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Installation
Tutorials
How-To Guides
Explanation
Extending PhenoTypic
API Reference
Developer Guide
Downloads
GitHub
Section Navigation
Image Class Methods
Image Class Methods
Color Space Operations
Visualization & Plotting
Color Space Operations
Visualization & Plotting
GridImage Class Methods
GridImage Class Methods
ImagePipeline Class Methods
ImagePipeline Class Methods
CLI Reference
Configuration Reference
Glossary
Modules
phenotypic.abc_
phenotypic.abc_.register_detection_mode
phenotypic.abc_.MeasureFeatures
phenotypic.abc_.ImageOperation
phenotypic.abc_.ImageEnhancer
phenotypic.abc_.ImageCorrector
phenotypic.abc_.ObjectDetector
phenotypic.abc_.ObjectRefiner
phenotypic.abc_.ThresholdDetector
phenotypic.abc_.GpuDetector
phenotypic.abc_.GridOperation
phenotypic.abc_.GridFinder
phenotypic.abc_.GridCorrector
phenotypic.abc_.GridObjectRefiner
phenotypic.abc_.GridMeasureFeatures
phenotypic.abc_.BaseOperation
phenotypic.abc_.MeasurementInfo
phenotypic.abc_.GridObjectDetector
phenotypic.abc_.PrefabPipeline
phenotypic.abc_.FootprintMixin
phenotypic.abc_.PostMeasurement
phenotypic.abc_.DetectionMode
phenotypic.analysis
phenotypic.analysis.EdgeCorrector
phenotypic.analysis.LinearSoftplusModel
phenotypic.analysis.LogGrowthModel
phenotypic.analysis.TukeyOutlierRemover
phenotypic.correction
phenotypic.correction.ColorCheckerProfile
phenotypic.correction.ColorCorrector
phenotypic.correction.StableDenoise
phenotypic.correction.GridAligner
phenotypic.correction.ImageCropper
phenotypic.correction.ImagePadder
phenotypic.correction.BayesShrinkCorrector
phenotypic.correction.VisuShrinkCorrector
phenotypic.data
phenotypic.data.load_synthetic_colony
phenotypic.data.load_synth_yeast_plate
phenotypic.data.make_synthetic_colony
phenotypic.data.make_synthetic_plate
phenotypic.data.make_synthetic_filamentous_plate
phenotypic.data.load_plate_12hr
phenotypic.data.load_plate_72hr
phenotypic.data.load_plate_series
phenotypic.data.load_early_colony
phenotypic.data.load_faint_early_colony
phenotypic.data.load_colony
phenotypic.data.load_smear_plate_12hr
phenotypic.data.load_smear_plate_24hr
phenotypic.data.load_yeast_plate
phenotypic.data.load_fungi_plate
phenotypic.data.load_yeast_plate_full
phenotypic.data.load_fungi_plate_full
phenotypic.detect
phenotypic.detect.CannyDetector
phenotypic.detect.ChanVeseDetector
phenotypic.detect.CompositeDetector
phenotypic.detect.FilamentousFungiDetector
phenotypic.detect.HysteresisDetector
phenotypic.detect.InoculumDetector
phenotypic.detect.MadHysteresisDetector
phenotypic.detect.IsodataDetector
phenotypic.detect.LiDetector
phenotypic.detect.ManualDetector
phenotypic.detect.ManualGridDetector
phenotypic.detect.ManualPointDetector
phenotypic.detect.MeanDetector
phenotypic.detect.MinimumDetector
phenotypic.detect.OtsuDetector
phenotypic.detect.RankOtsuDetector
phenotypic.detect.RoundPeaksDetector
phenotypic.detect.SecondaryOtsuDetector
phenotypic.detect.SinePeakDetector
phenotypic.detect.TriangleDetector
phenotypic.detect.WatershedDetector
phenotypic.detect.YenDetector
phenotypic.enhance
phenotypic.enhance.AnscombeForward
phenotypic.enhance.AnscombeInverse
phenotypic.enhance.BayesShrinkEnhancer
phenotypic.enhance.BilateralDenoise
phenotypic.enhance.BM3DDenoiser
phenotypic.enhance.CLAHE
phenotypic.enhance.CoherenceEnhancingDiffusion
phenotypic.enhance.ContrastStretching
phenotypic.enhance.FrangiVesselness
phenotypic.enhance.GaussianBlur
