How to calculate thickness of a tube-like 3D mesh with a hole in Python or Meshlab?

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I have a 3D geometry of an organ with a cavity. It is in a 3D numpy array but can convert to STL. My task is to calculate its 3D wall thickness of it. I tried doing it in 2D and then considering it in 3D. But I wonder if there is a way to do it in 3D?

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