cellpose
a generalist algorithm for cellular segmentation

carsen stringer & marius pachitariu

What to segment
Channel to segment
Nuclear channel (if cyto)
Avg cell diameter (in resized pixels, see axes below)
Invert image
Return output in original size

(smallest diameter actually used is 15 pixels for cytoplasm model and 7.5 pixels for nuclei model to reduce computation time, computation may take up to 30sec)