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 ~/images_cyto/test/ --pretrained_model cyto --chan 2 --chan2 3 --save_png
You can specify the diameter for all the images or set to 0 if you want the algorithm to estimate it on an image by image basis. Here is how to run on nuclear data (grayscale) where the diameter is automatically estimated:
python -m cellpose --dir ~/images_nuclei/test/ --pretrained_model nuclei --diameter 0. --save_png
Warning
The path given to --dir
must be an absolute path.