MinimalOMEROImageJ

Based on the OMERO guide: https://omero-guides.readthedocs.io/projects/fiji/en/latest/imagej_python.html

Setup:

Create a new conda environment and activate it

$ conda create -n imagej_python python=3.6
$ conda activate imagej_python

Install the required packages

$ conda install -c conda-forge pyimagej
$ conda install -c ome omero-py
$ conda install -c conda-forge notebook

Start jupyter notebook

$ jupyter notebook

In the first function you will need to change the path to your local Fiji application.

Known Issues

ij.ui().show('Image', ij.py.to_java(plane)) Does not work on Mac, rest of the code should work, you just can't view it