FIJI Commands To Manipulate CellProfiler CPPIPE files

Hi everybody,

In case that’s useful to somebody else, I’ve wrote a few commands to open, display, modify and save the .cppipe files generated by CellProfiler 3, within FIJI.

  • Link to the repository
  • Link to the jar file (to be put in FIJI’s jars or plugins folder)
    The reason it’s on FIJI is really just for the convenience of the user, because there’s no image processing here, but just some text parsing, display and editing. Maybe it could be useful for other people, so I’m happy to share it.

It’s working for its current purpose, but it’s clearly not foolproof. In particular it has been tested only for a small set of pipelines generated by CellProfiler v3.1.8.