Shrink-wrap style margin?

Greetings slicers,

I have a micro-CT scan of an insect. The exoskeleton and associated dense internal cuticular structures are in a segment. What I would like to do is use the margin tool to erode away just the external exoskeleton part of the segmentation, but not act on the internal structure segmentation - kind of like a “shrink wrap” followed by margin, if that makes sense, to remove just the exoskeleton but keep the internal structures segmentation intact. Is there a way to do this? (Automated or semi-automated, that is - I can always do it by hand, but I was looking for a way to speed up the process.)

Many thanks in advance for any ideas anyone has!


For this, I would create an “air” segment by Thresholding (if there air inside then you can remove it by applying Smoothing > Opening and Islands > Keep largest) or Flood filling (in SegmentEditorExtraEffects extension). Then, expand this “air” segment using Margin > Grow effect.

For more sophisticated stripping (variable shell thickness), you can try SwissSkullStripper extension - it is developed for stripping the skull, but it can be used for other shells, too. You have to provide one example image (Atlas volume) and a mask (Atlas mask volume; a labelmap that only covers the region that you want to keep).