How can I use the marcoes I’ve written in fiji in a python environment? I’ve read that there is a specific way to import your installation of fiji into python then use them from there, but I’m not having luck. Additionally, when in python, the marcoes would have to be run headless. Is this the case automatically?
The pyimagej package should let you do what you want. It automatically runs in headless mode and has a simple helper function IJ.py.run_macro() that can take a macro string and run it.