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PhenoTypic PhenoTypic
    • Getting Started
    • Python API
    • GUI
    • How-To Guides
    • Explanation
    • Extending PhenoTypic
    • Measurements
    • Metadata
  • API Reference
    • Developer Guide
    • Downloads
  • GitHub
    • Getting Started
    • Python API
    • GUI
    • How-To Guides
    • Explanation
    • Extending PhenoTypic
    • Measurements
    • Metadata
  • API Reference
    • Developer Guide
    • Downloads
  • GitHub

Section Navigation

  • Image Class Methods
    • Image Class Methods
    • Color Space Operations
    • Plotting capabilities
  • Color Space Operations
  • Plotting capabilities
  • OME-Zarr store layout
  • 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_.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.analysis
    • phenotypic.analysis.cubical_persistence
    • 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.PersistencePairsResult
    • 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.CropImage
    • phenotypic.correction.PadImage
    • 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.TwoKFilamentousDetector
    • phenotypic.detect.FilFinderDetector
    • 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.ContrastGamma
    • phenotypic.enhance.ContrastLog
    • phenotypic.enhance.ContrastSigmoid
    • phenotypic.enhance.FocusEdgeFrangi
    • phenotypic.enhance.BlurGauss
    • 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.FocusEdgeMonogenicPhase
    • phenotypic.enhance.FocusEdgeTwoKPhase
    • phenotypic.enhance.FocusEdgeColorPhase
    • 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.MeasureSymZones
    • 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.schema
    • phenotypic.schema.parse_qualified_header
    • phenotypic.schema.qualified_header
    • phenotypic.schema.header_to_module
    • phenotypic.schema.Entry
    • phenotypic.schema.MeasurementInfo
    • phenotypic.schema.MetadataInfo
    • phenotypic.schema.REMBI_MODULE
    • phenotypic.schema.METADATA_MATCH
    • phenotypic.schema.IMAGE
    • phenotypic.schema.GENETIC
    • phenotypic.schema.SAMPLE
    • phenotypic.schema.PLATE
    • phenotypic.schema.CONDITION
    • phenotypic.schema.CULTURE
    • phenotypic.schema.EXPERIMENT
    • phenotypic.schema.STUDY
    • phenotypic.schema.ACQUISITION
    • phenotypic.schema.BBOX
    • phenotypic.schema.ColorComposition
    • phenotypic.schema.ColorHSV
    • phenotypic.schema.ColorLab
    • phenotypic.schema.Colorxy
    • phenotypic.schema.ColorXYZ
    • phenotypic.schema.CURATION
    • phenotypic.schema.LINEAR_CAP_AND_LAG_MODEL
    • phenotypic.schema.EDGE_CORRECTION
    • phenotypic.schema.ErrorCategory
    • phenotypic.schema.GRID
    • phenotypic.schema.GRID_LINREG_STATS
    • phenotypic.schema.NEIGHBOR_DIST
    • phenotypic.schema.GRID_SPREAD
    • phenotypic.schema.INTENSITY
    • phenotypic.schema.LINEAR_LAG_MODEL
    • phenotypic.schema.LOG_GROWTH_MODEL
    • phenotypic.schema.MODEL_METRICS
    • phenotypic.schema.OBJECT
    • phenotypic.schema.QUALITY_CHECK
    • phenotypic.schema.QUALITY_COUNT
    • phenotypic.schema.QUALITY_ICC
    • phenotypic.schema.QUALITY_MAD
    • phenotypic.schema.QUALITY_OCCUPANCY
    • phenotypic.schema.QUALITY_SE
    • phenotypic.schema.QUALITY_TUKEY
    • phenotypic.schema.QUALITY_ZMAX
    • phenotypic.schema.RADIAL_EXPANSION
    • phenotypic.schema.SHAPE
    • phenotypic.schema.SIZE
    • phenotypic.schema.ORIENTATION_ZONES
    • phenotypic.schema.ORIENTATION_ZONE_DIAGNOSTIC
    • phenotypic.schema.ORIENTATION_ZONE_PRIMARY
    • phenotypic.schema.SYMMETRIC_ZONES
    • phenotypic.schema.TEXTURE
  • phenotypic.sdk_
    • phenotypic.sdk_.aggregate_publication_marker_path
    • phenotypic.sdk_.atomic_write_bytes
    • phenotypic.sdk_.atomic_write_json
    • phenotypic.sdk_.atomic_write_parquet
    • phenotypic.sdk_.atomic_write_text
    • phenotypic.sdk_.atomic_write_with_writer