phenotypic.enhance.SubtractGaussian
phenotypic.enhance.GrayOpening
phenotypic.enhance.HessianFilter
phenotypic.enhance.HomomorphicFilter
phenotypic.enhance.ImageInverter
phenotypic.enhance.LaplaceEnhancer
phenotypic.enhance.MedianFilter
phenotypic.enhance.MeijeringRidgeFilter
phenotypic.enhance.MultiscaleLoGEnhancer
phenotypic.enhance.NonLocalMeansDenoiser
phenotypic.enhance.OpeningSubtractBg
phenotypic.enhance.PhaseCongruencyEnhancer
phenotypic.enhance.RankMedianEnhancer
phenotypic.enhance.SubtractRollingBall
phenotypic.enhance.SatoRidgeFilter
phenotypic.enhance.SobelFilter
phenotypic.enhance.UnsharpMask
phenotypic.enhance.VisuShrinkEnhancer
phenotypic.enhance.WhiteTophatEnhance
phenotypic.enhance.SubtractWhiteTophat
phenotypic.enhance.SetDetectMode
phenotypic.grid
phenotypic.grid.GridApply
phenotypic.grid.AutoGridFinder
phenotypic.grid.ManualGridFinder
phenotypic.measure
phenotypic.measure.MeasureBounds
phenotypic.measure.MeasureColor
phenotypic.measure.MeasureIntensity
phenotypic.measure.MeasureShape
phenotypic.measure.MeasureSize
phenotypic.measure.MeasureSymmetricZones
phenotypic.measure.MeasureTexture
phenotypic.measure.MeasureGridSpread
phenotypic.measure.MeasureGridLinRegStats
phenotypic.measure.MeasureGridSpatial
phenotypic.prefab
phenotypic.prefab.HeavyWatershedPipeline
phenotypic.prefab.HeavyOtsuPipeline
phenotypic.prefab.GridSectionPipeline
phenotypic.prefab.HeavyRoundPeaksPipeline
phenotypic.prefab.RoundPeaksPipeline
phenotypic.prefab.FilamentousFungiPipeline
phenotypic.prefab.SpImagerPipeline
phenotypic.refine
phenotypic.refine.AsymmetricSpurTrimmer
phenotypic.refine.BorderObjectRemover
phenotypic.refine.CenterDeviationReducer
phenotypic.refine.GMMCoreExtractor
phenotypic.refine.GridAlignmentRefiner
phenotypic.refine.GridOversizedObjectRemover
phenotypic.refine.LowCircularityRemover
phenotypic.refine.MaskCloser
phenotypic.refine.MaskDilator
phenotypic.refine.MaskEroder
phenotypic.refine.MaskFill
phenotypic.refine.MaskGradient
phenotypic.refine.MaskOpener
phenotypic.refine.ReduceMultipleGridObjects
phenotypic.refine.NearestNeighborMerger
phenotypic.refine.ResidualOutlierRemover
phenotypic.refine.SeparateObjects
phenotypic.refine.SineAlignmentRefiner
phenotypic.refine.Skeletonize
phenotypic.refine.SmallObjectRemover
phenotypic.refine.SmallToLargeMerger
phenotypic.refine.Thinning
phenotypic.refine.TransitiveDistanceMerger
phenotypic.refine.WhiteTophat
phenotypic.refine.GridSectionLargest
phenotypic.tools_
phenotypic.tools_.is_binary_mask
phenotypic.tools_.timed_execution
phenotypic.tools_.ClipControlMixin
phenotypic.tools_.FootprintMixin
phenotypic.tools_.GridInferenceMixin
phenotypic.tools_.HDF
phenotypic.tools_.LazyWidgetMixin
phenotypic.tools_.colourspace
phenotypic.tools_.constants_
phenotypic.tools_.constants_.ConstantLabels
phenotypic.tools_.constants_.GAMMA_ENCODINGS
phenotypic.tools_.constants_.GRID_LINREG_STATS_EXTRACTOR
phenotypic.tools_.constants_.IMAGE_MODE
phenotypic.tools_.constants_.IMAGE_TYPES
phenotypic.tools_.constants_.IO
phenotypic.tools_.constants_.METADATA
phenotypic.tools_.constants_.OBJECT
phenotypic.tools_.constants_.PIPE_STATUS
phenotypic.tools_.exceptions_
phenotypic.tools_.exceptions_.ArrayKeyValueShapeMismatchError
phenotypic.tools_.exceptions_.DataIntegrityError
phenotypic.tools_.exceptions_.EmptyImageError
phenotypic.tools_.exceptions_.GrayscaleOutOfRangeError
phenotypic.tools_.exceptions_.GridImageInputError
