotypic.prefab.GridSectionPipeline attribute), [1], [2] texture_quant_lvl (phenotypic.prefab.GridSectionPipeline attribute), [1], [2] texture_scale (phenotypic.prefab.GridSectionPipeline attribute), [1], [2] (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1], [2] texture_warn (phenotypic.prefab.GridSectionPipeline attribute), [1], [2] (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1], [2] Thinning (class in phenotypic.refine), [1], [2] thresh_method (phenotypic.detect.RoundPeaksDetector attribute), [1], [2] ThresholdDetector (class in phenotypic.abc_), [1], [2] TIFF_EXTENSIONS (phenotypic.tools.constants_.IO attribute), [1], [2] time_label (phenotypic.analysis.LogGrowthModel attribute), [1], [2] timed_execution() (in module phenotypic.tools), [1], [2] (in module phenotypic.tools.funcs_) title() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2]

to_json() (phenotypic.abc_.PrefabPipeline method), [1], [2] (phenotypic.ImagePipeline method) (phenotypic.prefab.GridSectionPipeline method), [1], [2] (phenotypic.prefab.HeavyOtsuPipeline method), [1], [2] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1], [2] (phenotypic.prefab.HeavyWatershedPipeline method), [1], [2] (phenotypic.prefab.RoundPeaksPipeline method), [1], [2] tol (phenotypic.grid.AutoGridFinder attribute), [1], [2] translate() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2] TriangleDetector (class in phenotypic.detect), [1], [2] truncate (phenotypic.enhance.GaussianBlur attribute), [1], [2] (phenotypic.enhance.GaussianSubtract attribute), [1], [2] TukeyOutlierRemover (class in phenotypic.analysis), [1], [2]

U

UnknownError, [1], [2] UnsharpMask (class in phenotypic.enhance), [1], [2] UnsupportedFileTypeError, [1], [2] UnsupportedImageFormat, [1], [2] upper() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2]

use_quantiles (phenotypic.detect.CannyDetector attribute), [1], [2] uuid (phenotypic.GridImage property) (phenotypic.Image property) UUID (phenotypic.tools.constants_.METADATA attribute), [1], [2] UuidAssignmentError, [1], [2] UUIDReassignmentError, [1], [2]

V

validate_measure_integrity() (in module phenotypic.tools.funcs_) validate_operation_integrity() (in module phenotypic.tools.funcs_)

verbose (phenotypic.analysis.LogGrowthModel attribute), [1], [2] (phenotypic.ImagePipeline attribute) (phenotypic.prefab.HeavyRoundPeaksPipeline attribute), [1], [2]

W

WatershedDetector (class in phenotypic.detect), [1], [2] WhiteTophatEnhancer (class in phenotypic.enhance), [1], [2] WhiteTophatModifier (class in phenotypic.refine), [1], [2] widget() (phenotypic.abc_.GridCorrector method), [1], [2] (phenotypic.abc_.GridObjectDetector method), [1], [2] (phenotypic.abc_.GridObjectRefiner method), [1], [2] (phenotypic.abc_.GridOperation method), [1], [2] (phenotypic.abc_.ImageCorrector method), [1], [2] (phenotypic.abc_.ImageEnhancer method), [1], [2] (phenotypic.abc_.ImageOperation method), [1], [2] (phenotypic.abc_.ObjectDetector method), [1], [2] (phenotypic.abc_.ObjectRefiner method), [1], [2] (phenotypic.abc_.PrefabPipeline method), [1], [2] (phenotypic.abc_.ThresholdDetector method), [1], [2] (phenotypic.correction.GridAligner method), [1], [2] (phenotypic.detect.CannyDetector method), [1], [2] (phenotypic.detect.IsodataDetector method), [1], [2] (phenotypic.detect.LiDetector method), [1], [2] (phenotypic.detect.MeanDetector method), [1], [2] (phenotypic.detect.MinimumDetector method), [1], [2] (phenotypic.detect.OtsuDetector method), [1], [2] (phenotypic.detect.RoundPeaksDetector method), [1], [2] (phenotypic.detect.TriangleDetector method), [1], [2] (phenotypic.detect.WatershedDetector method), [1], [2] (phenotypic.detect.YenDetector method), [1], [2] (phenotypic.enhance.BilateralDenoise method), [1], [2] (phenotypic.enhance.BM3DDenoiser method), [1], [2] (phenotypic.enhance.CLAHE method), [1], [2] (phenotypic.enhance.ContrastStretching method), [1], [2] (phenotypic.enhance.GaussianBlur method), [1], [2] (phenotypic.enhance.GaussianSubtract method), [1], [2] (phenotypic.enhance.LaplaceEnhancer method), [1], [2] (phenotypic.enhance.MedianFilter method), [1], [2] (phenotypic.enhance.RankMedianEnhancer method), [1], [2] (phenotypic.enhance.RollingBallRemoveBG method), [1], [2] (phenotypic.enhance.SobelFilter method), [1], [2] (phenotypic.enhance.UnsharpMask method), [1], [2] (phenotypic.enhance.WhiteTophatEnhancer method), [1], [2] (phenotypic.ImagePipeline method) (phenotypic.prefab.GridSectionPipeline method), [1], [2] (phenotypic.prefab.HeavyOtsuPipeline method), [1], [2] (phenotypic.prefab.HeavyRoundPeaksPipeline method), [1], [2] (phenotypic.prefab.HeavyWatershedPipeline method), [1], [2] (phenotypic.prefab.RoundPeaksPipeline method), [1], [2] (phenotypic.refine.BorderObjectRemover method), [1], [2] (phenotypic.refine.CenterDeviationReducer method), [1], [2] (phenotypic.refine.GridOversizedObjectRemover method), [1], [2] (phenotypic.refine.LowCircularityRemover method), [1], [2] (phenotypic.refine.MaskFill method), [1], [2] (phenotypic.refine.MaskOpener method), [1], [2] (phenotypic.refine.MinResidualErrorReducer method), [1], [2] (phenotypic.refine.ResidualOutlierRemover method), [1], [2] (phenotypic.refine.Skeletonize method), [1], [2] (phenotypic.refine.SmallObjectRemover method), [1], [2] (phenotypic.refine.Thinning method), [1], [2] (phenotypic.refine.WhiteTophatModifier method), [1], [2]

