Index

A

add_colorbar() (in module livecellx.core.pl_utils) add_component() (livecellx.core.SingleCellStatic method) add_daughter() (livecellx.core.SingleCellTrajectory method) add_feature() (livecellx.core.SingleCellStatic method) add_mother() (livecellx.core.SingleCellTrajectory method) ADD_MOTHER_DAUGHER_MODE (livecellx.core.sct_operator.SctOperator attribute) add_mother_daughter_relation() (livecellx.core.sct_operator.SctOperator method) add_new_sc() (livecellx.core.sct_operator.SctOperator method) add_nonoverlapping_sct() (livecellx.core.SingleCellTrajectory method) add_organelle() (livecellx.core.SingleCellStatic method)

add_sc() (livecellx.core.SingleCellTrajectory method) add_sc_by_time() (livecellx.core.SingleCellTrajectory method) add_single_cell() (livecellx.core.SingleCellTrajectory method) add_single_cell_by_time() (livecellx.core.SingleCellTrajectory method) add_trajectory() (livecellx.core.SingleCellTrajectoryCollection method) annotate_click() (livecellx.core.sct_operator.SctOperator method) ANNOTATE_CLICK_MODE (livecellx.core.sct_operator.SctOperator attribute) assign_uuid() (livecellx.core.SingleCellStatic static method) associate_detections_with_trackers() (in module livecellx.track.sort_tracker) AUTOENCODER_FEATURE_KEY (livecellx.core.SingleCellStatic attribute)

C

CACHE_IMG_CROP_KEY (livecellx.core.SingleCellStatic attribute) class2samples_to_annotation_data_structure() (livecellx.core.sct_operator.SctOperator method) clear_contour_cache() (livecellx.core.SingleCellStatic method) clear_sc_layer_callback() (livecellx.core.sc_seg_operator.ScSegOperator method) clear_sc_opeartors() (livecellx.core.sct_operator.SctOperator method) clear_selection() (livecellx.core.sct_operator.SctOperator method) close() (livecellx.core.sc_seg_operator.ScSegOperator method) (livecellx.core.sct_operator.SctOperator method) combine_two_scs_monte_carlo() (in module livecellx.segment.ou_simulator) combine_video_frames_and_masks() (in module livecellx.track.classify_utils) COMPONENTS_KEY (livecellx.core.SingleCellStatic attribute) compute_distance_by_contour() (in module livecellx.segment.ou_simulator) compute_features() (livecellx.core.SingleCellTrajectory method) compute_haralick_features() (in module livecellx.trajectory.feature_extractors) compute_iomin() (livecellx.core.SingleCellStatic method) compute_iou() (livecellx.core.SingleCellStatic method) compute_match_label_map() (in module livecellx.segment.utils)

compute_overlap_mask() (livecellx.core.SingleCellStatic method) compute_overlap_percent() (livecellx.core.SingleCellStatic method) compute_regionprops() (livecellx.core.SingleCellStatic method) compute_skimage_regionprops() (in module livecellx.trajectory.feature_extractors) CONNECT_MODE (livecellx.core.sct_operator.SctOperator attribute) connect_two_scts() (livecellx.core.sct_operator.SctOperator method) convert() (in module livecellx.annotation.labelme2coco) copy() (livecellx.core.SingleCellStatic method) (livecellx.core.SingleCellTrajectory method) correct_segment() (livecellx.core.sc_seg_operator.ScSegOperator method) create_sc_layer() (livecellx.core.sc_seg_operator.ScSegOperator method) create_sc_seg_napari_ui() (in module livecellx.core.sc_seg_operator) create_scs_edit_viewer() (in module livecellx.core.sct_operator) create_sct_napari_ui() (in module livecellx.core.sct_operator) create_scts_operator_viewer() (in module livecellx.core.sct_operator) csn_correct_seg_callback() (livecellx.core.sc_seg_operator.ScSegOperator method) CSN_CORRECT_SEG_MODE (livecellx.core.sc_seg_operator.ScSegOperator attribute)

D

default() (livecellx.core.io_utils.LiveCellEncoder method) DEFAULT_CSN_MODEL (livecellx.core.sc_seg_operator.ScSegOperator attribute) DEFAULT_OUT_DIR (livecellx.core.datasets.LiveCellImageDataset attribute) (livecellx.core.datasets.SingleImageDataset attribute)

