Ok I’m going to reply to each point:
Can you specify more exactly what steps you’re using, and include any extra code/script/macro that is involved?
(A)Honestly, I wouldn’t trust myself enough to attempt any extra code/script , so we are just using the basic functionality of the app.
Also, does this need to work in batch or is it feasible to export the images one at a time interactively?
(A)Exporting images one at a time would be preferable at this moment in time, to allow for QC. I wouldn’t rule our batching but that’s a problem for another day.
Finally, do you need ImageJ ROIs that can be further manipulated or do you only require a RGB image that looks the same (i.e. what you can get by copying a snapshot)?
(A)Yes, I only need an RGB image that looks like the snapshot,. But I need it superimposed onto the original slide scan.
Since I never really use the macro functionality myself the code in QuPath for this purpose is a bit neglected. But if it doesn’t do the job you need here should be another way if it can be precisely defined.
(A)I’m new to the software so any help would be appreciated, neglected or otherwise! J