Index

_

__str__() (image_analysis_3D.featurization_utils.errors.ProcessorTypeError method) _fix_scipy_ndimage_result() (in module image_analysis_3D.featurization_utils.granularity_utils)

_subsample_3d() (in module image_analysis_3D.featurization_utils.granularity_utils) _upsample_3d() (in module image_analysis_3D.featurization_utils.granularity_utils)

A

add_masks_where_missing() (in module image_analysis_3D.segmentation_utils.general_segmentation_utils) add_min_max_boundry_slices() (in module image_analysis_3D.segmentation_utils.general_segmentation_utils)

animate_view() (in module image_analysis_3D.visualization_utils.animation_utils) apply_butterworth_filter() (in module image_analysis_3D.segmentation_utils.general_segmentation_utils) avoid_path_crash_bandicoot() (in module image_analysis_3D.file_utils.notebook_init_utils)

B

bandicoot_check() (in module image_analysis_3D.file_utils.notebook_init_utils) bisection_costes_threshold_calculation() (in module image_analysis_3D.featurization_utils.colocalization_utils)

build_complete_bipartite_graph() (in module image_analysis_3D.segmentation_utils.nuclei_segmentation) butterworth_grid_optimization() (in module image_analysis_3D.segmentation_utils.general_segmentation_utils)

C

calculate_bbox_area() (in module image_analysis_3D.segmentation_utils.general_segmentation_utils) calculate_centroid() (in module image_analysis_3D.featurization_utils.neighbors_utils) calculate_mask_iou() (in module image_analysis_3D.segmentation_utils.general_segmentation_utils) calculate_overlap() (in module image_analysis_3D.segmentation_utils.general_segmentation_utils) calculate_surface_area() (in module image_analysis_3D.featurization_utils.area_size_shape_utils) call_chammi75_featurization_pipeline() (in module image_analysis_3D.featurization_utils.chammi75_featurization) call_SAMMed3D_pipeline() (in module image_analysis_3D.featurization_utils.sammed3d_featurizer) call_whole_image_sammed3d_pipeline() (in module image_analysis_3D.featurization_utils.sammed3d_featurizer) centroid_within_bbox_detection() (in module image_analysis_3D.segmentation_utils.general_segmentation_utils) check_coordinate_inside_box() (in module image_analysis_3D.file_utils.segmentation_decoupling) (in module image_analysis_3D.segmentation_utils.segmentation_decoupling) check_for_all_same_labels() (in module image_analysis_3D.segmentation_utils.general_segmentation_utils) check_for_missing_args() (in module image_analysis_3D.file_utils.arg_parsing_utils) check_for_xy_squareness() (in module image_analysis_3D.image_utils.image_utils)

check_for_zero_objects() (in module image_analysis_3D.featurization_utils.sammed3d_featurizer) check_if_centroid_within_mask() (in module image_analysis_3D.segmentation_utils.general_segmentation_utils) check_number_of_files() (in module image_analysis_3D.file_utils.file_checking) check_well_dir_name_format() (in module image_analysis_3D.file_utils.preprocessing_funcs) classify_cells_into_shells() (in module image_analysis_3D.featurization_utils.neighbors_utils) clean_border_objects() (in module image_analysis_3D.segmentation_utils.general_segmentation_utils) collapse_labels() (in module image_analysis_3D.segmentation_utils.general_segmentation_utils) collapse_labels_from_paths() (in module image_analysis_3D.segmentation_utils.nuclei_segmentation) compare_masks_for_merged() (in module image_analysis_3D.file_utils.segmentation_decoupling) (in module image_analysis_3D.segmentation_utils.segmentation_decoupling) create_cytoplasm_masks() (in module image_analysis_3D.segmentation_utils.general_segmentation_utils) create_results_dataframe() (in module image_analysis_3D.featurization_utils.neighbors_utils) crop_3D_image() (in module image_analysis_3D.featurization_utils.neighbors_utils) (in module image_analysis_3D.image_utils.image_utils)

D

decouple_masks() (in module image_analysis_3D.segmentation_utils.general_segmentation_utils)

