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livecellx 0.0.0 documentation
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livecellx 0.0.0 documentation

General

  • Installation
  • Quick start guide
  • Livecellx Tutorials
    • SingleCellStatic: saving & loading
    • SingleCellTrajectory: saving & loading
    • Visualizing and analyzing EBSS data
    • Editing SingleCellStatic Objects Using a Viewer
    • Create Napari UI for editing SingleCellTrajectoryCollection (SCTC)
    • Annotation by clicking single cells in the Napari UI
    • Annotate Mitosis Events (and other cell events)
    • Segment A549 cells using a trained cellpose
    • Train a cellpose to segment A549 cells
    • Create UMAP of single cell features
    • Create UMAP of single cell features on EBSS starvation data
    • Display attributes of single cells and trajectory
  • API
    • livecellx.annotation.labelme2coco.get_coco_from_labelme_folder
    • livecellx.annotation.labelme2coco.convert
    • livecellx.core.datasets.read_img_default
    • livecellx.core.io_sc.process_mask_wrapper
    • livecellx.core.io_sc.prep_scs_from_mask_dataset
    • livecellx.core.io_utils.save_png
    • livecellx.core.io_utils.save_tiff
    • livecellx.core.io_utils.save_general
    • livecellx.core.pl_utils.add_colorbar
    • livecellx.core.sc_seg_operator.create_sc_seg_napari_ui
    • livecellx.core.sct_operator.create_sct_napari_ui
    • livecellx.core.sct_operator.create_scts_operator_viewer
    • livecellx.core.sct_operator.create_scs_edit_viewer
    • livecellx.segment.ou_simulator.viz_check_combined_sc_result
    • livecellx.segment.ou_simulator.compute_distance_by_contour
    • livecellx.segment.ou_simulator.combine_two_scs_monte_carlo
    • livecellx.segment.ou_simulator.gen_synthetic_overlap_scs
    • livecellx.segment.ou_simulator.gen_gauss_sc_bg
    • livecellx.segment.ou_simulator.gen_sc_bg_crop
    • livecellx.segment.ou_simulator.move_two_scs
    • livecellx.segment.utils.get_contours_from_pred_masks
    • livecellx.segment.utils.match_mask_labels_by_iou
    • livecellx.segment.utils.filter_labels_match_map
    • livecellx.segment.utils.compute_match_label_map
    • livecellx.segment.utils.process_scs_from_one_label_mask
    • livecellx.segment.utils.judge_connected_bfs
    • livecellx.track.classify_utils.video_frames_and_masks_from_sample
    • livecellx.track.classify_utils.combine_video_frames_and_masks
    • livecellx.track.sort_tracker.associate_detections_with_trackers
    • livecellx.trajectory.contour_utils.get_cellTool_contour_points
    • livecellx.trajectory.contour_utils.viz_contours
    • livecellx.trajectory.feature_extractors.compute_haralick_features
    • livecellx.trajectory.feature_extractors.compute_skimage_regionprops
  • Classes
    • livecellx.core.SingleCellStatic
      • livecellx.core.SingleCellStatic.add_component
      • livecellx.core.SingleCellStatic.add_feature
      • livecellx.core.SingleCellStatic.add_organelle
      • livecellx.core.SingleCellStatic.assign_uuid
      • livecellx.core.SingleCellStatic.clear_contour_cache
      • livecellx.core.SingleCellStatic.compute_iomin
      • livecellx.core.SingleCellStatic.compute_iou
      • livecellx.core.SingleCellStatic.compute_overlap_mask
      • livecellx.core.SingleCellStatic.compute_overlap_percent
      • livecellx.core.SingleCellStatic.compute_regionprops
      • livecellx.core.SingleCellStatic.copy
