Command line

The full list of options and what they do can be found on the Command Line Interface (CLI) documentation page: Cellpose CLI. A description of the most important settings can be found on the Settings page.

Command Line Usage

Run python -m cellpose and specify parameters as below. For instance to run on a folder with images where cytoplasm is green and nucleus is blue and save the output as a png (using default diameter 30):

python -m cellpose --dir /home/carsen/images_cyto/test/ --save_png

To run on a single 3D image:

python -m cellpose --image_path /home/carsen/image3D.tif --do_3D --flow3D_smooth 2 --save_tif

Warning

The path given to --dir is recommended to be an absolute path.