E

euclidean_distance_from_centroid() (in module image_analysis_3D.featurization_utils.neighbors_utils) euclidian_2D_distance() (in module image_analysis_3D.file_utils.segmentation_decoupling) (in module image_analysis_3D.segmentation_utils.segmentation_decoupling) expand_box() (in module image_analysis_3D.image_utils.image_utils) extract() (image_analysis_3D.featurization_utils.sammed3d_featurizer.SAMMed3DFeatureExtractor method)

extract_batch() (image_analysis_3D.featurization_utils.sammed3d_featurizer.SAMMed3DFeatureExtractor method) extract_features() (image_analysis_3D.featurization_utils.sammed3d_featurizer.MicroscopySAMMed3DPipeline method) extract_features_batch() (image_analysis_3D.featurization_utils.sammed3d_featurizer.MicroscopySAMMed3DPipeline method) extract_unique_masks() (in module image_analysis_3D.file_utils.segmentation_decoupling) (in module image_analysis_3D.segmentation_utils.segmentation_decoupling)

F

featurize_2D_image_w_chammi75() (in module image_analysis_3D.featurization_utils.chammi75_featurization) fill_holes_in_mask() (in module image_analysis_3D.segmentation_utils.cell_segmentation) fill_object_gaps() (in module image_analysis_3D.segmentation_utils.nuclei_segmentation) find_files_available() (in module image_analysis_3D.file_utils.file_reading)

format_morphology_feature_name() (in module image_analysis_3D.featurization_utils.feature_writing_utils) forward() (image_analysis_3D.featurization_utils.chammi75_featurization.PerImageNormalize method) (image_analysis_3D.featurization_utils.chammi75_featurization.SaturationNoiseInjector method) (image_analysis_3D.featurization_utils.sammed3d_featurizer.TransformerBlock3D method)

G

generate_coordinates_for_reconstruction() (in module image_analysis_3D.segmentation_utils.general_segmentation_utils) generate_distance_pairs() (in module image_analysis_3D.segmentation_utils.general_segmentation_utils) get_chammi75_model() (in module image_analysis_3D.featurization_utils.chammi75_featurization) get_combinations_of_indices() (in module image_analysis_3D.file_utils.segmentation_decoupling) (in module image_analysis_3D.segmentation_utils.segmentation_decoupling) get_coordinates() (in module image_analysis_3D.featurization_utils.neighbors_utils) get_dimensionality() (in module image_analysis_3D.file_utils.segmentation_decoupling) (in module image_analysis_3D.segmentation_utils.segmentation_decoupling)

get_labels_for_post_hoc_reassignment() (in module image_analysis_3D.segmentation_utils.general_segmentation_utils) get_larger_bbox() (in module image_analysis_3D.file_utils.segmentation_decoupling) (in module image_analysis_3D.segmentation_utils.segmentation_decoupling) get_number_of_unique_labels() (in module image_analysis_3D.file_utils.segmentation_decoupling) (in module image_analysis_3D.segmentation_utils.segmentation_decoupling) get_outline() (in module image_analysis_3D.featurization_utils.intensity_utils) get_to_the_unested_dir() (in module image_analysis_3D.file_utils.preprocessing_funcs) get_well_fov_dirs() (in module image_analysis_3D.file_utils.preprocessing_funcs) graph_creation() (in module image_analysis_3D.segmentation_utils.general_segmentation_utils)

I

image_analysis_3D.errors.exceptions module image_analysis_3D.featurization_utils.area_size_shape_utils module image_analysis_3D.featurization_utils.chammi75_featurization module image_analysis_3D.featurization_utils.colocalization_utils module image_analysis_3D.featurization_utils.errors module image_analysis_3D.featurization_utils.feature_writing_utils module image_analysis_3D.featurization_utils.granularity_utils module image_analysis_3D.featurization_utils.intensity_utils module image_analysis_3D.featurization_utils.neighbors_utils module image_analysis_3D.featurization_utils.resource_profiling_util module image_analysis_3D.featurization_utils.sammed3d_featurizer module image_analysis_3D.featurization_utils.texture_utils module image_analysis_3D.file_utils.arg_parsing_utils module