      • livecellx.core.SingleCellStatic.gen_contour_mask
      • livecellx.core.SingleCellStatic.gen_contour_mask_skimage_deprecated
      • livecellx.core.SingleCellStatic.gen_skimage_bbox_img_crop
      • livecellx.core.SingleCellStatic.get_bbox
      • livecellx.core.SingleCellStatic.get_bbox_from_contour
      • livecellx.core.SingleCellStatic.get_bbox_on_crop
      • livecellx.core.SingleCellStatic.get_center
      • livecellx.core.SingleCellStatic.get_components
      • livecellx.core.SingleCellStatic.get_contour
      • livecellx.core.SingleCellStatic.get_contour_coords_on_crop
      • livecellx.core.SingleCellStatic.get_contour_coords_on_img_crop
      • livecellx.core.SingleCellStatic.get_contour_img
      • livecellx.core.SingleCellStatic.get_contour_label_mask
      • livecellx.core.SingleCellStatic.get_contour_mask
      • livecellx.core.SingleCellStatic.get_contour_mask_closed_form
      • livecellx.core.SingleCellStatic.get_feature_pd_series
      • livecellx.core.SingleCellStatic.get_img
      • livecellx.core.SingleCellStatic.get_img_crop
      • livecellx.core.SingleCellStatic.get_img_shape
      • livecellx.core.SingleCellStatic.get_label_mask
      • livecellx.core.SingleCellStatic.get_label_mask_crop
      • livecellx.core.SingleCellStatic.get_mask
      • livecellx.core.SingleCellStatic.get_mask_crop
      • livecellx.core.SingleCellStatic.get_napari_shape_bbox_vec
      • livecellx.core.SingleCellStatic.get_napari_shape_contour_vec
      • livecellx.core.SingleCellStatic.get_napari_shape_vec
      • livecellx.core.SingleCellStatic.get_organelles
      • livecellx.core.SingleCellStatic.get_sc_img
      • livecellx.core.SingleCellStatic.get_sc_label_mask
      • livecellx.core.SingleCellStatic.get_sc_mask
      • livecellx.core.SingleCellStatic.inflate_from_json_dict
      • livecellx.core.SingleCellStatic.load_from_json_dict
      • livecellx.core.SingleCellStatic.load_single_cells_json
      • livecellx.core.SingleCellStatic.load_single_cells_jsons
      • livecellx.core.SingleCellStatic.remove_component
      • livecellx.core.SingleCellStatic.remove_organelle
      • livecellx.core.SingleCellStatic.sample_contour_point
      • livecellx.core.SingleCellStatic.segment_by_cellpose
      • livecellx.core.SingleCellStatic.segment_by_detectron
      • livecellx.core.SingleCellStatic.show
      • livecellx.core.SingleCellStatic.show_contour_img
      • livecellx.core.SingleCellStatic.show_contour_mask
      • livecellx.core.SingleCellStatic.show_label_mask
      • livecellx.core.SingleCellStatic.show_mask
      • livecellx.core.SingleCellStatic.show_panel
      • livecellx.core.SingleCellStatic.show_whole_img
      • livecellx.core.SingleCellStatic.show_whole_mask
      • livecellx.core.SingleCellStatic.to_json_dict
      • livecellx.core.SingleCellStatic.update_bbox
      • livecellx.core.SingleCellStatic.update_contour
      • livecellx.core.SingleCellStatic.update_regionprops
      • livecellx.core.SingleCellStatic.update_sc_mask_by_crop
      • livecellx.core.SingleCellStatic.write_json
      • livecellx.core.SingleCellStatic.write_single_cells_json
      • livecellx.core.SingleCellStatic.AUTOENCODER_FEATURE_KEY
      • livecellx.core.SingleCellStatic.CACHE_IMG_CROP_KEY
      • livecellx.core.SingleCellStatic.COMPONENTS_KEY
      • livecellx.core.SingleCellStatic.HARALICK_FEATURE_KEY
      • livecellx.core.SingleCellStatic.MORPHOLOGY_FEATURE_KEY
      • livecellx.core.SingleCellStatic.id_generator
