livecellx.core.SingleCellStatic¶
- class livecellx.core.SingleCellStatic(timeframe=0, bbox=None, regionprops=None, img_dataset=None, mask_dataset=None, dataset_dict=None, feature_dict=None, contour=None, meta=None, uns=None, id=None, cache=None, update_mask_dataset_by_contour=False, empty_cell=False, tmp=None, use_cache_contour_mask=False, use_img_crop_cache=False, cached_img_shape=None)[source]¶
Single cell at one time frame
Methods
add_component(component[, component_type])Add a component to this unit
add_feature(name, features[, typecheck])add_organelle(organelle)Add an organelle to this cell (convenience method)
assign_uuid([exclude_set, max_try])compute_iomin(other_cell[, bbox])compute_iou(other_cell[, bbox])compute_overlap_mask(other_cell[, bbox])compute_overlap_percent(other_cell[, bbox])compute overlap defined by: overlap = intersection / self's area.
compute_regionprops([crop, ignore_errors])copy()gen_contour_mask(contour[, img, shape, ...])gen_contour_mask_skimage_deprecated(contour)gen_skimage_bbox_img_crop(bbox, img[, ...])get_bbox([padding])get_bbox_from_contour(contour[, dtype])get the bounding box of a contour
get_bbox_on_crop([bbox, padding])get_center([crop])get_components([component_type])Get components of a specific type or all components
Get the contour for this unit
get_contour_coords_on_crop([bbox, padding])get_contour_coords_on_img_crop([padding])A utility function to calculate pixel coord in image crop's coordinate system from the contour coordinates in the whole image's coordinate system.
get_contour_img([crop, bg_val])return a contour image with out of self cell region set to background_val
get_contour_label_mask([padding, crop, ...])get_contour_mask([padding, crop, bbox, dtype])get_contour_mask_closed_form([padding, crop])If contour points are pixel-wise closed, use this function to fill the contour.
Generate a pandas Series containing features for a single cell.
get_img()Get the image for this unit
get_img_crop([padding, bbox])get_img_shape([use_cache])get_label_mask([dtype])Get the label mask for this unit
get_label_mask_crop([bbox, dtype])get_mask([dtype])Get the mask for this unit
get_mask_crop([bbox, dtype])get_napari_shape_contour_vec([...])get_napari_shape_vec(coords)get_organelles([organelle_type])Get organelles of a specific type or all organelles (convenience method)
get_sc_img([crop, bg_val])return a contour image with out of self cell region set to background_val
get_sc_label_mask([padding, crop, bbox, dtype])get_sc_mask([padding, crop, bbox, dtype])inflate_from_json_dict(json_dict[, ...])load from json dict
load_from_json_dict(json_dict[, ...])load from json dict
load_single_cells_json(path[, verbose])load a json file containing a list of single cells
load_single_cells_jsons(paths)remove_component(component[, component_type])Remove a component from this unit
remove_organelle(organelle)Remove an organelle from this cell (convenience method)
sample_contour_point(max_contour_num[, ...])sample contour points from the trajectory and modify contour attr
show([crop, padding, ax])show_contour_img([padding, ax, crop, cmap])show_contour_mask([padding, ax, crop, cmap])show_label_mask([padding, ax, crop, cmap])show_mask([crop, padding, ax, cmap])show_panel([padding, figsize, img_cmap, ...])show_whole_img([ax, cmap])show_whole_mask([ax, cmap])to_json_dict([include_dataset_json, ...])returns a dict that can be converted to json
update_bbox([bbox])update_contour(contour[, update_bbox, ...])update_sc_mask_by_crop(mask[, ...])Updates the single cell mask by cropping the input mask to the bounding box of the single cell and updating the contour.
write_json([path, dataset_json_dir])write_single_cells_json(single_cells, path)Write a JSON file containing a list of single cells.
Attributes