Running CellProfiler on Python (Jupyter Notebook)


I am trying to use Python, specifically Jupyter Notebook, to run Cell Profiler. I tried importing the cellprofiler package, but I got this error:
----> 1 import cellprofiler.pipeline
2 import pandas as pd

ModuleNotFoundError: No module named ‘cellprofiler.pipeline’; ‘cellprofiler’ is not a package

Please let me know what I can do

Hi @mayil,

Just to check - have you installed CellProfiler and it’s dependencies as a python package?


That’s the problem I’m having. I was not able to install the python packages for CellProfiler. I tried doing it on Python 3, but it said there was no such package. So I tried using Python 2, and it found the packages but received errors.

How would you recommend installing CellProfiler python packages? I have a windows

@mayil Two years ago, we got some CellProfiler-based notebooks running using Conda; see:

And in particular the environment.yml there.

@agoodman may have better / more recent instructions on how best to do it these days, though.