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Tutorials
Getting Started
Python API
GUI
Guides
How-To Guides
Explanation
Extending PhenoTypic
Measurements
Measurements
Metadata
API Reference
More
Developer Guide
Downloads
Choose version
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
GUI internals
phenotypic.gui.builder
phenotypic.gui.builder._state.BlockNode
phenotypic.gui.builder._state.Edge
phenotypic.gui.builder._state._DagBuilderScope
phenotypic.gui.builder._state._DagBuilderState
phenotypic.gui.builder._state.INPUT_IMAGE_CLASS_NAME
phenotypic.gui.builder._state.PIPELINE_CLASS_NAME
phenotypic.gui.builder._state._seed_input_image
phenotypic.gui.builder._conversion_dag.to_pipeline_dag
phenotypic.gui.builder._conversion_dag.from_pipeline_dag
phenotypic.gui.builder._validation.validate
phenotypic.gui.builder._validation.Issue
Pipeline builder dispatch kinds
Pipeline builder validation rules
CLI Reference
Configuration Reference
Glossary
Modules
phenotypic.abc_
phenotypic.abc_.register_detection_mode
phenotypic.abc_.figure
phenotypic.abc_.MeasureFeatures
phenotypic.abc_.ImageOperation
phenotypic.abc_.ImageEnhancer
phenotypic.abc_.ImageDenoiser
phenotypic.abc_.FocusEdge
phenotypic.abc_.FocusBlob
phenotypic.abc_.Smoothing
phenotypic.abc_.BackgroundSubtraction
phenotypic.abc_.MorphologicalFiltering
phenotypic.abc_.ContrastAdjustment
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.abc_.Control
phenotypic.abc_.FigureSpec
phenotypic.abc_.FigureProvider
phenotypic.abc_.BoundFigures
phenotypic.analysis
phenotypic.analysis.filter_spec_json
phenotypic.analysis.filter_spec_query
phenotypic.analysis.render_error_analysis_html
phenotypic.analysis.render_error_analysis_report
phenotypic.analysis.LinearCapAndLagModel
phenotypic.analysis.EdgeCorrector
phenotypic.analysis.ErrorCutoffFinder
phenotypic.analysis.ExpectedVsDetectedCount
phenotypic.analysis.GridOccupancy
phenotypic.analysis.ICC
phenotypic.analysis.LinearLagModel
phenotypic.analysis.LogGrowthModel
phenotypic.analysis.MADOutlierRemover
phenotypic.analysis.MaxModifiedZScore
phenotypic.analysis.RelativeMAD
phenotypic.analysis.ReplicateAgreement
phenotypic.analysis.TukeyOutlierFraction
phenotypic.analysis.TukeyOutlierRemover
phenotypic.correction
phenotypic.correction.CaptureMetadata
phenotypic.correction.ColorCheckerProfile
phenotypic.correction.ColorCorrector
phenotypic.correction.ColorDenoise
phenotypic.correction.DenoiseBlockMatch
phenotypic.correction.GridAligner
phenotypic.correction.ImageCropper
phenotypic.correction.ImagePadder
phenotypic.correction.BayesShrinkCorrector
phenotypic.correction.VisuShrinkCorrector
phenotypic.data
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_early_colony
phenotypic.data.load_faint_early_colony
phenotypic.data.load_colony
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.UserThreshold
phenotypic.detect.ManualGridPointDetector
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.BayesShrinkEnhancer
phenotypic.enhance.LocalEdgeDenoise
phenotypic.enhance.EnhanceBlockMatch
phenotypic.enhance.EnhanceLocalContrast
phenotypic.enhance.StructureSmoothing
phenotypic.enhance.ContrastStretching
