SA: Make everything a little less fragile

- Skeletonize everything beforehand so that root ROI gets skeletonized only once
- Be more accurate in counts when "Root ROI" contains multiple branches
- Improve warning messages

NB: The "Root Protection ROI" is really hacky. There are at least dozens of
scenarios where counts will not reflect the iteration. However, the 'Color map'
output should remain accurate.