I would like to use ImageJ and some of its macros and call them from inside a jupyter notebook. I am aware of PyimageJ, and I have been able to install it and load an image for display using ImageJ methods. But I am having some difficulties in getting the grasp of how to call and run the java-based plugins that come with imageJ nor load user-written macros.
I have been looking at this example: https://omero-guides.readthedocs.io/en/latest/fiji/docs/imagej_python.html
The example in question is actually for Omero, which I do not require nor have access to (registration for Omero is required).
I think I lack a more transversal understanding of working across different platforms, Could anyone please give me a hand?
Many thanks in advance.