Can ITK extract the skeleton for a 3D mask?

You can use SGEXT, a library that I develop and maintain, which uses a less noisy skeletonization algorithm, and also generates a graph (what you called a network) from it. Also includes tools to manipulate graphs, and other modules specific to my research.

I am right now parallelizing the 3D thinning algorithm to make it faster. The library is not yet in a super-easy to use state (it will be), but I encourage you to try it if you need its functionality. In the short future it will also be completely wrapped to use in python (right now is at 70%).

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