phenotypic.enhance.FocusEdgeFrangi
phenotypic.enhance.GaussianBlur
phenotypic.enhance.SubtractGaussian
phenotypic.enhance.GrayOpening
phenotypic.enhance.FocusEdgeHessian
phenotypic.enhance.FlattenIllumination
phenotypic.enhance.ImageInverter
phenotypic.enhance.FocusEdgeLaplace
phenotypic.enhance.MedianFilter
phenotypic.enhance.FocusEdgeMeijering
phenotypic.enhance.FocusBlobLoG
phenotypic.enhance.NonLocalMeansDenoiser
phenotypic.enhance.SubtractOpening
phenotypic.enhance.FocusEdgePhase
phenotypic.enhance.RankMedianEnhancer
phenotypic.enhance.SubtractRollingBall
phenotypic.enhance.FocusEdgeSato
phenotypic.enhance.FocusEdgeSobel
phenotypic.enhance.SharpenEdgeGauss
phenotypic.enhance.VisuShrinkEnhancer
phenotypic.enhance.WhiteTophatEnhance
phenotypic.enhance.SubtractWhiteTophat
phenotypic.enhance.SetDetectMode
phenotypic.enhance.CompositeEnhance
phenotypic.grid
phenotypic.grid.GridApply
phenotypic.grid.AutoGridFinder
phenotypic.grid.CenteredAutoGridFinder
phenotypic.grid.ManualGridFinder
phenotypic.grid.CenteredAutoGridFinderFallbackWarning
phenotypic.measure
phenotypic.measure.MeasureBounds
phenotypic.measure.MeasureColor
phenotypic.measure.MeasureIntensity
phenotypic.measure.MeasureOrientationZones
phenotypic.measure.MeasureShape
phenotypic.measure.MeasureSize
phenotypic.measure.MeasureSymmetricZones
phenotypic.measure.MeasureTexture
phenotypic.measure.MeasureGridSpread
phenotypic.measure.MeasureGridLinRegStats
phenotypic.measure.MeasureNeighborDist
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.TrimAsymmetry
phenotypic.refine.RemoveBorderObjects
phenotypic.refine.KeepNearestCenter
phenotypic.refine.ExtractColonyCore
phenotypic.refine.GridAlignmentRefiner
phenotypic.refine.GridOversizedObjectRemover
phenotypic.refine.RemoveLowCircularity
phenotypic.refine.ManualRefine
phenotypic.refine.MaskClosing
phenotypic.refine.MaskDilation
phenotypic.refine.MaskErosion
phenotypic.refine.MaskFill
phenotypic.refine.MaskGradient
phenotypic.refine.MaskOpening
phenotypic.refine.ReduceSectionsByLine
phenotypic.refine.NearestNeighborMerger
phenotypic.refine.RemoveGridOutliers
phenotypic.refine.SeparateObjects
phenotypic.refine.RefineBySineFit
phenotypic.refine.Skeletonize
phenotypic.refine.SmallObjectRemover
phenotypic.refine.SmallToLargeMerger
phenotypic.refine.Thinning
phenotypic.refine.MergeFragmentChains
phenotypic.refine.MaskWhiteTophat
phenotypic.refine.KeepSectionLargest
phenotypic.refine.RemoveByFeature
phenotypic.sdk_
phenotypic.sdk_.atomic_write_bytes
phenotypic.sdk_.atomic_write_text
phenotypic.sdk_.canonical_metadata_order
phenotypic.sdk_.ensure_metadata_prefix
phenotypic.sdk_.is_binary_mask
phenotypic.sdk_.is_metadata_header
phenotypic.sdk_.metadata_category_for_label
phenotypic.sdk_.metadata_category_prefixes
phenotypic.sdk_.order_measurement_columns
phenotypic.sdk_.timed_execution
phenotypic.sdk_.analysis_csv_path
phenotypic.sdk_.analysis_full_parquet_path
phenotypic.sdk_.analysis_html_path
phenotypic.sdk_.analysis_parquet_path
phenotypic.sdk_.analysis_scatter_json_path
phenotypic.sdk_.best_pipeline_path
phenotypic.sdk_.best_params_path
phenotypic.sdk_.chunk_lock_path
phenotypic.sdk_.chunk_manifest_path
