@hanslovsky I am using pyimagej to use existing imageJ apis/plugins within a larger python program. More specifically, I use it in a tool to export Electron Microscope annotations from the Thermo MAPS software (https://www.fei.com/software/maps/) and stitch the images around each annotation.
I am using python because the larger project is in python and I’m familiar with it. I decided to use pyimagej because the stitching of EM images is superior in Fiji compared to other python solutions like stitching using opencv. pyimagej allows me to integrate these powerful imageJ APIs into my python workflow. Also, it gives me the flexibility of using imageJ APIs that are very hard to find in other tools (e.g. changing image exif data like pixel size).