    • livecellx.core.SingleCellTrajectory
      • livecellx.core.SingleCellTrajectory.add_daughter
      • livecellx.core.SingleCellTrajectory.add_mother
      • livecellx.core.SingleCellTrajectory.add_nonoverlapping_sct
      • livecellx.core.SingleCellTrajectory.add_sc
      • livecellx.core.SingleCellTrajectory.add_sc_by_time
      • livecellx.core.SingleCellTrajectory.add_single_cell
      • livecellx.core.SingleCellTrajectory.add_single_cell_by_time
      • livecellx.core.SingleCellTrajectory.compute_features
      • livecellx.core.SingleCellTrajectory.copy
      • livecellx.core.SingleCellTrajectory.get_all_scs
      • livecellx.core.SingleCellTrajectory.get_img
      • livecellx.core.SingleCellTrajectory.get_mask
      • livecellx.core.SingleCellTrajectory.get_prev_by_sc
      • livecellx.core.SingleCellTrajectory.get_sc
      • livecellx.core.SingleCellTrajectory.get_sc_bboxes
      • livecellx.core.SingleCellTrajectory.get_sc_feature_table
      • livecellx.core.SingleCellTrajectory.get_scs_napari_shapes
      • livecellx.core.SingleCellTrajectory.get_single_cell
      • livecellx.core.SingleCellTrajectory.get_sorted_scs
      • livecellx.core.SingleCellTrajectory.get_time_span
      • livecellx.core.SingleCellTrajectory.get_time_span_length
      • livecellx.core.SingleCellTrajectory.get_timeframe_span
      • livecellx.core.SingleCellTrajectory.get_timeframe_span_length
      • livecellx.core.SingleCellTrajectory.inflate_other_trajectories
      • livecellx.core.SingleCellTrajectory.inflate_other_trajectories_by_dict
      • livecellx.core.SingleCellTrajectory.is_empty
      • livecellx.core.SingleCellTrajectory.load_from_json_dict
      • livecellx.core.SingleCellTrajectory.load_from_json_file
      • livecellx.core.SingleCellTrajectory.next_time
      • livecellx.core.SingleCellTrajectory.num_scs
      • livecellx.core.SingleCellTrajectory.pop_sc
      • livecellx.core.SingleCellTrajectory.pop_sc_by_time
      • livecellx.core.SingleCellTrajectory.pop_single_cell_by_time
      • livecellx.core.SingleCellTrajectory.remove_daughter
      • livecellx.core.SingleCellTrajectory.remove_mother
      • livecellx.core.SingleCellTrajectory.show_on_grid
      • livecellx.core.SingleCellTrajectory.show_trajectory_on_grid
      • livecellx.core.SingleCellTrajectory.split
      • livecellx.core.SingleCellTrajectory.subsct
      • livecellx.core.SingleCellTrajectory.to_json_dict
      • livecellx.core.SingleCellTrajectory.write_json
      • livecellx.core.SingleCellTrajectory.META_DAUGHTER_IDS
      • livecellx.core.SingleCellTrajectory.META_MOTHER_IDS
      • livecellx.core.SingleCellTrajectory.timeframe_set
      • livecellx.core.SingleCellTrajectory.times
    • livecellx.core.SingleCellTrajectoryCollection
      • livecellx.core.SingleCellTrajectoryCollection.add_trajectory
      • livecellx.core.SingleCellTrajectoryCollection.filter_trajectories
      • livecellx.core.SingleCellTrajectoryCollection.filter_trajectories_by_length
      • livecellx.core.SingleCellTrajectoryCollection.get_all_scs
      • livecellx.core.SingleCellTrajectoryCollection.get_all_tids
      • livecellx.core.SingleCellTrajectoryCollection.get_all_track_ids
      • livecellx.core.SingleCellTrajectoryCollection.get_all_trajectories
      • livecellx.core.SingleCellTrajectoryCollection.get_feature_table
      • livecellx.core.SingleCellTrajectoryCollection.get_max_tid
      • livecellx.core.SingleCellTrajectoryCollection.get_time_span