phenotypic.sdk_.chunk_parquet_filename
phenotypic.sdk_.chunk_parquet_path
phenotypic.sdk_.chunk_state_path
phenotypic.sdk_.chunks_dir
phenotypic.sdk_.checkpoint_lock_filename
phenotypic.sdk_.checkpoint_lock_path
phenotypic.sdk_.dashboard_html_path
phenotypic.sdk_.dataset_hdf_dir
phenotypic.sdk_.dataset_measurements_dir
phenotypic.sdk_.dataset_overlays_dir
phenotypic.sdk_.dataset_results_dir
phenotypic.sdk_.overlays_dir
phenotypic.sdk_.curation_labels_parquet_path
phenotypic.sdk_.custom_categories_json_path
phenotypic.sdk_.default_output_dir_name
phenotypic.sdk_.deliverables_dir
phenotypic.sdk_.error_analysis_csv_path
phenotypic.sdk_.error_analysis_html_path
phenotypic.sdk_.error_analysis_parquet_path
phenotypic.sdk_.error_category_parquet_path
phenotypic.sdk_.errors_dir
phenotypic.sdk_.event_log_path
phenotypic.sdk_.ensure_typed_json_suffix
phenotypic.sdk_.failures_jsonl_path
phenotypic.sdk_.generalization_path
phenotypic.sdk_.has_config_suffix
phenotypic.sdk_.job_metadata_path
phenotypic.sdk_.load_image_from_hdf
phenotypic.sdk_.load_master_measurements
phenotypic.sdk_.logs_dir
phenotypic.sdk_.manifest_json_path
phenotypic.sdk_.master_measurements_csv_path
phenotypic.sdk_.master_measurements_parquet_path
phenotypic.sdk_.measurements_by_feature_dir
phenotypic.sdk_.measurements_csv_path
phenotypic.sdk_.measurements_parquet_path
phenotypic.sdk_.metadata_csv_deliverable_path
phenotypic.sdk_.matches_any_suffix
phenotypic.sdk_.migrate_legacy_machine_state
phenotypic.sdk_.migrate_legacy_qc
phenotypic.sdk_.clear_machine_state
phenotypic.sdk_.overlay_manifest_path
phenotypic.sdk_.param_importance_path
phenotypic.sdk_.pareto_best_pipeline_path
phenotypic.sdk_.pareto_dir
phenotypic.sdk_.pareto_front_parquet_path
phenotypic.sdk_.pareto_importance_path
phenotypic.sdk_.phenotypic_cache_dir
phenotypic.sdk_.phenotypic_cache_pipeline_json_path
phenotypic.sdk_.pipeline_json_path
phenotypic.sdk_.processing_report_html_path
phenotypic.sdk_.processing_state_path
phenotypic.sdk_.progress_dir
phenotypic.sdk_.qc_dir
phenotypic.sdk_.qc_duckdb_path
phenotypic.sdk_.qc_review_state_path
phenotypic.sdk_.readme_md_path
phenotypic.sdk_.read_run_manifest
phenotypic.sdk_.recompile_dir
phenotypic.sdk_.recompile_status_dir
phenotypic.sdk_.rembi_manifest_path
phenotypic.sdk_.resolve_best_pipeline_path
phenotypic.sdk_.resolve_event_log_path
phenotypic.sdk_.resolve_execution_mode
phenotypic.sdk_.resolve_manifest_json_path
phenotypic.sdk_.resolve_pipeline_config_path
phenotypic.sdk_.resolve_processing_state_path
phenotypic.sdk_.resolve_progress_dir
phenotypic.sdk_.resolve_qc_dir
phenotypic.sdk_.resolve_split_assignment_path
phenotypic.sdk_.resolve_study_db_path
phenotypic.sdk_.resolve_tuning_spec_path
phenotypic.sdk_.results_dir
phenotypic.sdk_.sentinel_resubmitted_path
phenotypic.sdk_.shard_parquet_filename
phenotypic.sdk_.slurm_scripts_dir
phenotypic.sdk_.task_status_filename
phenotypic.sdk_.task_status_path
phenotypic.sdk_.trials_parquet_path
phenotypic.sdk_.tune_cache_dir
phenotypic.sdk_.tune_cache_run_marker_path
phenotypic.sdk_.tune_cache_split_assignment_path
phenotypic.sdk_.tune_cache_splits_dir
phenotypic.sdk_.tune_cache_study_db_path
phenotypic.sdk_.tuning_spec_path
phenotypic.sdk_.verified_parquet_path
phenotypic.sdk_.ClipControlMixin
phenotypic.sdk_.FootprintMixin
phenotypic.sdk_.GridInferenceMixin
phenotypic.sdk_.HDF
phenotypic.sdk_.LazyWidgetMixin
phenotypic.sdk_.ChunkManifestKey
phenotypic.sdk_.ChunkStateKey
phenotypic.sdk_.DashboardManifestKey
phenotypic.sdk_.DashboardManifestSlurmInfoKey
phenotypic.sdk_.EnvVar
phenotypic.sdk_.HdfAttr
phenotypic.sdk_.JobMetadataKey
phenotypic.sdk_.ModulePath
phenotypic.sdk_.ProcessingStateKey
phenotypic.sdk_.BundleLayout
phenotypic.sdk_.colourspace
phenotypic.sdk_.colourspace.decode_srgb
phenotypic.sdk_.colourspace.encode_srgb
phenotypic.sdk_.constants_
phenotypic.sdk_.constants_.ConstantLabels
phenotypic.sdk_.constants_.GAMMA_ENCODINGS
phenotypic.sdk_.constants_.GRID_LINREG_STATS_EXTRACTOR
phenotypic.sdk_.constants_.IMAGE_MODE
phenotypic.sdk_.constants_.IMAGE_TYPES
phenotypic.sdk_.constants_.IO
phenotypic.sdk_.constants_.PIPE_STATUS
phenotypic.sdk_.exceptions_
phenotypic.sdk_.exceptions_.ArrayKeyValueShapeMismatchError
phenotypic.sdk_.exceptions_.DataIntegrityError
phenotypic.sdk_.exceptions_.EmptyImageError
phenotypic.sdk_.exceptions_.GrayscaleOutOfRangeError
phenotypic.sdk_.exceptions_.GridImageInputError
phenotypic.sdk_.exceptions_.IllegalAssignmentError
phenotypic.sdk_.exceptions_.IllegalElementAssignmentError
phenotypic.sdk_.exceptions_.ImageOperationError
phenotypic.sdk_.exceptions_.ImmutableComponentError
phenotypic.sdk_.exceptions_.InputShapeMismatchError
phenotypic.sdk_.exceptions_.InterfaceError
phenotypic.sdk_.exceptions_.InvalidHsvSchemaError
phenotypic.sdk_.exceptions_.InvalidMapValueError
phenotypic.sdk_.exceptions_.InvalidMaskScalarValueError
phenotypic.sdk_.exceptions_.InvalidMaskValueError
phenotypic.sdk_.exceptions_.InvalidShapeError
phenotypic.sdk_.exceptions_.MetadataKeySpacesError
phenotypic.sdk_.exceptions_.MetadataKeyValueError
phenotypic.sdk_.exceptions_.MetadataValueNonScalarError
phenotypic.sdk_.exceptions_.NoArrayError
phenotypic.sdk_.exceptions_.NoComponentError
phenotypic.sdk_.exceptions_.NoImageDataError
phenotypic.sdk_.exceptions_.NoObjectsError
phenotypic.sdk_.exceptions_.NoOutputError
phenotypic.sdk_.exceptions_.ObjectNotFoundError
phenotypic.sdk_.exceptions_.OperationFailedError
phenotypic.sdk_.exceptions_.OperationIntegrityError
phenotypic.sdk_.exceptions_.OutputValueError
phenotypic.sdk_.exceptions_.PhenoTypicError
phenotypic.sdk_.exceptions_.UUIDReassignmentError
phenotypic.sdk_.exceptions_.UnknownError
phenotypic.sdk_.exceptions_.UnsupportedFileTypeError
phenotypic.sdk_.exceptions_.UnsupportedImageFormat
phenotypic.sdk_.exceptions_.UuidAssignmentError
phenotypic.sdk_.napari_
phenotypic.sdk_.napari_.add_image_layer
phenotypic.sdk_.napari_.LabelEditorWidget
phenotypic.sdk_.napari_.PointPickerWidget
phenotypic.sdk_.register
phenotypic.sdk_.register.available_analysis_plugins
phenotypic.sdk_.register.available_plotters
phenotypic.sdk_.register.get_analysis_plugin
phenotypic.sdk_.register.get_plotter
phenotypic.sdk_.register.register_analysis
phenotypic.sdk_.register.register_plotter
phenotypic.sdk_.register.AnalysisPluginRegistry
