All modules for which code is available
- phenotypic._core._grid_image
- phenotypic._core._image
- phenotypic._core._image_parts.accessors._color_accessor
- phenotypic._core._image_parts.accessors._detect_mat_accessor
- phenotypic._core._image_parts.accessors._grayscale_accessor
- phenotypic._core._image_parts.accessors._grid_accessor
- phenotypic._core._image_parts.accessors._metadata_accessor
- phenotypic._core._image_parts.accessors._objects_accessor
- phenotypic._core._image_parts.accessors._objmap_accessor
- phenotypic._core._image_parts.accessors._objmask_accessor
- phenotypic._core._image_parts.accessors._plot_accessor
- phenotypic._core._image_parts.accessors._rgb_accessor
- phenotypic._core._image_parts.detection_modes._detection_mode
- phenotypic.abc_._base_operation
- phenotypic.abc_._enhance_markers._background_subtraction
- phenotypic.abc_._enhance_markers._contrast_adjustment
- phenotypic.abc_._enhance_markers._focus_blob
- phenotypic.abc_._enhance_markers._focus_edge
- phenotypic.abc_._enhance_markers._morphological_filtering
- phenotypic.abc_._enhance_markers._smoothing
- phenotypic.abc_._figure_provider
- phenotypic.abc_._gpu_detector
- phenotypic.abc_._grid_corrector
- phenotypic.abc_._grid_finder
- phenotypic.abc_._grid_measure
- phenotypic.abc_._grid_object_detector
- phenotypic.abc_._grid_object_refiner
- phenotypic.abc_._grid_operation
- phenotypic.abc_._image_corrector
- phenotypic.abc_._image_denoiser
- phenotypic.abc_._image_enhancer
- phenotypic.abc_._image_operation
- phenotypic.abc_._measure_features
- phenotypic.abc_._object_detector
- phenotypic.abc_._object_refiner
- phenotypic.abc_._post_measurement
- phenotypic.abc_._prefab_pipeline
- phenotypic.abc_._threshold_detector
- phenotypic.analysis._double_softplus
- phenotypic.analysis._edge_correction
- phenotypic.analysis._error_cutoffs
- phenotypic.analysis._error_report
- phenotypic.analysis._linear_softplus
- phenotypic.analysis._log_growth_model
- phenotypic.analysis._mad_outlier
- phenotypic.analysis._tukey_outlier
- phenotypic.analysis.abc_._model_fitter
- phenotypic.analysis.abc_._quality_check
- phenotypic.analysis.abc_._set_analyzer
- phenotypic.analysis.qc._expected_vs_detected
- phenotypic.analysis.qc._icc
- phenotypic.analysis.qc._max_modz
- phenotypic.analysis.qc._relative_mad
- phenotypic.analysis.qc._replicate_agreement
- phenotypic.analysis.qc._tukey_fraction
- phenotypic.correction._bayesshrink_corrector
- phenotypic.correction._color_correction._capture_metadata
- phenotypic.correction._color_correction._color_checker_profile
- phenotypic.correction._color_correction._color_corrector
- phenotypic.correction._color_denoise
- phenotypic.correction._denoise_block_match
- phenotypic.correction._grid_aligner
- phenotypic.correction._image_cropper
- phenotypic.correction._image_padder
- phenotypic.correction._visushrink_corrector
- phenotypic.data._sample_image_data
- phenotypic.data._synthetic_data
- phenotypic.detect._canny_detector
- phenotypic.detect._chan_vese_detector
- phenotypic.detect._composite_detector
- phenotypic.detect._filamentous_fungi_detector
- phenotypic.detect._hysteresis_detector
- phenotypic.detect._inoculum_detector
- phenotypic.detect._isodata_detector
- phenotypic.detect._li_detector
- phenotypic.detect._mad_hysteresis_detector
- phenotypic.detect._manual_grid_point_detector
- phenotypic.detect._manual_point_detector
- phenotypic.detect._mean_detector
- phenotypic.detect._minimum_detector
- phenotypic.detect._otsu_detector
- phenotypic.detect._rank_otsu
- phenotypic.detect._round_peaks_detector
- phenotypic.detect._secondary_otsu
- phenotypic.detect._sine_peak_detector
- phenotypic.detect._triangle_detector
- phenotypic.detect._user_threshold
