Recommendations for segmenting internal cavities

Community
1

Hi, I’m working with a microCT of bone osteoderms. I need to segment internal cavities and external compact bone. I started with threshold tool to segment compact bone and went successful. But the internal cavities is a lot more complex and some are connected with the exterior. I started segmenting full manually using the painting tool, but it take a LOT of time (2 - 3 days only 1 osteoderms). I’m asking for advice to follow some strategy to fill those cavities in a more automatic or semiautomatic way. Thanks in advance.

Below is and screenshot of the osteoderm:

image

2

Yes, we have several automated tools that could segment these structures effortlessly. The key is to prevent leaking through small holes.

From a single image slice it is hard to tell which method will work the best, but I would recommend to start with trying cavity extraction using SurfaceWrapSolidify extension. See this segmentation recipe for step-by-step instructions.