I have an issue that I have not been able to overcome trying to run Cell profiler after installing it with Conda. The Cell profiler GUI will open up with no issues and I can interact with the program including using the test mode. However I cannot get the analyze images button to work. It will appear to start with no error codes and the last line of the command prompt will display: Worker 0: Starting job but it will remain stuck there until I click stop analysis.
I have been able to download and install the cellprofiler-3.1.8.exe from the website and run the same pipeline successfully.