Dear Caroline, sorry you’re having trouble but that doesn’t sound like the recommended install procedure. Did you try following the steps in the readme using the Fiji update site?

https://github.com/jefferis/fiji-cmtk-gu...

Iirc if you are going to install manually you need to ensure that jython compiles the py file and it ends up in the class path. I forget the details but can look into it if there’s a reason why the update site won’t work for you.

All the best,

Greg.