Efficient Segmentation of Fossil Vertebrae from Matrix in 3D Slicer

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1

Hi all,

I’m working with an undergrad student to segment individual fossil vertebrae from a CT-scanned articulated specimen (paleontological data). We’re using 3D Slicer, and the matrix and bone have very similar densities, making thresholding difficult.

We’ve managed to get a decent volume rendering using adjusted thresholds, but we’re still struggling with effective segmentation techniques to isolate bones cleanly.

Our key challenges:

  • Bone and matrix are hard to distinguish by intensity alone.
  • We’d like to avoid painstaking slice-by-slice manual painting, if possible.
  • We’re working with articulated vertebrae, so some separation between elements would be helpful.

Questions:

  1. Are there any recommended tutorials or workflows specifically for fossil or archaeological materials?
  2. Is there a better way to improve segmentation beyond thresholding — e.g., region growing, AI tools, or semi-automated methods?
  3. Any tips on segmenting multiple similar elements (e.g., vertebrae) efficiently?

Thanks so much for any guidance! We’ve found medical examples helpful, but fossil data seems to need a different approach.

Best,
B

2

All of those are available in Slicer.

Try painting a few seeds and the use the Grow from the seeds effect in Segment Editor. Lately, I am using the NNInteractive extension with quite a bit of success in similar settings. However, you if you have large volume, you will need to crop the volume into smaller chunks so that NNInteractive works effectively.

See the documentation at: SlicerNNInteractive/README.md at main · coendevente/SlicerNNInteractive · GitHub