Create RunImgeJScript Module

hinerm commented 3 years ago

Like the RunImageJMacro module, the RunImageJScript module is designed for running ImageJ processes from within CellProfiler.

In RunImageJScript we accomplish this by using the PyImageJ bridge between Python and ImageJ. This allows lightweight wrapping between CellProfiler image data structures and ImageJ (ImgLib2) types.

Advantages:

All ImageJ script languages are supported, including .ijm
No disk (de)serialization required for transferring data between CP and ImageJ
Script parameters are automatically detected and exposed in the GUI

Known limitations:

Only image and simple (primitives/String) script parameters currently supported
PyImageJ is built on Jpype which cannot coexist with the java bridge used in CP. This requires PyImageJ to run in a dedicated process, which does incur an overhead due to pickling data between processes.

hinerm commented 3 years ago

A sample script for use in testing: https://gist.github.com/hinerm/4693a4e918e452e8d0e16a3edb9b7387

0x00b1 commented 3 years ago

This is awesome @hinerm

hinerm commented 3 years ago

@0x00b1 I think @alicelucas made her changes to the tests - is there anything else you'd like to see before merging this?

alicelucas commented 3 years ago

Nice, congratulation @hinerm ! 🎉

CellProfiler / CellProfiler-plugins

Create RunImgeJScript Module #120