phenotypic.tools_.exceptions_.IllegalAssignmentError
phenotypic.tools_.exceptions_.IllegalElementAssignmentError
phenotypic.tools_.exceptions_.ImageOperationError
phenotypic.tools_.exceptions_.ImmutableComponentError
phenotypic.tools_.exceptions_.InputShapeMismatchError
phenotypic.tools_.exceptions_.InterfaceError
phenotypic.tools_.exceptions_.InvalidHsvSchemaError
phenotypic.tools_.exceptions_.InvalidMapValueError
phenotypic.tools_.exceptions_.InvalidMaskScalarValueError
phenotypic.tools_.exceptions_.InvalidMaskValueError
phenotypic.tools_.exceptions_.InvalidShapeError
phenotypic.tools_.exceptions_.MetadataKeySpacesError
phenotypic.tools_.exceptions_.MetadataKeyValueError
phenotypic.tools_.exceptions_.MetadataValueNonScalarError
phenotypic.tools_.exceptions_.NoArrayError
phenotypic.tools_.exceptions_.NoComponentError
phenotypic.tools_.exceptions_.NoImageDataError
phenotypic.tools_.exceptions_.NoObjectsError
phenotypic.tools_.exceptions_.NoOutputError
phenotypic.tools_.exceptions_.ObjectNotFoundError
phenotypic.tools_.exceptions_.OperationFailedError
phenotypic.tools_.exceptions_.OperationIntegrityError
phenotypic.tools_.exceptions_.OutputValueError
phenotypic.tools_.exceptions_.PhenoTypicError
phenotypic.tools_.exceptions_.UUIDReassignmentError
phenotypic.tools_.exceptions_.UnknownError
phenotypic.tools_.exceptions_.UnsupportedFileTypeError
phenotypic.tools_.exceptions_.UnsupportedImageFormat
phenotypic.tools_.exceptions_.UuidAssignmentError
phenotypic.tools_.napari_
phenotypic.tools_.napari_.PointPickerWidget
phenotypic.tools_.panel_
phenotypic.tools_.panel_.PANEL_AVAILABLE
phenotypic.tools_.panel_.PLOTLY_AVAILABLE
phenotypic.tools_.panel_.PANEL_IMPORT_ERROR
phenotypic.tools_.panel_.display_or_return
phenotypic.tools_.panel_.ensure_panel_extension
phenotypic.tools_.panel_.in_ipython
phenotypic.tools_.panel_.in_jupyter
phenotypic.tools_.panel_.require_panel
phenotypic.tools_.register
phenotypic.tools_.register.available_analysis_plugins
phenotypic.tools_.register.available_dashboards
phenotypic.tools_.register.available_plotters
phenotypic.tools_.register.get_analysis_plugin
phenotypic.tools_.register.get_dashboard
phenotypic.tools_.register.get_plotter
phenotypic.tools_.register.register_analysis
phenotypic.tools_.register.register_dashboard
phenotypic.tools_.register.register_plotter
phenotypic.tools_.register.AnalysisPluginRegistry
phenotypic.tools_.register.BaseRegistry
phenotypic.tools_.register.DashboardRegistry
phenotypic.tools_.register.PlotterRegistry
phenotypic.tools_.slurm
phenotypic.tools_.slurm.calculate_optimal_array_chunks
phenotypic.tools_.slurm.estimate_concurrent_capacity
phenotypic.tools_.slurm.format_sbatch_directives
phenotypic.tools_.slurm.generate_dispatcher_chain
phenotypic.tools_.slurm.generate_dispatcher_script
phenotypic.tools_.slurm.get_slurm_array_limit
phenotypic.tools_.slurm.get_slurm_max_submit_jobs
phenotypic.tools_.slurm.parse_job_id
phenotypic.tools_.slurm.submit_drip_feed_start
phenotypic.tools_.slurm.submit_script
phenotypic.tools_.slurm.validate_array_chunk
phenotypic.tools_.slurm_
phenotypic.util
phenotypic.util.geometric_median
phenotypic.util.ImageMetricsCalculator
phenotypic.util.NoiseMetrics
phenotypic.util.ContrastMetrics
phenotypic.util.StructureMetrics
phenotypic.util.BackgroundMetrics
phenotypic.util.QualityScores
API Reference
phenotypic.tools_
phenotypic.tools_.colourspace
phenotypic.tools_.colourspace
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