Hi David,

I forgot to reply you sorry ! Well about the merge channel block, to be honest it is not really suited to do a protocols block for that, because the input would be a folder and we have no real output except file make that not really straightforward for protocol classical usage. Still it could be in form of a script so we do the merging operation before (and outside) the protocol then execute the protocol on merged images 🙂
About your second question, what you can try is to “convexify” your ROI (you have a block for that) !

– Stephane