# Multi-phase segmentation of a rock core

**URL:** <https://discourse.slicer.org/t/multi-phase-segmentation-of-a-rock-core/41620>\
**Category:** Support\
**Tags:** segmentation\
**Created:** [February 11, 2025, 3:34am UTC](https://discourse.slicer.org/t/multi-phase-segmentation-of-a-rock-core/41620 "2025-02-11T03:34:23Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![jddorellanao](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jddorellanao/32/79418_2.png) [@jddorellanao](https://discourse.slicer.org/u/jddorellanao)\
**Post date:** [February 11, 2025, 3:34am UTC](https://discourse.slicer.org/t/multi-phase-segmentation-of-a-rock-core/41620/1 "2025-02-11T03:34:23Z")

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

 ![IMG_4963](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/0/a/0a76ddc75bdc8ebf0359f8c8d6ef23a5405e9085.jpeg)

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 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.

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**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [February 11, 2025, 2:17pm UTC](https://discourse.slicer.org/t/multi-phase-segmentation-of-a-rock-core/41620/2 "2025-02-11T14:17:33Z")

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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.