locan.scripts.script_rois

Define regions of interest with napari and save as roi files.

With this script you can choose a file name, open the localization file in napari. Draw regions of interest as additional shapes in napari. Upon closing napari each shape is taken as single roi and saved as _roi.yaml file.

To run the script:

locan rois -f <file> -t <file type> -i <roi file indicator> --bin_size <>
--rescale <string with tuple or rescale>

Try for instance:

locan rois -f "locan/tests/test_data/five_blobs.txt" -t 1 -i "_roi" --bin_size 10

See also

locan.visualize.render_napari.utilities.select_by_drawing_napari

Functions

main([args])	rtype: None
sc_draw_roi_napari([file_path, file_type, ...])	Define regions of interest by drawing a boundary.