      • livecellx.core.SingleCellTrajectoryCollection.get_track_ids
      • livecellx.core.SingleCellTrajectoryCollection.get_trajectory
      • livecellx.core.SingleCellTrajectoryCollection.histogram_traj_length
      • livecellx.core.SingleCellTrajectoryCollection.load_from_json_dict
      • livecellx.core.SingleCellTrajectoryCollection.load_from_json_dict_parallel
      • livecellx.core.SingleCellTrajectoryCollection.load_from_json_file
      • livecellx.core.SingleCellTrajectoryCollection.pop_sct
      • livecellx.core.SingleCellTrajectoryCollection.pop_sct_by_id
      • livecellx.core.SingleCellTrajectoryCollection.pop_trajectory
      • livecellx.core.SingleCellTrajectoryCollection.pop_trajectory_by_id
      • livecellx.core.SingleCellTrajectoryCollection.remove_empty_sct
      • livecellx.core.SingleCellTrajectoryCollection.show_tracks
      • livecellx.core.SingleCellTrajectoryCollection.subset
      • livecellx.core.SingleCellTrajectoryCollection.subset_random
      • livecellx.core.SingleCellTrajectoryCollection.to_json_dict
      • livecellx.core.SingleCellTrajectoryCollection.write_json
    • livecellx.core.datasets.LiveCellImageDataset
      • livecellx.core.datasets.LiveCellImageDataset.get_dataset_name
      • livecellx.core.datasets.LiveCellImageDataset.get_dataset_path
      • livecellx.core.datasets.LiveCellImageDataset.get_default_json_path
      • livecellx.core.datasets.LiveCellImageDataset.get_img_by_idx
      • livecellx.core.datasets.LiveCellImageDataset.get_img_by_time
      • livecellx.core.datasets.LiveCellImageDataset.get_img_by_url
      • livecellx.core.datasets.LiveCellImageDataset.get_img_path
      • livecellx.core.datasets.LiveCellImageDataset.get_sorted_times
      • livecellx.core.datasets.LiveCellImageDataset.has_time
      • livecellx.core.datasets.LiveCellImageDataset.infer_shape
      • livecellx.core.datasets.LiveCellImageDataset.insert_cache
      • livecellx.core.datasets.LiveCellImageDataset.load_from_json_dict
      • livecellx.core.datasets.LiveCellImageDataset.load_from_json_file
      • livecellx.core.datasets.LiveCellImageDataset.reindex_time2url_sequential
      • livecellx.core.datasets.LiveCellImageDataset.subset_by_time
      • livecellx.core.datasets.LiveCellImageDataset.time_span
      • livecellx.core.datasets.LiveCellImageDataset.to_dask
      • livecellx.core.datasets.LiveCellImageDataset.to_json_dict
      • livecellx.core.datasets.LiveCellImageDataset.update_time2url
      • livecellx.core.datasets.LiveCellImageDataset.update_time2url_from_dir_path
      • livecellx.core.datasets.LiveCellImageDataset.write_json
      • livecellx.core.datasets.LiveCellImageDataset.DEFAULT_OUT_DIR
    • livecellx.core.datasets.SingleImageDataset
      • livecellx.core.datasets.SingleImageDataset.get_dataset_name
      • livecellx.core.datasets.SingleImageDataset.get_dataset_path
      • livecellx.core.datasets.SingleImageDataset.get_default_json_path
      • livecellx.core.datasets.SingleImageDataset.get_img_by_idx
      • livecellx.core.datasets.SingleImageDataset.get_img_by_time
      • livecellx.core.datasets.SingleImageDataset.get_img_by_url
      • livecellx.core.datasets.SingleImageDataset.get_img_path
      • livecellx.core.datasets.SingleImageDataset.get_sorted_times
      • livecellx.core.datasets.SingleImageDataset.has_time
      • livecellx.core.datasets.SingleImageDataset.infer_shape
      • livecellx.core.datasets.SingleImageDataset.insert_cache