    • phenotypic.sdk_.publication_commit
    • phenotypic.sdk_.build_measurement_table_descriptor
    • phenotypic.sdk_.build_metadata_table_descriptor
    • phenotypic.sdk_.embedded_measurement_columns
    • phenotypic.sdk_.read_embedded_measurement_column
    • phenotypic.sdk_.read_embedded_measurement_descriptor
    • phenotypic.sdk_.replace_embedded_measurement_table
    • phenotypic.sdk_.replace_image_tables
    • phenotypic.sdk_.write_embedded_measurement_table
    • phenotypic.sdk_.write_image_tables
    • phenotypic.sdk_.write_metadata_table
    • phenotypic.sdk_.canonical_metadata_order
    • phenotypic.sdk_.ensure_metadata_prefix
    • phenotypic.sdk_.external_metadata_preserved_columns
    • phenotypic.sdk_.is_binary_mask
    • phenotypic.sdk_.is_metadata_header
    • phenotypic.sdk_.metadata_category_for_label
    • phenotypic.sdk_.metadata_category_prefixes
    • phenotypic.sdk_.metadata_member_for_header
    • phenotypic.sdk_.metadata_member_for_label
    • phenotypic.sdk_.metadata_only_mask
    • phenotypic.sdk_.metadata_owner_for_header
    • phenotypic.sdk_.metadata_owner_for_label
    • phenotypic.sdk_.normalize_metadata_columns
    • phenotypic.sdk_.order_measurement_columns
    • phenotypic.sdk_.metadata_migration_authority
    • phenotypic.sdk_.migrate_metadata_bundle
    • phenotypic.sdk_.migrate_metadata_file
    • phenotypic.sdk_.migrate_preflighted_metadata_bundle
    • phenotypic.sdk_.preflight_metadata_schema
    • phenotypic.sdk_.rollback_metadata_migration
    • phenotypic.sdk_.validated_published_metadata_migration_targets
    • phenotypic.sdk_.timed_execution
    • phenotypic.sdk_.describe_durability
    • phenotypic.sdk_.durable_writes_enabled
    • phenotypic.sdk_.new_part_path
    • phenotypic.sdk_.promote_store
    • phenotypic.sdk_.read_phenotypic_attributes
    • phenotypic.sdk_.sweep_orphan_parts
    • phenotypic.sdk_.valid_staged_store
    • phenotypic.sdk_.aggregate_proof_is_current
    • phenotypic.sdk_.assert_identity_current
    • phenotypic.sdk_.clear_verification_cache
    • phenotypic.sdk_.finalization_input_object
    • phenotypic.sdk_.resolve_run_state
    • phenotypic.sdk_.run_identity
    • phenotypic.sdk_.aggregation_shard_dir
    • phenotypic.sdk_.analysis_full_parquet_path
    • phenotypic.sdk_.analysis_manifest_path
    • phenotypic.sdk_.best_pipeline_path
    • phenotypic.sdk_.best_params_path
    • phenotypic.sdk_.bytes_fingerprint
    • 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_measurements_dir
    • phenotypic.sdk_.dataset_overlays_dir
    • phenotypic.sdk_.dataset_results_dir
    • phenotypic.sdk_.dataset_zarr_dir
    • phenotypic.sdk_.datasets_needing_migration
    • phenotypic.sdk_.overlays_dir
    • phenotypic.sdk_.plots_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_.file_fingerprint
    • phenotypic.sdk_.generalization_path
    • phenotypic.sdk_.generation_staging_path
    • phenotypic.sdk_.gui_launch_owner_path
    • phenotypic.sdk_.slurm_lifecycle_path
    • phenotypic.sdk_.image_completion_marker_path
    • phenotypic.sdk_.image_record_path
    • phenotypic.sdk_.read_image_record
    • phenotypic.sdk_.record_provenance
    • phenotypic.sdk_.record_rejection
    • phenotypic.sdk_.has_config_suffix
    • phenotypic.sdk_.job_metadata_path
    • phenotypic.sdk_.load_image_from_store
    • phenotypic.sdk_.logs_dir
    • phenotypic.sdk_.manifest_json_path
    • phenotypic.sdk_.master_carries_user_metadata
    • phenotypic.sdk_.user_metadata_headers
    • phenotypic.sdk_.master_measurements_parquet_path
    • phenotypic.sdk_.measurements_by_feature_dir
    • phenotypic.sdk_.measurements_csv_path
    • phenotypic.sdk_.measurements_parquet_path
    • phenotypic.sdk_.migration_backup_dir
    • phenotypic.sdk_.migration_backup_path
    • phenotypic.sdk_.migration_lock_path
    • phenotypic.sdk_.migration_receipt_path
    • phenotypic.sdk_.named_analysis_csv_path