- phenotypic.detect._watershed_detector
- phenotypic.detect._yen_detector
- phenotypic.enhance._bayesshrink_enhancer
- phenotypic.enhance._contrast_streching
- phenotypic.enhance._enhance_block_match
- phenotypic.enhance._enhance_local_contrast
- phenotypic.enhance._flatten_illumination
- phenotypic.enhance._focus_blob_log
- phenotypic.enhance._focus_edge_frangi
- phenotypic.enhance._focus_edge_hessian
- phenotypic.enhance._focus_edge_laplace
- phenotypic.enhance._focus_edge_meijering
- phenotypic.enhance._focus_edge_phase
- phenotypic.enhance._focus_edge_sato
- phenotypic.enhance._focus_edge_sobel
- phenotypic.enhance._gaussian_blur
- phenotypic.enhance._gray_opening
- phenotypic.enhance._image_inverter
- phenotypic.enhance._local_edge_denoise
- phenotypic.enhance._median_filter
- phenotypic.enhance._non_local_means
- phenotypic.enhance._rank_median_enhancer
- phenotypic.enhance._set_detect_mode
- phenotypic.enhance._sharpen_edge_gauss
- phenotypic.enhance._structure_smoothing
- phenotypic.enhance._subtract_gaussian
- phenotypic.enhance._subtract_opening
- phenotypic.enhance._subtract_rolling_ball
- phenotypic.enhance._subtract_white_tophat
- phenotypic.enhance._visushrink_enhancer
- phenotypic.enhance._white_tophat_enhance
- phenotypic.grid._auto_grid_finder
- phenotypic.grid._centered_auto_grid_finder
- phenotypic.grid._grid_apply
- phenotypic.grid._manual_grid_finder
- phenotypic.gui
- phenotypic.gui.analysis._app
- phenotypic.gui.builder
- phenotypic.gui.builder._conversion_dag
- phenotypic.gui.builder._state
- phenotypic.gui.builder._validation
- phenotypic.gui.results_viewer.__main__
- phenotypic.gui.results_viewer._app
- phenotypic.gui.shell._app
- phenotypic.gui.shell._launcher
- phenotypic.gui.shell._sandbox
- phenotypic.gui.shell._session
- phenotypic.gui.tune._app
- phenotypic.gui.tune._run_root
- phenotypic.measure._measure_bounds
- phenotypic.measure._measure_color
- phenotypic.measure._measure_grid_linreg_stats
- phenotypic.measure._measure_grid_spatial
- phenotypic.measure._measure_grid_spread
- phenotypic.measure._measure_intensity
- phenotypic.measure._measure_shape
- phenotypic.measure._measure_size
- phenotypic.measure._measure_symmetric_zones
- phenotypic.measure._measure_texture
- phenotypic.phenotypicCLI
- phenotypic.post._append_string
- phenotypic.post._expand_metadata
- phenotypic.post._merge_metadata
- phenotypic.post._prepend_string
- phenotypic.prefab._filamentous_fungi_pipeline
- phenotypic.prefab._grid_section_pipeline
- phenotypic.prefab._heavy_otsu_pipeline
- phenotypic.prefab._heavy_round_peaks_pipeline
- phenotypic.prefab._heavy_watershed_pipeline
- phenotypic.prefab._round_peaks_pipeline
- phenotypic.prefab._spimager_pipeline
- phenotypic.refine._extract_colony_core
- phenotypic.refine._grid_alignment_refiner
- phenotypic.refine._grid_oversized_object_remover
- phenotypic.refine._keep_nearest_center
- phenotypic.refine._keep_section_largest
- phenotypic.refine._manual_refine
- phenotypic.refine._mask_closing
- phenotypic.refine._mask_dilation
- phenotypic.refine._mask_erosion
- phenotypic.refine._mask_fill
- phenotypic.refine._mask_gradient
- phenotypic.refine._mask_opening
- phenotypic.refine._mask_white_tophat
- phenotypic.refine._merge_fragment_chains
- phenotypic.refine._nearest_neighbor_merger
- phenotypic.refine._reduce_multiple_grid_objects
- phenotypic.refine._refine_by_sine_fit
- phenotypic.refine._remove_border_objects
- phenotypic.refine._remove_by_feature
- phenotypic.refine._remove_grid_outliers
- phenotypic.refine._remove_low_circularity
- phenotypic.refine._separate_objects
- phenotypic.refine._skeletonize
- phenotypic.refine._small_object_remover
- phenotypic.refine._small_to_large_merger
- phenotypic.refine._thinning