DEFAULT_TIME (livecellx.core.datasets.SingleImageDataset attribute) delete_selected_sct() (livecellx.core.sct_operator.SctOperator method) DELETE_TRAJECTORY_MODE (livecellx.core.sct_operator.SctOperator attribute) DISCONNECT_MODE (livecellx.core.sct_operator.SctOperator attribute) disconnect_sct() (livecellx.core.sct_operator.SctOperator method)

E

edit_sc() (livecellx.core.sct_operator.SctOperator method)

edit_selected_sc() (livecellx.core.sct_operator.SctOperator method) encode() (livecellx.core.io_utils.LiveCellEncoder method)

F

filter_cells_by_size_callback() (livecellx.core.sc_seg_operator.ScSegOperator method) filter_labels_match_map() (in module livecellx.segment.utils)

filter_trajectories() (livecellx.core.SingleCellTrajectoryCollection method) filter_trajectories_by_length() (livecellx.core.SingleCellTrajectoryCollection method) focus_on_sc_callback() (livecellx.core.sc_seg_operator.ScSegOperator method)

G

gen_contour_mask() (livecellx.core.SingleCellStatic static method) gen_contour_mask_skimage_deprecated() (livecellx.core.SingleCellStatic static method) gen_gauss_sc_bg() (in module livecellx.segment.ou_simulator) gen_sc_bg_crop() (in module livecellx.segment.ou_simulator) gen_skimage_bbox_img_crop() (livecellx.core.SingleCellStatic static method) gen_synthetic_overlap_scs() (in module livecellx.segment.ou_simulator) gen_trajectories_shapes() (livecellx.core.napari_visualizer.NapariVisualizer method) get_all_scs() (livecellx.core.sct_operator.SctOperator method) (livecellx.core.SingleCellTrajectory method) (livecellx.core.SingleCellTrajectoryCollection method) get_all_tids() (livecellx.core.SingleCellTrajectoryCollection method) get_all_track_ids() (livecellx.core.SingleCellTrajectoryCollection method) get_all_trajectories() (livecellx.core.SingleCellTrajectoryCollection method) get_bbox() (livecellx.core.SingleCellStatic method) get_bbox_from_contour() (livecellx.core.SingleCellStatic static method) get_bbox_on_crop() (livecellx.core.SingleCellStatic method) get_cellTool_contour_points() (in module livecellx.trajectory.contour_utils) get_center() (livecellx.core.SingleCellStatic method) get_coco_from_labelme_folder() (in module livecellx.annotation.labelme2coco) get_components() (livecellx.core.SingleCellStatic method) get_contour() (livecellx.core.SingleCellStatic method) get_contour_coords_on_crop() (livecellx.core.SingleCellStatic method) get_contour_coords_on_img_crop() (livecellx.core.SingleCellStatic method) get_contour_img() (livecellx.core.SingleCellStatic method) get_contour_label_mask() (livecellx.core.SingleCellStatic method) get_contour_mask() (livecellx.core.SingleCellStatic method) get_contour_mask_closed_form() (livecellx.core.SingleCellStatic method) get_contours_from_pred_masks() (in module livecellx.segment.utils) get_dataset_name() (livecellx.core.datasets.LiveCellImageDataset method) (livecellx.core.datasets.SingleImageDataset method) get_dataset_path() (livecellx.core.datasets.LiveCellImageDataset method) (livecellx.core.datasets.SingleImageDataset method) get_default_json_path() (livecellx.core.datasets.LiveCellImageDataset method) (livecellx.core.datasets.SingleImageDataset method) get_feature_pd_series() (livecellx.core.SingleCellStatic method) get_feature_table() (livecellx.core.SingleCellTrajectoryCollection method) get_img() (livecellx.core.SingleCellStatic method) (livecellx.core.SingleCellTrajectory method) get_img_by_idx() (livecellx.core.datasets.LiveCellImageDataset method) (livecellx.core.datasets.SingleImageDataset method)

