I am a beginner in image analysis and I am trying to develop my first pipeline with Cellprofiler (3.1.8).
I have to segment nuclei from a gray image and then measure the intensity of the immunostainings around the nuclei. The first step is by far the most difficult!
I installed the plugins available on github ( and they all appear in the modules except “classifypixelsunet”.
Maybe I have incorrectly installed tensorflow and keras (installed with python 2.7)?
It seems to me that CP 3.X uses python 3.XX. So I tried to install a later version of Python (3.7.15) but I can not install tensorflow with this version of python (needs Python 3.6 version?).
Can you help me install and use this plugin that looks very promising to improve my pipeline.
Thank you.
PS .: My config: Mac OSx Mojave, I7 8700k, 64GB, no graphic card.


CellProfiler uses python 2.7, not 3.X.

Hope that helps!

Thank you for your reply,
I tried to remove Python3,7 and keep only Python 2.7 but that did not solve my problem.
I probably made a mistake in installing keras?
I am not a computer scientist and I will probably not find the way to solve the problem … I will wait for a “special version that installs itself for a pathologist who wants to play with a neural network” is available.
In the meantime, I’m working with Ilastik + CellProfiler and the impressive results I’m getting are going to be enough for my project.
Thank you for your help and long live CellProfiler !!!
Best regards