The imaging platform has two goals that are related to ImageJ: to make ImageJ macros accessible as modules in a CellProfiler pipeline and to make CellProfiler pipelines executable as macros within ImageJ. We also have integrated the Bio-Formats library into CellProfiler to read and write image formats.
The ImageJ / CellProfiler collaboration is unusual in that CellProfiler is written in Python and uses libraries that are incompatible with Jython so it would seem that CellProfiler can’t run in the ImageJ process and can’t easily access Bio-Formats. But we do. We’re working on our own technology for running Python and Java together using JNI and we’re having quite good success bridging the gap. The collaboration’s goal is to showcase this sort of integration and demonstrate how other tools might be linked to ImageJ despite apparent language barriers.