get_img_by_time() (livecellx.core.datasets.LiveCellImageDataset method) (livecellx.core.datasets.SingleImageDataset method) get_img_by_url() (livecellx.core.datasets.LiveCellImageDataset method) (livecellx.core.datasets.SingleImageDataset method) get_img_crop() (livecellx.core.SingleCellStatic method) get_img_path() (livecellx.core.datasets.LiveCellImageDataset method) (livecellx.core.datasets.SingleImageDataset method) get_img_shape() (livecellx.core.SingleCellStatic method) get_label_mask() (livecellx.core.SingleCellStatic method) get_label_mask_crop() (livecellx.core.SingleCellStatic method) get_mask() (livecellx.core.SingleCellStatic method) (livecellx.core.SingleCellTrajectory method) get_mask_crop() (livecellx.core.SingleCellStatic method) get_max_tid() (livecellx.core.SingleCellTrajectoryCollection method) get_meta() (livecellx.core.sct_operator.SctOperator method) get_napari_shape_bbox_vec() (livecellx.core.SingleCellStatic method) get_napari_shape_contour_vec() (livecellx.core.SingleCellStatic method) get_napari_shape_vec() (livecellx.core.SingleCellStatic method) get_organelles() (livecellx.core.SingleCellStatic method) get_prev_by_sc() (livecellx.core.SingleCellTrajectory method) get_sc() (livecellx.core.SingleCellTrajectory method) get_sc_bboxes() (livecellx.core.SingleCellTrajectory method) get_sc_feature_table() (livecellx.core.SingleCellTrajectory method) get_sc_img() (livecellx.core.SingleCellStatic method) get_sc_label_mask() (livecellx.core.SingleCellStatic method) get_sc_mask() (livecellx.core.SingleCellStatic method) get_scs_napari_shapes() (livecellx.core.SingleCellTrajectory method) get_single_cell() (livecellx.core.SingleCellTrajectory method) get_sorted_scs() (livecellx.core.SingleCellTrajectory method) get_sorted_times() (livecellx.core.datasets.LiveCellImageDataset method) (livecellx.core.datasets.SingleImageDataset method) get_time_span() (livecellx.core.SingleCellTrajectory method) (livecellx.core.SingleCellTrajectoryCollection method) get_time_span_length() (livecellx.core.SingleCellTrajectory method) get_timeframe_span() (livecellx.core.SingleCellTrajectory method) get_timeframe_span_length() (livecellx.core.SingleCellTrajectory method) get_track_ids() (livecellx.core.SingleCellTrajectoryCollection method) get_trajectory() (livecellx.core.SingleCellTrajectoryCollection method)

H

HARALICK_FEATURE_KEY (livecellx.core.SingleCellStatic attribute) has_time() (livecellx.core.datasets.LiveCellImageDataset method) (livecellx.core.datasets.SingleImageDataset method)

hide_function_widgets() (livecellx.core.sc_seg_operator.ScSegOperator method) (livecellx.core.sct_operator.SctOperator method) histogram_traj_length() (livecellx.core.SingleCellTrajectoryCollection method)

I

id_generator (livecellx.core.SingleCellStatic attribute) infer_shape() (livecellx.core.datasets.LiveCellImageDataset method) (livecellx.core.datasets.SingleImageDataset method) inflate_from_json_dict() (livecellx.core.SingleCellStatic method) inflate_other_trajectories() (livecellx.core.SingleCellTrajectory method)

inflate_other_trajectories_by_dict() (livecellx.core.SingleCellTrajectory method) insert_cache() (livecellx.core.datasets.LiveCellImageDataset method) (livecellx.core.datasets.SingleImageDataset method) is_empty() (livecellx.core.SingleCellTrajectory method) item_separator (livecellx.core.io_utils.LiveCellEncoder attribute) iterencode() (livecellx.core.io_utils.LiveCellEncoder method)

J

JSON_IMG_DATASET_PATH (livecellx.core.sc_key_manager.SingleCellMetaKeyManager attribute)

JSON_MASK_DATASET_PATH (livecellx.core.sc_key_manager.SingleCellMetaKeyManager attribute) judge_connected_bfs() (in module livecellx.segment.utils)

K

key_separator (livecellx.core.io_utils.LiveCellEncoder attribute)

L

LiveCellEncoder (class in livecellx.core.io_utils) LiveCellImageDataset (class in livecellx.core.datasets) livecellx.annotation module livecellx.classification module livecellx.core module, [1] livecellx.model_zoo module livecellx.preprocess module livecellx.segment module livecellx.track module livecellx.trajectory module

livecellx.trajectory.contour module load_annotations() (livecellx.core.sct_operator.SctOperator method) load_default_csn_model() (livecellx.core.sc_seg_operator.ScSegOperator static method) load_from_json_dict() (livecellx.core.datasets.LiveCellImageDataset method) (livecellx.core.datasets.SingleImageDataset method) (livecellx.core.SingleCellStatic method) (livecellx.core.SingleCellTrajectory method) (livecellx.core.SingleCellTrajectoryCollection method) load_from_json_dict_parallel() (livecellx.core.SingleCellTrajectoryCollection method) load_from_json_file() (livecellx.core.datasets.LiveCellImageDataset static method) (livecellx.core.datasets.SingleImageDataset static method) (livecellx.core.SingleCellTrajectory static method) (livecellx.core.SingleCellTrajectoryCollection static method) load_single_cells_json() (livecellx.core.SingleCellStatic static method) load_single_cells_jsons() (livecellx.core.SingleCellStatic static method) lookup_sc_shape_index() (livecellx.core.sct_operator.SctOperator method)

