# Strategies for working with large microCT files

**URL:** <https://discourse.slicer.org/t/strategies-for-working-with-large-microct-files/45847>\
**Category:** Support\
**Tags:** segmentation\
**Created:** [January 21, 2026, 1:23am UTC](https://discourse.slicer.org/t/strategies-for-working-with-large-microct-files/45847 "2026-01-21T01:23:34Z")\
**Posts on this page:** 1\
**Showing post:** 7

<div class="post-metadata">

**Author:** ![Antmaker](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/antmaker/32/81424_2.png) [@Antmaker](https://discourse.slicer.org/u/Antmaker)\
**Post date:** [February 10, 2026, 12:18am UTC](https://discourse.slicer.org/t/strategies-for-working-with-large-microct-files/45847/7 "2026-02-10T00:18:36Z")

</div>

@muratmaga and @arumiat, thank you both for such great and detailed suggestions. I have made some progress in my workflow by incorporating suggestions you made here and other posts in combination with my trial-and-error.

I’m going to recap the discussion here for future readers.

### Objective / Use case

Segment medical device microCT scans that contain non-organic (plastic, metal, etc) and organic (blood clots) components/substances and quantify the statistics (esp. volume) of each segmented components.

### Challenge

The image stacks are large (approximately 70GB-80GB) and the segments are non-continuous (scattered like stars in the night sky). Because of how large the model size is, the computer takes a long time to do a simple segment by threshold and “Show 3D” feature will crash the application even when running with ~800GB of RAM.

### Current solution(s)

- Create pseudo-ROI using [“Draw tube” effect](https://discourse.slicer.org/t/cropping-a-cylindrical-volume-jar-in-a-circular-roi/42750) and “Scissors” effect (add/remove shapes) to create the final segment for pseudo-ROI.

- Use this pseudo-ROI as a mask by selecting it in the “Editable area” dropdown menu of the “Masking” tab when any of the “Segment Editor” effects is selected.

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/0/5/05654e384890843b89ccdbb3e7daad228df00db0.png)

- Utilizing [“Colorize Volume” from the “Sandbox” module](https://discourse.slicer.org/t/new-colorize-volume-module/32254/7) instead of “Show 3D” of the “Segment Editor” module to view in 3D.

---

_[View the full topic](https://discourse.slicer.org/t/strategies-for-working-with-large-microct-files/45847)._