- phenotypic.refine._trim_asymmetry
- phenotypic.schema._bbox
- phenotypic.schema._color_composition
- phenotypic.schema._color_hsv
- phenotypic.schema._color_lab
- phenotypic.schema._color_xy
- phenotypic.schema._color_xyz
- phenotypic.schema._curation
- phenotypic.schema._double_softplus_model
- phenotypic.schema._edge_correction
- phenotypic.schema._error_category
- phenotypic.schema._experimental_tags._acquisition
- phenotypic.schema._experimental_tags._condition
- phenotypic.schema._experimental_tags._experiment
- phenotypic.schema._experimental_tags._genetic
- phenotypic.schema._experimental_tags._incubation
- phenotypic.schema._experimental_tags._plate
- phenotypic.schema._experimental_tags._sample
- phenotypic.schema._grid
- phenotypic.schema._grid_linreg_stats
- phenotypic.schema._grid_spatial
- phenotypic.schema._grid_spread
- phenotypic.schema._intensity
- phenotypic.schema._linear_softplus_model
- phenotypic.schema._log_growth_model
- phenotypic.schema._measurement_info
- phenotypic.schema._metadata
- 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_se
- phenotypic.schema._quality_tukey
- phenotypic.schema._quality_zmax
- phenotypic.schema._radial_expansion
- phenotypic.schema._shape
- phenotypic.schema._size
- phenotypic.schema._symmetric_zones
- phenotypic.schema._texture
- phenotypic.sdk_._atomic_io
- phenotypic.sdk_._io_constants
- phenotypic.sdk_.branch_pathfinding._cost_surface
- phenotypic.sdk_.branch_pathfinding._dataclasses
- phenotypic.sdk_.branch_pathfinding._diagnostics
- phenotypic.sdk_.branch_pathfinding._dijkstra_kernels
- phenotypic.sdk_.branch_pathfinding._fragment_prescreening
- phenotypic.sdk_.branch_pathfinding._path_quality
- phenotypic.sdk_.branch_pathfinding._voronoi_partition
- phenotypic.sdk_.colourspace
- phenotypic.sdk_.constants_
- phenotypic.sdk_.exceptions_
- phenotypic.sdk_.funcs_
- phenotypic.sdk_.hdf_
- phenotypic.sdk_.mixin._clip_control_mixin
- phenotypic.sdk_.mixin._footprint_mixin
- phenotypic.sdk_.mixin._grid_inference_mixin
- phenotypic.sdk_.mixin._lazy_widget_mixin
- phenotypic.sdk_.mixin._point_picker_mixin
- phenotypic.sdk_.napari_._label_editor_widget
- phenotypic.sdk_.napari_._layers
- phenotypic.sdk_.napari_._point_picker_widget
- phenotypic.sdk_.register._analysis_plugin_registry
- phenotypic.sdk_.register._base_registry
- phenotypic.sdk_.register._plotter_registry
- phenotypic.sdk_.slurm._config
- phenotypic.sdk_.slurm._dispatcher
- phenotypic.sdk_.slurm._sbatch
- phenotypic.sdk_.typing_
- phenotypic.sdk_.viz.figures._mpl_theme
- phenotypic.sdk_.viz.figures._theme
- phenotypic.sdk_.viz.notebook._adapter
- phenotypic.settings_
- phenotypic.tune._engine
- phenotypic.tune._evaluation._builder
- phenotypic.tune._evaluation._evaluator
- phenotypic.tune._evaluation._generalization
- phenotypic.tune._evaluation._held_out
- phenotypic.tune._scoring._composite
- phenotypic.tune._scoring._gt_loader
- phenotypic.tune._scoring._qc_scorer
- phenotypic.tune._scoring._reference_free_scorer
- phenotypic.tune._scoring._scorer
- phenotypic.tune._scoring._supervised
- phenotypic.tune._screening
- phenotypic.tune._screening_freeze
- phenotypic.tune._search_space._discovery
- phenotypic.tune._search_space._domains
- phenotypic.tune._search_space._infer
- phenotypic.tune._search_space._inferred
- phenotypic.tune._search_space._space
- phenotypic.tune._search_space._targets
- phenotypic.tune._spec
- phenotypic.tune._strategies._config
- phenotypic.tune._study_store
- phenotypic.tune._tune_cli._auto_space
- phenotypic.tune._tune_cli._run
- phenotypic.util._geometric_median
- phenotypic.util._measurement_outputs
- phenotypic.util._robust_color_stats
- phenotypic.util._well_pos_decoder
- phenotypic.util.image_metrics