M

MANUAL_CORRECT_SEG_MODE (livecellx.core.sc_seg_operator.ScSegOperator attribute) map_colors() (livecellx.core.napari_visualizer.NapariVisualizer static method) MASK_LABEL (livecellx.core.sc_key_manager.SingleCellMetaKeyManager attribute) match_mask_labels_by_iou() (in module livecellx.segment.utils) META_DAUGHTER_IDS (livecellx.core.SingleCellTrajectory attribute) META_MOTHER_IDS (livecellx.core.SingleCellTrajectory attribute) module livecellx.annotation livecellx.classification livecellx.core, [1] livecellx.model_zoo livecellx.preprocess livecellx.segment livecellx.track livecellx.trajectory livecellx.trajectory.contour

MORPHOLOGY_FEATURE_KEY (livecellx.core.SingleCellStatic attribute) move_two_scs() (in module livecellx.segment.ou_simulator)

N

NapariVisualizer (class in livecellx.core.napari_visualizer) next_time() (livecellx.core.SingleCellTrajectory method)

notify_sct_to_remove_sc_operator() (livecellx.core.sc_seg_operator.ScSegOperator method) notify_sct_to_update() (livecellx.core.sc_seg_operator.ScSegOperator method) num_scs() (livecellx.core.SingleCellTrajectory method)

P

pop_sc() (livecellx.core.SingleCellTrajectory method) pop_sc_by_time() (livecellx.core.SingleCellTrajectory method) pop_sct() (livecellx.core.SingleCellTrajectoryCollection method) pop_sct_by_id() (livecellx.core.SingleCellTrajectoryCollection method) pop_single_cell_by_time() (livecellx.core.SingleCellTrajectory method)

pop_trajectory() (livecellx.core.SingleCellTrajectoryCollection method) pop_trajectory_by_id() (livecellx.core.SingleCellTrajectoryCollection method) prep_scs_from_mask_dataset() (in module livecellx.core.io_sc) process_mask_wrapper() (in module livecellx.core.io_sc) process_scs_from_one_label_mask() (in module livecellx.segment.utils)

R

read_img_default() (in module livecellx.core.datasets) read_single_img_from_mem() (livecellx.core.datasets.SingleImageDataset method) reindex_time2url_sequential() (livecellx.core.datasets.LiveCellImageDataset method) (livecellx.core.datasets.SingleImageDataset method) remove_component() (livecellx.core.SingleCellStatic method) remove_daughter() (livecellx.core.SingleCellTrajectory method) remove_empty_contour_sct() (livecellx.core.sct_operator.SctOperator method) remove_empty_sct() (livecellx.core.SingleCellTrajectoryCollection method) remove_mother() (livecellx.core.SingleCellTrajectory method)

remove_organelle() (livecellx.core.SingleCellStatic method) remove_sc_layer() (livecellx.core.sc_seg_operator.ScSegOperator method) remove_sc_operator() (livecellx.core.sct_operator.SctOperator method) remove_scs() (livecellx.core.sct_operator.SctOperator method) remove_shape_layer() (livecellx.core.sct_operator.SctOperator method) replace_sc_contour() (livecellx.core.sc_seg_operator.ScSegOperator method) resample_contour() (livecellx.core.sc_seg_operator.ScSegOperator static method) resample_contours_callback() (livecellx.core.sc_seg_operator.ScSegOperator method) restore_sc_contour_callback() (livecellx.core.sc_seg_operator.ScSegOperator method) restore_shapes_data() (livecellx.core.sct_operator.SctOperator method)

