Bioimage Analysis / Desktop app / Python package
Cellpose
Generate instance masks for cells or nuclei in microscopy images and inspect them in a graphical interface.
Best fit
Imaging researchers who need a first pass at separating cells before counting or measuring them.
What you need
Python and a supported Cellpose installation; the optional GUI helps with inspection, and a compatible GPU can accelerate larger jobs.
What to check
Check masks on held-out images. Crowding, unfamiliar contrast, or a change in model version can alter which cells are merged or split.