image_analysis_3D.file_utils.file_checking module image_analysis_3D.file_utils.file_reading module image_analysis_3D.file_utils.notebook_init_utils module image_analysis_3D.file_utils.preprocessing_funcs module image_analysis_3D.file_utils.read_in_channel_mapping module image_analysis_3D.file_utils.segmentation_decoupling module image_analysis_3D.image_utils.image_utils module image_analysis_3D.segmentation_utils.cell_segmentation module image_analysis_3D.segmentation_utils.general_segmentation_utils module image_analysis_3D.segmentation_utils.nuclei_segmentation module image_analysis_3D.segmentation_utils.segmentation_decoupling module image_analysis_3D.visualization_utils.animation_utils module init_notebook() (in module image_analysis_3D.file_utils.notebook_init_utils)

L

linear_costes_threshold_calculation() (in module image_analysis_3D.featurization_utils.colocalization_utils)

M

mahalanobis_distance_from_centroid() (in module image_analysis_3D.featurization_utils.neighbors_utils) mask_label_reassignment() (in module image_analysis_3D.segmentation_utils.general_segmentation_utils) MaxWorkerError measure_3D_area_size_shape() (in module image_analysis_3D.featurization_utils.area_size_shape_utils) measure_3D_colocalization() (in module image_analysis_3D.featurization_utils.colocalization_utils) measure_3D_granularity() (in module image_analysis_3D.featurization_utils.granularity_utils) measure_3D_intensity_CPU() (in module image_analysis_3D.featurization_utils.intensity_utils) measure_3D_number_of_neighbors() (in module image_analysis_3D.featurization_utils.neighbors_utils) measure_3D_texture() (in module image_analysis_3D.featurization_utils.texture_utils) merge_sets() (in module image_analysis_3D.file_utils.segmentation_decoupling) (in module image_analysis_3D.segmentation_utils.general_segmentation_utils) (in module image_analysis_3D.segmentation_utils.segmentation_decoupling) merge_sets_df() (in module image_analysis_3D.file_utils.segmentation_decoupling) (in module image_analysis_3D.segmentation_utils.segmentation_decoupling) MicroscopySAMMed3DPipeline (class in image_analysis_3D.featurization_utils.sammed3d_featurizer) missing_slice_check() (in module image_analysis_3D.segmentation_utils.general_segmentation_utils) module image_analysis_3D.errors.exceptions image_analysis_3D.featurization_utils.area_size_shape_utils image_analysis_3D.featurization_utils.chammi75_featurization image_analysis_3D.featurization_utils.colocalization_utils image_analysis_3D.featurization_utils.errors image_analysis_3D.featurization_utils.feature_writing_utils image_analysis_3D.featurization_utils.granularity_utils image_analysis_3D.featurization_utils.intensity_utils image_analysis_3D.featurization_utils.neighbors_utils image_analysis_3D.featurization_utils.resource_profiling_util image_analysis_3D.featurization_utils.sammed3d_featurizer image_analysis_3D.featurization_utils.texture_utils image_analysis_3D.file_utils.arg_parsing_utils image_analysis_3D.file_utils.file_checking image_analysis_3D.file_utils.file_reading image_analysis_3D.file_utils.notebook_init_utils image_analysis_3D.file_utils.preprocessing_funcs image_analysis_3D.file_utils.read_in_channel_mapping image_analysis_3D.file_utils.segmentation_decoupling image_analysis_3D.image_utils.image_utils image_analysis_3D.segmentation_utils.cell_segmentation image_analysis_3D.segmentation_utils.general_segmentation_utils image_analysis_3D.segmentation_utils.nuclei_segmentation image_analysis_3D.segmentation_utils.segmentation_decoupling image_analysis_3D.visualization_utils.animation_utils

mp4_to_gif() (in module image_analysis_3D.visualization_utils.animation_utils)

N

neighbors_expand_box() (in module image_analysis_3D.featurization_utils.neighbors_utils)

new_crop_border() (in module image_analysis_3D.image_utils.image_utils)

