Machine and Deep Learning

ilastik Ilastik

https://www.ilastik.org/
https://www.ilastik.org/documentation/fiji_export/plugin

Leverage machine learning algorithms to easily segment, classify, track and count your cells or other experimental data. Most operations are interactive, even on large datasets: you just draw the labels and immediately see the result. No machine learning expertise required.


Logo Cellpose

http://www.cellpose.org/
https://cellpose.readthedocs.io/en/latest/gui.html#starting-the-gui

A generalist algorithm for cell and nucleus segmentation.

https://cellpose.readthedocs.io/en/latest/installation.html#with-an-environment-file


StarDist

https://github.com/maweigert/neubias_academy_stardist
https://imagej.net/StarDist  (Fiji Plugin)
(or one with splines instead of starconvexes: experimental: https://gitlab.ebi.ac.uk/smandal/splinedist)