phenotypic.sdk_.register.BaseRegistry
phenotypic.sdk_.register.PlotterRegistry
phenotypic.sdk_.slurm
phenotypic.sdk_.slurm.calculate_optimal_array_chunks
phenotypic.sdk_.slurm.estimate_concurrent_capacity
phenotypic.sdk_.slurm.format_sbatch_directives
phenotypic.sdk_.slurm.generate_dispatcher_chain
phenotypic.sdk_.slurm.generate_dispatcher_script
phenotypic.sdk_.slurm.get_slurm_array_limit
phenotypic.sdk_.slurm.get_slurm_max_submit_jobs
phenotypic.sdk_.slurm.parse_job_id
phenotypic.sdk_.slurm.submit_drip_feed_start
phenotypic.sdk_.slurm.submit_script
phenotypic.sdk_.slurm.validate_array_chunk
phenotypic.sdk_.slurm_
phenotypic.tune
phenotypic.tune.build_pipeline
phenotypic.tune.infer_group_key
phenotypic.tune.compute_generalization_gap
phenotypic.tune.run_held_out
phenotypic.tune.compute_param_importance
phenotypic.tune.compute_param_importance_report
phenotypic.tune.count_free_params
phenotypic.tune.screening_warmup_floor
phenotypic.tune.select_params_to_freeze
phenotypic.tune.freeze_value
phenotypic.tune.build_reduced_space
phenotypic.tune.run_tuning
phenotypic.tune.infer_search_space
phenotypic.tune.run_auto_space
phenotypic.tune.Categorical
phenotypic.tune.IntRange
phenotypic.tune.FloatRange
phenotypic.tune.Fixed
phenotypic.tune.Knob
phenotypic.tune.SearchSpace
phenotypic.tune.Evaluator
phenotypic.tune.EvaluationResult
phenotypic.tune.HeldOutConfig
phenotypic.tune.GeneralizationReport
phenotypic.tune.TuningEngine
phenotypic.tune.TuningSpec
phenotypic.tune.Budget
phenotypic.tune.StudyStore
phenotypic.tune.JournalStudyStore
phenotypic.tune.Trial
phenotypic.tune.ImportanceReport
phenotypic.tune.ScreeningController
phenotypic.tune.ScreeningConfig
phenotypic.tune.ScreeningResult
phenotypic.tune.TuneSpec
phenotypic.tune.InferredSearchSpace
phenotypic.tune.Excluded
phenotypic.tune.score
phenotypic.tune.score.Scorer
phenotypic.tune.score.QCScorer
phenotypic.tune.score.ReferenceFreeScorer
phenotypic.tune.score.GroundTruthMasks
phenotypic.tune.score.SupervisedScorer
phenotypic.tune.score.CompositeScorer
phenotypic.tune.strategy
phenotypic.tune.strategy.SearchStrategy
phenotypic.tune.strategy.PruningChannel
phenotypic.tune.strategy.NoOpChannel
phenotypic.tune.strategy.GridStrategy
phenotypic.tune.strategy.RandomStrategy
phenotypic.tune.strategy.StrategyConfig
phenotypic.tune.strategy.GridConfig
phenotypic.tune.strategy.RandomConfig
phenotypic.tune.strategy.OptunaConfig
phenotypic.util
phenotypic.util.geometric_median
phenotypic.util.generate_output_key
phenotypic.util.split_measurements
phenotypic.util.robust_color_center
phenotypic.util.medoid_ciede2000
phenotypic.util.delta_e2000_spread
phenotypic.util.hsv_to_cone
phenotypic.util.cone_to_hsv
phenotypic.util.lab_to_srgb_hex
phenotypic.util.decode_well_position
phenotypic.util.ImageMetricsCalculator
phenotypic.util.NoiseMetrics
phenotypic.util.ContrastMetrics
phenotypic.util.StructureMetrics
phenotypic.util.BackgroundMetrics
phenotypic.util.QualityScores
API Reference
phenotypic.tune
phenotypic.tune.StudyStore
phenotypic.tune.StudyStore
#
phenotypic.tune.
StudyStore
#
alias of
JournalStudyStore
On this page
StudyStore
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