win_size (phenotypic.enhance.BilateralDenoise attribute), [1], [2] with_traceback() (phenotypic.tools.exceptions_.ArrayKeyValueShapeMismatchError method), [1], [2] (phenotypic.tools.exceptions_.DataIntegrityError method), [1], [2] (phenotypic.tools.exceptions_.EmptyImageError method), [1], [2] (phenotypic.tools.exceptions_.GridImageInputError method), [1], [2] (phenotypic.tools.exceptions_.IllegalAssignmentError method), [1], [2] (phenotypic.tools.exceptions_.IllegalElementAssignmentError method), [1], [2] (phenotypic.tools.exceptions_.ImageOperationError method), [1], [2] (phenotypic.tools.exceptions_.ImmutableComponentError method), [1], [2] (phenotypic.tools.exceptions_.InputShapeMismatchError method), [1], [2] (phenotypic.tools.exceptions_.InterfaceError method), [1], [2] (phenotypic.tools.exceptions_.InvalidHsvSchemaError method), [1], [2] (phenotypic.tools.exceptions_.InvalidMapValueError method), [1], [2] (phenotypic.tools.exceptions_.InvalidMaskScalarValueError method), [1], [2] (phenotypic.tools.exceptions_.InvalidMaskValueError method), [1], [2] (phenotypic.tools.exceptions_.InvalidShapeError method), [1], [2] (phenotypic.tools.exceptions_.MetadataKeySpacesError method), [1], [2] (phenotypic.tools.exceptions_.MetadataKeyValueError method), [1], [2] (phenotypic.tools.exceptions_.MetadataValueNonScalarError method), [1], [2] (phenotypic.tools.exceptions_.NoArrayError method), [1], [2] (phenotypic.tools.exceptions_.NoComponentError method), [1], [2] (phenotypic.tools.exceptions_.NoImageDataError method), [1], [2] (phenotypic.tools.exceptions_.NoObjectsError method), [1], [2] (phenotypic.tools.exceptions_.NoOutputError method), [1], [2] (phenotypic.tools.exceptions_.ObjectNotFoundError method), [1], [2] (phenotypic.tools.exceptions_.OperationFailedError method), [1], [2] (phenotypic.tools.exceptions_.OperationIntegrityError method), [1], [2] (phenotypic.tools.exceptions_.OutputValueError method), [1], [2] (phenotypic.tools.exceptions_.PhenoTypicError method), [1], [2] (phenotypic.tools.exceptions_.UnknownError method), [1], [2] (phenotypic.tools.exceptions_.UnsupportedFileTypeError method), [1], [2] (phenotypic.tools.exceptions_.UnsupportedImageFormat method), [1], [2] (phenotypic.tools.exceptions_.UuidAssignmentError method), [1], [2] (phenotypic.tools.exceptions_.UUIDReassignmentError method), [1], [2]

Y

YenDetector (class in phenotypic.detect), [1], [2]

Z

zfill() (phenotypic.abc_.MeasurementInfo method), [1], [2] (phenotypic.tools.constants_.BBOX method), [1], [2] (phenotypic.tools.constants_.GRID method), [1], [2] (phenotypic.tools.constants_.METADATA method), [1], [2] (phenotypic.tools.constants_.PIPE_STATUS method), [1], [2]