    • phenotypic.sdk_.named_analysis_parquet_path
    • phenotypic.sdk_.named_analysis_paths
    • phenotypic.sdk_.metadata_csv_deliverable_path
    • phenotypic.sdk_.terminal_failures_jsonl_path
    • phenotypic.sdk_.matches_any_suffix
    • phenotypic.sdk_.migrate_legacy_machine_state
    • phenotypic.sdk_.migrate_legacy_qc
    • phenotypic.sdk_.clear_machine_state
    • 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_.pipeline_publication_lock
    • phenotypic.sdk_.pipeline_publication_lock_path
    • phenotypic.sdk_.paths_fingerprint
    • 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_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_split_assignment_path
    • phenotypic.sdk_.resolve_study_db_path
    • phenotypic.sdk_.resolve_tuning_spec_path
    • phenotypic.sdk_.restart_epoch_path
    • phenotypic.sdk_.results_dir
    • phenotypic.sdk_.run_completion_marker_path
    • phenotypic.sdk_.sentinel_resubmitted_path
    • phenotypic.sdk_.shard_parquet_filename
    • phenotypic.sdk_.slurm_scripts_dir
    • phenotypic.sdk_.source_cache_key
    • phenotypic.sdk_.is_zarr_store_name
    • phenotypic.sdk_.store_stem
    • phenotypic.sdk_.source_image_stem
    • phenotypic.sdk_.source_image_suffix
    • phenotypic.sdk_.store_publication_token
    • phenotypic.sdk_.store_revision_identity
    • 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_journal_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_.verification_cache_path
    • phenotypic.sdk_.verified_parquet_path
    • phenotypic.sdk_.validate_analysis_id
    • phenotypic.sdk_.zarr_store_path
    • phenotypic.sdk_.FootprintMixin
    • phenotypic.sdk_.GridInferenceMixin
    • phenotypic.sdk_.HDF
    • phenotypic.sdk_.InputLayerMixin
    • phenotypic.sdk_.LazyWidgetMixin
    • phenotypic.sdk_.NormControlMixin
    • phenotypic.sdk_.NormalizedOutputMixin
    • phenotypic.sdk_.PreparedEmbeddedMeasurementTable
    • phenotypic.sdk_.PreparedImageTables
    • phenotypic.sdk_.MetadataMigrationAuthority
    • phenotypic.sdk_.MetadataMigrationReport
    • phenotypic.sdk_.MetadataMigrationResult
    • phenotypic.sdk_.MetadataMigrationTarget
    • phenotypic.sdk_.PhenotypicAttr
    • phenotypic.sdk_.ImageState
    • phenotypic.sdk_.RunDiagnostics
    • phenotypic.sdk_.RunIdentity
    • phenotypic.sdk_.RunState
    • phenotypic.sdk_.ChunkManifestKey
    • phenotypic.sdk_.ChunkStateKey
    • phenotypic.sdk_.DashboardManifestKey
    • phenotypic.sdk_.DashboardManifestSlurmInfoKey
    • phenotypic.sdk_.EnvVar
    • phenotypic.sdk_.JobMetadataKey
    • phenotypic.sdk_.ModulePath
    • phenotypic.sdk_.ProcessingStateKey
    • phenotypic.sdk_.AnalysisArtifactPaths
    • 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_.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.generation_script_key
      • phenotypic.sdk_.slurm.get_slurm_array_limit
      • phenotypic.sdk_.slurm.get_slurm_max_submit_jobs
      • phenotypic.sdk_.slurm.parse_job_id
      • phenotypic.sdk_.slurm.parse_slurm_time
      • phenotypic.sdk_.slurm.sbatch_submission_environment
      • phenotypic.sdk_.slurm.submit_drip_feed_start
      • phenotypic.sdk_.slurm.submit_script
      • phenotypic.sdk_.slurm.validate_array_chunk
      • phenotypic.sdk_.slurm.write_slurm_array_script
      • phenotypic.sdk_.slurm.SlurmArrayScriptSpec
    • 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.sdk_
  • phenotypic.sdk_.write_embedded_measurement_table

phenotypic.sdk_.write_embedded_measurement_table#

phenotypic.sdk_.write_embedded_measurement_table(store_part: Path, table: PreparedEmbeddedMeasurementTable) → Path[source]#

Write the prepared Parquet payload and its two Zarr v3 groups.

Parameters:
  • store_part (Path)

  • table (PreparedEmbeddedMeasurementTable)

Return type:

Path

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  • write_embedded_measurement_table()

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