      • livecellx.core.datasets.SingleImageDataset.load_from_json_dict
      • livecellx.core.datasets.SingleImageDataset.load_from_json_file
      • livecellx.core.datasets.SingleImageDataset.read_single_img_from_mem
      • livecellx.core.datasets.SingleImageDataset.reindex_time2url_sequential
      • livecellx.core.datasets.SingleImageDataset.subset_by_time
      • livecellx.core.datasets.SingleImageDataset.time_span
      • livecellx.core.datasets.SingleImageDataset.to_dask
      • livecellx.core.datasets.SingleImageDataset.to_json_dict
      • livecellx.core.datasets.SingleImageDataset.update_time2url
      • livecellx.core.datasets.SingleImageDataset.update_time2url_from_dir_path
      • livecellx.core.datasets.SingleImageDataset.write_json
      • livecellx.core.datasets.SingleImageDataset.DEFAULT_OUT_DIR
      • livecellx.core.datasets.SingleImageDataset.DEFAULT_TIME
    • livecellx.core.io_utils.LiveCellEncoder
      • livecellx.core.io_utils.LiveCellEncoder.default
      • livecellx.core.io_utils.LiveCellEncoder.encode
      • livecellx.core.io_utils.LiveCellEncoder.iterencode
      • livecellx.core.io_utils.LiveCellEncoder.item_separator
      • livecellx.core.io_utils.LiveCellEncoder.key_separator
    • livecellx.core.napari_visualizer.NapariVisualizer
      • livecellx.core.napari_visualizer.NapariVisualizer.gen_trajectories_shapes
      • livecellx.core.napari_visualizer.NapariVisualizer.map_colors
      • livecellx.core.napari_visualizer.NapariVisualizer.viz_traj
    • livecellx.core.sc_key_manager.SingleCellMetaKeyManager
      • livecellx.core.sc_key_manager.SingleCellMetaKeyManager.JSON_IMG_DATASET_PATH
      • livecellx.core.sc_key_manager.SingleCellMetaKeyManager.JSON_MASK_DATASET_PATH
      • livecellx.core.sc_key_manager.SingleCellMetaKeyManager.MASK_LABEL
    • livecellx.core.sc_seg_operator.ScSegOperator
      • livecellx.core.sc_seg_operator.ScSegOperator.clear_sc_layer_callback
      • livecellx.core.sc_seg_operator.ScSegOperator.close
      • livecellx.core.sc_seg_operator.ScSegOperator.correct_segment
      • livecellx.core.sc_seg_operator.ScSegOperator.create_sc_layer
      • livecellx.core.sc_seg_operator.ScSegOperator.csn_correct_seg_callback
      • livecellx.core.sc_seg_operator.ScSegOperator.filter_cells_by_size_callback
      • livecellx.core.sc_seg_operator.ScSegOperator.focus_on_sc_callback
      • livecellx.core.sc_seg_operator.ScSegOperator.hide_function_widgets
      • livecellx.core.sc_seg_operator.ScSegOperator.load_default_csn_model
      • livecellx.core.sc_seg_operator.ScSegOperator.notify_sct_to_remove_sc_operator
      • livecellx.core.sc_seg_operator.ScSegOperator.notify_sct_to_update
      • livecellx.core.sc_seg_operator.ScSegOperator.remove_sc_layer
      • livecellx.core.sc_seg_operator.ScSegOperator.replace_sc_contour
      • livecellx.core.sc_seg_operator.ScSegOperator.resample_contour
      • livecellx.core.sc_seg_operator.ScSegOperator.resample_contours_callback
      • livecellx.core.sc_seg_operator.ScSegOperator.restore_sc_contour_callback
      • livecellx.core.sc_seg_operator.ScSegOperator.save_seg_callback
      • livecellx.core.sc_seg_operator.ScSegOperator.setup_edit_contour_shape_layer
      • livecellx.core.sc_seg_operator.ScSegOperator.show_selected_mode_widget
      • livecellx.core.sc_seg_operator.ScSegOperator.update_shape_layer_by_sc
      • livecellx.core.sc_seg_operator.ScSegOperator.CSN_CORRECT_SEG_MODE
