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_._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_enhancer
- phenotypic.abc_._image_operation
- phenotypic.abc_._measure_features
- phenotypic.abc_._measurement_info
- phenotypic.abc_._object_detector
- phenotypic.abc_._object_refiner
- phenotypic.abc_._post_measurement
- phenotypic.abc_._prefab_pipeline
- phenotypic.abc_._threshold_detector
- phenotypic.analysis._edge_correction
- phenotypic.analysis._linear_softplus
- phenotypic.analysis._log_growth_model
- phenotypic.analysis._tukey_outlier
- phenotypic.analysis.abc_._model_fitter
- phenotypic.analysis.abc_._set_analyzer
- phenotypic.correction._bayesshrink_corrector
- phenotypic.correction._color_correction._color_checker_profile
- phenotypic.correction._color_correction._color_corrector
- phenotypic.correction._grid_aligner
- phenotypic.correction._image_cropper
- phenotypic.correction._image_padder
- phenotypic.correction._stable_denoise
- 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_detector
- phenotypic.detect._manual_grid_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._watershed_detector
- phenotypic.detect._yen_detector
- phenotypic.enhance._anscombe_forward
- phenotypic.enhance._anscombe_inverse
- phenotypic.enhance._bayesshrink_enhancer
- phenotypic.enhance._bilateral_denoise
- phenotypic.enhance._bm3d_denoiser
- phenotypic.enhance._clahe
- phenotypic.enhance._coherence_enhancing_diffusion
- phenotypic.enhance._contrast_streching
- phenotypic.enhance._frangi_vesselness
- phenotypic.enhance._gaussian_blur
- phenotypic.enhance._gray_opening
- phenotypic.enhance._hessian_filter
- phenotypic.enhance._homomorphic_filter
- phenotypic.enhance._image_inverter
- phenotypic.enhance._laplace_enhancer
- phenotypic.enhance._median_filter
- phenotypic.enhance._meijering_ridge_filter
- phenotypic.enhance._multiscale_log_enhancer
- phenotypic.enhance._non_local_means
- phenotypic.enhance._opening_subtract_bg
- phenotypic.enhance._phase_congruency
- phenotypic.enhance._rank_median_enhancer
- phenotypic.enhance._sato_ridge_filter
- phenotypic.enhance._set_detect_mode
- phenotypic.enhance._sobel_filter
- phenotypic.enhance._subtract_gaussian
- phenotypic.enhance._subtract_rolling_ball
- phenotypic.enhance._subtract_white_tophat
- phenotypic.enhance._unsharp_mask
- phenotypic.enhance._visushrink_enhancer
- phenotypic.enhance._white_tophat_enhance
- phenotypic.grid._auto_grid_finder
- phenotypic.grid._grid_apply
- phenotypic.grid._manual_grid_finder
- phenotypic.gui
- 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._asymmetric_spur_trimmer
- phenotypic.refine._border_object_modifier
- phenotypic.refine._center_deviation_reducer
- phenotypic.refine._circularity_modifier
- phenotypic.refine._gmm_core_extractor
- phenotypic.refine._grid_alignment_refiner
- phenotypic.refine._grid_oversized_object_remover
- phenotypic.refine._grid_section_largest
- phenotypic.refine._mask_closer
- phenotypic.refine._mask_dilator
- phenotypic.refine._mask_eroder
- phenotypic.refine._mask_fill
- phenotypic.refine._mask_gradient
- phenotypic.refine._mask_opener
- phenotypic.refine._min_residual_error_reducer
- phenotypic.refine._nearest_neighbor_merger
- phenotypic.refine._residual_outlier_remover
- phenotypic.refine._separate_objects
- phenotypic.refine._sine_alignment_refiner
- phenotypic.refine._skeletonize
- phenotypic.refine._small_object_remover
- phenotypic.refine._small_to_large_merger
- phenotypic.refine._thinning
- phenotypic.refine._transitive_distance_merger
- phenotypic.refine._white_tophat_modifier
- phenotypic.settings_
- phenotypic.sweep._generate_sweep
- phenotypic.sweep._sweep_types._sweep
- phenotypic.tools_.branch_pathfinding._cost_surface
- phenotypic.tools_.branch_pathfinding._dataclasses
- phenotypic.tools_.branch_pathfinding._diagnostics
- phenotypic.tools_.branch_pathfinding._dijkstra_kernels
- phenotypic.tools_.branch_pathfinding._fragment_prescreening
- phenotypic.tools_.branch_pathfinding._path_quality
- phenotypic.tools_.branch_pathfinding._voronoi_partition
- phenotypic.tools_.constants_
- phenotypic.tools_.exceptions_
- phenotypic.tools_.funcs_
- phenotypic.tools_.hdf_
- phenotypic.tools_.measurement_info_
- phenotypic.tools_.mixin._clip_control_mixin
- phenotypic.tools_.mixin._footprint_mixin
- phenotypic.tools_.mixin._grid_inference_mixin
- phenotypic.tools_.mixin._lazy_widget_mixin
- phenotypic.tools_.napari_._point_picker_widget
- phenotypic.tools_.panel_
- phenotypic.tools_.register._analysis_plugin_registry
- phenotypic.tools_.register._base_registry
- phenotypic.tools_.register._dashboard_registry
- phenotypic.tools_.register._plotter_registry
- phenotypic.tools_.slurm._config
- phenotypic.tools_.slurm._dispatcher
- phenotypic.tools_.slurm._sbatch
- phenotypic.util._geometric_median
- phenotypic.util.image_metrics