Troubleshooting

Problem	Solution
After setting the CellProfiler Plugins folder, CellProfiler won’t open and returns an error: no commands supplied in the terminal.	You have set the CellProfiler Plugins folder to the parent folder of the plugins repository (CellProfiler-plugins), not the folder that contains plugins (CellProfiler-plugins/active_plugins). In order to get it to open, remove setup.py from the folder. Change the CellProfiler Plugins path to the correct path and close CellProfiler. Return setup.py to the parent folder.
No plugins are visible in the “Add Modules” panel in CellProfiler.	You have not properly set the plugins path. Go to CellProfiler => Preferences and set the path in the CellProfiler plugins directory to the active_plugins folder in the GitHub repository that you just cloned. Select Save at the bottom of the Preferences window.
Some but not all plugins are visible in the in the “Add Modules” panel in CellProfiler.	Not-visible plugins have unmet dependencies. Follow installation instructions to install dependencies for plugins.