      • livecellx.core.sc_seg_operator.ScSegOperator.DEFAULT_CSN_MODEL
      • livecellx.core.sc_seg_operator.ScSegOperator.MANUAL_CORRECT_SEG_MODE
    • livecellx.core.sct_operator.SctOperator
      • livecellx.core.sct_operator.SctOperator.add_mother_daughter_relation
      • livecellx.core.sct_operator.SctOperator.add_new_sc
      • livecellx.core.sct_operator.SctOperator.annotate_click
      • livecellx.core.sct_operator.SctOperator.class2samples_to_annotation_data_structure
      • livecellx.core.sct_operator.SctOperator.clear_sc_opeartors
      • livecellx.core.sct_operator.SctOperator.clear_selection
      • livecellx.core.sct_operator.SctOperator.close
      • livecellx.core.sct_operator.SctOperator.connect_two_scts
      • livecellx.core.sct_operator.SctOperator.delete_selected_sct
      • livecellx.core.sct_operator.SctOperator.disconnect_sct
      • livecellx.core.sct_operator.SctOperator.edit_sc
      • livecellx.core.sct_operator.SctOperator.edit_selected_sc
      • livecellx.core.sct_operator.SctOperator.get_all_scs
      • livecellx.core.sct_operator.SctOperator.get_meta
      • livecellx.core.sct_operator.SctOperator.hide_function_widgets
      • livecellx.core.sct_operator.SctOperator.load_annotations
      • livecellx.core.sct_operator.SctOperator.lookup_sc_shape_index
      • livecellx.core.sct_operator.SctOperator.remove_empty_contour_sct
      • livecellx.core.sct_operator.SctOperator.remove_sc_operator
      • livecellx.core.sct_operator.SctOperator.remove_scs
      • livecellx.core.sct_operator.SctOperator.remove_shape_layer
      • livecellx.core.sct_operator.SctOperator.restore_shapes_data
      • livecellx.core.sct_operator.SctOperator.save_annotations
      • livecellx.core.sct_operator.SctOperator.select_shape
      • livecellx.core.sct_operator.SctOperator.selected_scs
      • livecellx.core.sct_operator.SctOperator.setup_by_timespan
      • livecellx.core.sct_operator.SctOperator.setup_from_sctc
      • livecellx.core.sct_operator.SctOperator.setup_shape_layer
      • livecellx.core.sct_operator.SctOperator.show_selected_mode_widget
      • livecellx.core.sct_operator.SctOperator.store_shape_layer_info
      • livecellx.core.sct_operator.SctOperator.toggle_shapes_text
      • livecellx.core.sct_operator.SctOperator.update_shape_layer
      • livecellx.core.sct_operator.SctOperator.update_shape_layer_by_sc
      • livecellx.core.sct_operator.SctOperator.update_shape_layer_by_track_id
      • livecellx.core.sct_operator.SctOperator.ADD_MOTHER_DAUGHER_MODE
      • livecellx.core.sct_operator.SctOperator.ANNOTATE_CLICK_MODE
      • livecellx.core.sct_operator.SctOperator.CONNECT_MODE
      • livecellx.core.sct_operator.SctOperator.DELETE_TRAJECTORY_MODE
      • livecellx.core.sct_operator.SctOperator.DISCONNECT_MODE
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livecellx.core.SingleCellTrajectoryCollection.get_all_trajectories¶

SingleCellTrajectoryCollection.get_all_trajectories()[source]¶
Return type:

List[SingleCellTrajectory]

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livecellx.core.SingleCellTrajectoryCollection.get_feature_table
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livecellx.core.SingleCellTrajectoryCollection.get_all_track_ids
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  • livecellx.core.SingleCellTrajectoryCollection.get_all_trajectories
    • SingleCellTrajectoryCollection.get_all_trajectories()