I am attempting to generate per well profiles from a Cell Painting experiment. The per object data is in an SQLite database.
I am following this protocol for the script: https://images.nature.com/full/nature-assets/nprot/journal/v11/n9/extref/nprot.2016.105-S1.pdf
I have very limited experience with scripting in general and am completely unfamiliar with python. I’m working in a Windows environment. So far I have been able to install all the packages and have generated the cellpntg environment and installed CellProfiler-Analyst as a git clone. The error I am running into I think has to do with the export PYTHONPATH=
pwd line. Since this is in Windows I updated it to be set PYTHONPATH=
cd but nothing seems to happen after I type it in.
When I go to the next step to create the cache within the code file I get the following error: C:\pathstring\Miniconda3\envs\cellpntg\python.exe: No module named cpa.profiling found.
Any help would be appreciated!