cellpose

cellpose is an anatomical segmentation algorithm written in Python 3 by Carsen Stringer and Marius Pachitariu. For support, please open an issue.

We make pip installable releases of cellpose, here is the pypi. You can install it as pip install cellpose[gui].

You can try it out without installing at cellpose.org. Also check out these resources:

  • twitter thread
  • Marius’s talk on cellpose
  • paper on biorxiv (see figure 1 below)
fig1