O

object_stitching_and_relation() (in module image_analysis_3D.segmentation_utils.nuclei_segmentation)

P

parse_args() (in module image_analysis_3D.file_utils.arg_parsing_utils) perform_morphology_dependent_segmentation() (in module image_analysis_3D.segmentation_utils.cell_segmentation) PerImageNormalize (class in image_analysis_3D.featurization_utils.chammi75_featurization) plot_distance_distributions() (in module image_analysis_3D.featurization_utils.neighbors_utils)

postprocess_segmentation() (in module image_analysis_3D.segmentation_utils.nuclei_segmentation) prepare_two_images_for_colocalization() (in module image_analysis_3D.featurization_utils.colocalization_utils) preprocess_volume() (image_analysis_3D.featurization_utils.sammed3d_featurizer.MicroscopySAMMed3DPipeline method) ProcessorTypeError

R

read_2D_image_for_zstacking() (in module image_analysis_3D.file_utils.preprocessing_funcs) read_in_channels() (in module image_analysis_3D.file_utils.file_reading) read_zstack_image() (in module image_analysis_3D.file_utils.file_reading) reassemble_each_mask() (in module image_analysis_3D.file_utils.segmentation_decoupling) (in module image_analysis_3D.segmentation_utils.segmentation_decoupling) reassign_labels() (in module image_analysis_3D.segmentation_utils.general_segmentation_utils) remove_edge_cases() (in module image_analysis_3D.segmentation_utils.general_segmentation_utils)

remove_label_id() (in module image_analysis_3D.segmentation_utils.general_segmentation_utils) remove_single_slice_objects() (in module image_analysis_3D.segmentation_utils.nuclei_segmentation) remove_underscores_from_string() (in module image_analysis_3D.featurization_utils.feature_writing_utils) reorder_organoid_labels() (in module image_analysis_3D.segmentation_utils.general_segmentation_utils) retrieve_channel_mapping() (in module image_analysis_3D.file_utils.read_in_channel_mapping) reverse_sliding_window_max_projection() (in module image_analysis_3D.segmentation_utils.general_segmentation_utils) run_post_hoc_mask_reassignment() (in module image_analysis_3D.segmentation_utils.general_segmentation_utils) run_post_hoc_refinement() (in module image_analysis_3D.segmentation_utils.general_segmentation_utils)

S

SAMMed3DFeatureExtractor (class in image_analysis_3D.featurization_utils.sammed3d_featurizer) SaturationNoiseInjector (class in image_analysis_3D.featurization_utils.chammi75_featurization) save_features_as_parquet() (in module image_analysis_3D.featurization_utils.feature_writing_utils) scale_image() (in module image_analysis_3D.featurization_utils.texture_utils) segment_cells_with_3D_watershed() (in module image_analysis_3D.segmentation_utils.cell_segmentation) (in module image_analysis_3D.segmentation_utils.general_segmentation_utils) segmentaion_on_two_D() (in module image_analysis_3D.segmentation_utils.nuclei_segmentation) select_objects_from_label() (in module image_analysis_3D.image_utils.image_utils)

single_3D_image_expand_bbox() (in module image_analysis_3D.image_utils.image_utils) sliding_window_two_point_five_D() (in module image_analysis_3D.segmentation_utils.general_segmentation_utils) solve_graph() (in module image_analysis_3D.segmentation_utils.general_segmentation_utils) solve_graph_improved() (in module image_analysis_3D.segmentation_utils.nuclei_segmentation) split_long_trajectories() (in module image_analysis_3D.segmentation_utils.nuclei_segmentation) square_off_xy_crop_bbox() (in module image_analysis_3D.image_utils.image_utils) stack_3d_segmentation() (in module image_analysis_3D.segmentation_utils.nuclei_segmentation) start_profiling() (in module image_analysis_3D.featurization_utils.resource_profiling_util) stop_profiling() (in module image_analysis_3D.featurization_utils.resource_profiling_util)

T

TransformerBlock3D (class in image_analysis_3D.featurization_utils.sammed3d_featurizer)

V

visualize_organoid_shells() (in module image_analysis_3D.featurization_utils.neighbors_utils)