Segmentation of thin surfaces

Hey Slicers,

I’m curious if anyone has any suggestions on strategies for segmentation of some specimens we’re working on. These are micro-CT scanned insects (dried, pinned specimens) that have thin cuticular membranes internally that I want to segment out. The membranes are very thin and wind up having absorbances pretty close to the background air. Here’s a representative image as an example:


The red is my segmentation in progress, and you can see how the membrane is very thin and also very close to the background absorbance.

Thus far, my strategy has been to use sphere brush and symmetric scissors with a set intensity range as much as possible, periodically using island removal to “de-speckle”. This results in lots of holes in the reconstructed surface, however, that I wind up going back and cleaning up manually using a brush. This can be somewhat time consuming, and I’m looking for ways to speed up the process.

I’ve tried flood filling and other algorithms a couple of times without a lot of success. Just curious if anyone has run into any algorithms or anything that do any kind of “surface following”, for lack of a better term, or if there are any fancy ITK filters called “Automatic Insect Membrane Determination”. (OK, that last one is a bit of a stretch.)

Thanks in advance for any ideas anyone has!


We had very similar problem when segmenting thin orbital bone. Couple of things that helped:

  • Crop and resample your volume to make the structures that you want to segment at least 4-5 voxel wide. Otherwise all the region-growing based method will fail, as due to random noise a few voxels may be missed and your structure may break to parts.
  • Apply filtering, which enhances thin structures. We have found that unsharp masking helped.
  • If the structure that you need to represent is a surface then instead of a volumetric representation, you may try to reconstruct a surface from points. See this complete example that works in Slicer as is, See also these additional VTK examples: Poisson surface reconstruction, comparison of 3 surface reconstruction methods that are available in VTK. If this approach works well then let me know and I can make a segment editor effect from it.
  • You may paint the structure manually on a couple of (non-neighbor) slices and use Fill between slices effect to create a complete segmentation out of it.

Hey Andras,

These are great ideas, and thanks for the reference.

I’ll report back on the surface ideas (it is indeed a surface we want out of this, not necessarily a volume) to see if it makes sense to make a segment editor effect.

Thanks again!!!