S

sample_contour_point() (livecellx.core.SingleCellStatic method) save_annotations() (livecellx.core.sct_operator.SctOperator method) save_general() (in module livecellx.core.io_utils) save_png() (in module livecellx.core.io_utils) save_seg_callback() (livecellx.core.sc_seg_operator.ScSegOperator method) save_tiff() (in module livecellx.core.io_utils) sc (livecellx.core.sc_seg_operator.ScSegOperator attribute) ScSegOperator (class in livecellx.core.sc_seg_operator) SctOperator (class in livecellx.core.sct_operator) segment_by_cellpose() (livecellx.core.SingleCellStatic method) segment_by_detectron() (livecellx.core.SingleCellStatic method) select_shape() (livecellx.core.sct_operator.SctOperator method) selected_scs() (livecellx.core.sct_operator.SctOperator method) setup_by_timespan() (livecellx.core.sct_operator.SctOperator method) setup_edit_contour_shape_layer() (livecellx.core.sc_seg_operator.ScSegOperator method) setup_from_sctc() (livecellx.core.sct_operator.SctOperator method) setup_shape_layer() (livecellx.core.sct_operator.SctOperator method) shape_layer (livecellx.core.sc_seg_operator.ScSegOperator attribute) show() (livecellx.core.SingleCellStatic method) show_contour_img() (livecellx.core.SingleCellStatic method) show_contour_mask() (livecellx.core.SingleCellStatic method)

show_label_mask() (livecellx.core.SingleCellStatic method) show_mask() (livecellx.core.SingleCellStatic method) show_on_grid() (livecellx.core.SingleCellTrajectory method) show_panel() (livecellx.core.SingleCellStatic method) show_selected_mode_widget() (livecellx.core.sc_seg_operator.ScSegOperator method) (livecellx.core.sct_operator.SctOperator method) show_tracks() (livecellx.core.SingleCellTrajectoryCollection method) show_trajectory_on_grid() (livecellx.core.SingleCellTrajectory static method) show_whole_img() (livecellx.core.SingleCellStatic method) show_whole_mask() (livecellx.core.SingleCellStatic method) SingleCellMetaKeyManager (class in livecellx.core.sc_key_manager) SingleCellStatic (class in livecellx.core) SingleCellTrajectory (class in livecellx.core) SingleCellTrajectoryCollection (class in livecellx.core) SingleImageDataset (class in livecellx.core.datasets) split() (livecellx.core.SingleCellTrajectory method) store_shape_layer_info() (livecellx.core.sct_operator.SctOperator method) subsct() (livecellx.core.SingleCellTrajectory method) subset() (livecellx.core.SingleCellTrajectoryCollection method) subset_by_time() (livecellx.core.datasets.LiveCellImageDataset method) (livecellx.core.datasets.SingleImageDataset method) subset_random() (livecellx.core.SingleCellTrajectoryCollection method)

T

time_span() (livecellx.core.datasets.LiveCellImageDataset method) (livecellx.core.datasets.SingleImageDataset method) timeframe_set (livecellx.core.SingleCellTrajectory property) times (livecellx.core.SingleCellTrajectory property) to_dask() (livecellx.core.datasets.LiveCellImageDataset method) (livecellx.core.datasets.SingleImageDataset method)

to_json_dict() (livecellx.core.datasets.LiveCellImageDataset method) (livecellx.core.datasets.SingleImageDataset method) (livecellx.core.SingleCellStatic method) (livecellx.core.SingleCellTrajectory method) (livecellx.core.SingleCellTrajectoryCollection method) toggle_shapes_text() (livecellx.core.sct_operator.SctOperator method)

U

update_bbox() (livecellx.core.SingleCellStatic method) update_contour() (livecellx.core.SingleCellStatic method) update_regionprops() (livecellx.core.SingleCellStatic method) update_sc_mask_by_crop() (livecellx.core.SingleCellStatic method) update_shape_layer() (livecellx.core.sct_operator.SctOperator method) update_shape_layer_by_sc() (livecellx.core.sc_seg_operator.ScSegOperator method) (livecellx.core.sct_operator.SctOperator method)

update_shape_layer_by_track_id() (livecellx.core.sct_operator.SctOperator method) update_time2url() (livecellx.core.datasets.LiveCellImageDataset method) (livecellx.core.datasets.SingleImageDataset method) update_time2url_from_dir_path() (livecellx.core.datasets.LiveCellImageDataset method) (livecellx.core.datasets.SingleImageDataset method)

V

video_frames_and_masks_from_sample() (in module livecellx.track.classify_utils) viewer (livecellx.core.sc_seg_operator.ScSegOperator attribute)

viz_check_combined_sc_result() (in module livecellx.segment.ou_simulator) viz_contours() (in module livecellx.trajectory.contour_utils) viz_traj() (livecellx.core.napari_visualizer.NapariVisualizer method)

W

write_json() (livecellx.core.datasets.LiveCellImageDataset method) (livecellx.core.datasets.SingleImageDataset method) (livecellx.core.SingleCellStatic method) (livecellx.core.SingleCellTrajectory method) (livecellx.core.SingleCellTrajectoryCollection method)

write_single_cells_json() (livecellx.core.SingleCellStatic static method)