# Stitching micro-CT images together
**URL:** https://discourse.vtk.org/t/stitching-micro-ct-images-together/15826
**Category:** Support
**Tags:** python
**Created:** [July 17, 2025, 11:22am UTC](https://discourse.vtk.org/t/stitching-micro-ct-images-together/15826 "2025-07-17T11:22:14Z")
**Posts on this page:** 9
**Page:** 1
### Author:  [@bistek](https://discourse.vtk.org/u/bistek)
#### Post date: [July 17, 2025, 11:22am UTC](https://discourse.vtk.org/t/stitching-micro-ct-images-together/15826/1 "2025-07-17T11:22:14Z")
Hello, we are searching a solution to stitch together 3d image datasets collected with a micro-CT scanner. He images are all collected at the same scale, have some overlap, and are possibly rotated one with respect to the other sinché the sample is moved between one scan and the other.
Thanks very much!
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### Author:  [@cory.quammen](https://discourse.vtk.org/u/cory.quammen)
#### Post date: [July 17, 2025, 3:12pm UTC](https://discourse.vtk.org/t/stitching-micro-ct-images-together/15826/2 "2025-07-17T15:12:01Z")
Hi, you might find more image-oriented software like [3D Slicer](https://www.slicer.org) more suitable for stitching together micro-CT images.
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### Author:  [@bistek](https://discourse.vtk.org/u/bistek)
#### Post date: [July 17, 2025, 3:22pm UTC](https://discourse.vtk.org/t/stitching-micro-ct-images-together/15826/3 "2025-07-17T15:22:12Z")
Hi, we have experienced very slow loading of large microCT images in 3D slicer. Maybe we are doing something wrong? And do you have specific function for stitching?
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### Author:  [@dgobbi](https://discourse.vtk.org/u/dgobbi)
#### Post date: [July 17, 2025, 8:18pm UTC](https://discourse.vtk.org/t/stitching-micro-ct-images-together/15826/4 "2025-07-17T20:18:43Z")
VTK itself doesn’t have any classes for image stitching, or at least, none that I’m aware of.
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### Author:  [@dave3d](https://discourse.vtk.org/u/dave3d)
#### Post date: [July 18, 2025, 2:19pm UTC](https://discourse.vtk.org/t/stitching-micro-ct-images-together/15826/5 "2025-07-18T14:19:17Z")
Image registration is more of ITK’s domain. It has a number of registration algorithms in the toolkit. It doesn’t have anything that’ll solve your problem automatically, but you should be able to code something to fill your needs. I’d ask over at the ITK discourse ([discourse.itk.org](http://discourse.itk.org)).
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### Author:  [@mau\_igna\_06](https://discourse.vtk.org/u/mau_igna_06)
#### Post date: [July 18, 2025, 2:50pm UTC](https://discourse.vtk.org/t/stitching-micro-ct-images-together/15826/6 "2025-07-18T14:50:05Z")
Hi,
Slicer has a tool for stitching volumes:
> **[GitHub - PerkLab/SlicerSandbox: Collection of utilities that are not polished...](https://github.com/PerkLab/SlicerSandbox#stitch-volumes)**
>
> Collection of utilities that are not polished implementations but can be useful to users
But probably you’ll have to make a registration first if you are mentioning there is some relative rotation between the images
EDIT: I just found there is also [this one](https://github.com/mikebind/SlicerStitchImageVolumes)
HIH
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### Author:  [@bistek](https://discourse.vtk.org/u/bistek)
#### Post date: [July 18, 2025, 3:06pm UTC](https://discourse.vtk.org/t/stitching-micro-ct-images-together/15826/7 "2025-07-18T15:06:59Z")
Yes thanks! I need registration then merging the datasets. Is this possible in Slicer?
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### Author:  [@mau\_igna\_06](https://discourse.vtk.org/u/mau_igna_06)
#### Post date: [July 18, 2025, 11:08pm UTC](https://discourse.vtk.org/t/stitching-micro-ct-images-together/15826/8 "2025-07-18T23:08:01Z")
Yes, more info here:
> **[Registration — 3D Slicer documentation](https://slicer.readthedocs.io/en/latest/user_guide/registration.html)**
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### Author:  [@Sandor](https://discourse.vtk.org/u/Sandor)
#### Post date: [July 30, 2025, 2:01pm UTC](https://discourse.vtk.org/t/stitching-micro-ct-images-together/15826/9 "2025-07-30T14:01:03Z")
We had great results with Fiji/ImageJ to stitch LSM scans, also its quite straightforward:
> **[Image Stitching](https://imagej.net/plugins/image-stitching)**
>
> The Stitching plugin (2d-5d) reconstructs big images/stacks from tiled input images/stacks, optimizing for the best overlap.
plugin already comes with the Fiji download
> **[Downloads](https://imagej.net/downloads)**
>
> This page provides download links for ImageJ.