Multi-phase segmentation of a rock core

[jddorellanao (Jhon O)]

I am currently working with microCT images of rocks, more specifically cores (like the following image)

Since the acquisition is done by the lab operator, the images he gives me have some problems

• When the CT was acquired the core was tilted, so the first image and the last image do not match:
  The top image:
  

  
  
  The base image:
  
  

• The segmentation consists of a multiphase discriminator: the pore space, the rock matrix, and one or more minerals, when trying to segment the pore space with threshold, the space outside the core is included:
  

  

Which is not wrong, but it is not the desire. I tried with scissors, but since the core is inclined, I can’t do it.

I would be grateful if you could guide me.

[pieper (Steve Pieper (Isomics, Inc.))]

You should be able to threshold the air outside the rock first, then when you do the inside of the rock don’t let it overwrite the air.