Two weeks ago I posted about invoking ImageJ functions from Python using Fiji’s Jython interpreter. A couple of updates on the topic:
First, I’ve made a repository with a template project encapsulating my tips from that post. It’s very simple to get a Fiji Jython script working from that template. As an example, here’s a script to evaluate segmentations using the metric used by the SNEMI3D segmentation challenge (a slightly modified version of the adapted Rand error).
Second, this entire discussion might be rendered obsolete by two incredible projects from the CellProfiler team: Python-Javabridge, which allows Python to interact seamlessly with Java code, and Python-Bioformats, which uses Python-Javabridge to read Bioformats images into Python. I have yet to play with them, but both look like cleaner alternatives to interact with ImageJ than my Jython scripting! At some point I’ll write a post exploring these tools, but if you get to it before me, please mention it in the comments!