during the last month I used Fiji python scripting for various APEER modules that basically run Fiji inside a docker container to do various things such as particle analysis or 3D segmentation and analysis.
For more details have a look here: APEER - Fiji Python Scripting Tutorial
I tried to collect most of the “more general” functions inside a bigger scripts, which you can find it here fijipytools.py.
It is fure sure not perfect and will contain bugs, but nevertheless some of you might find it useful. Feedback is welcome.
Thanks everybody here on image.sc for helping me with various questions I posted when creating those scripts and modules. Feel free to have a look. It is all free and fully open source.
Even if your are not interested in APEER you can always download the source code (required login) and use it for whatever you want.
The docker base image that was used to create those things can be found here: