I have a JSON file export of the annotations, and I am trying to figure parse the JSON file to upload those ROIs onto the OMERO server along with this image.
Have you tried following examples at https://docs.openmicroscopy.org/omero/5.5.1/developers/Python.html#rois
to created ROIs in OMERO from your JSON data?
How far did you get? (or do you need help getting setup with the OMERO Python API?).