CellProfiler 3 in Linux



Hi all,
I have enjoyed CP2 in our ubuntu cluster for a while. A main limitation was the ability to do 3D, so it is exciting that CP3 will have this functionality!

I see in the release note that a linux release is/will available, however, there does not seem to be an active link in the download page. Is it yet not available? will it be? any timescale?

Even if it was possible to compile it from source, that would already be good news.
Thanks for your great work!



Hi Marcelo,

You can definitely compile it from source! You can get the code on our GitHub repo. I believe a Linux executable is in the works as well but I’m not sure on the timeline.


Thanks bcimini!
I will give it a go. Best, marcelo


To all wanting to install 3.0.0 on Linux (Ubuntu 16.04 in my case) via the instructions in Ubuntu 16.04 installation, make sure to “git checkout v3.0.0”. If you checkout “stable” you get version 2.2.1 instead.

  • Damir