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muratmaga merged 1 commit into from
Jul 28, 2026
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Add Imaging Modalities section to tutorial index #48

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11 changes: 5 additions & 6 deletions README.md
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Expand Up @@ -3,6 +3,11 @@ These tutorials show how to use SlicerMorph (and other relevant Slicer) modules

## Tutorial descriptions

### Imaging Modalities
1. #### [**What is a microCT:** A short review of what microCT imaging is, and how it compares to medical CT and some additional details](https://github.com/SlicerMorph/Tutorials/blob/main/microCT/README.md)
2. #### [**What is photogrammetry:** Background on Structure-from-Motion photogrammetry for biological specimens — how it works, capture/scaling, and what it is good at](https://github.com/SlicerMorph/Tutorials/blob/main/photogrammetry/README.md)
3. #### [**What is surface 3D scanning:** Background on structured-light and laser surface scanning of specimens — how they work, capture considerations, and outputs](https://github.com/SlicerMorph/Tutorials/blob/main/surfaceScanning/README.md)

### Data Import/Export, Downsampling, Transformations
1. #### [**Getting Data:** Shows how to use the Slicer's `Sample Data` and SlicerMorph's `ImportFromURL` modules to download and access sample data to be used in tutorials](https://github.com/SlicerMorph/Tutorials/tree/main/SampleData)
3. #### [**ImageStacks:** Tutorial on how to import non-DICOM imagestacks easily into Slicer.](https://github.com/SlicerMorph/Tutorials/tree/main/ImageStacks)
Expand Down Expand Up @@ -84,14 +89,8 @@ These tutorials show how to use SlicerMorph (and other relevant Slicer) modules
3. #### [**MonaiLabel:** How to train new AI based segmentation models from scratch](https://www.youtube.com/watch?v=3HTh2dqZqew)

### Others
0. #### [**What is a microCT:** A short review of what microCT imaging is, and how it compares to medical CT and some additional details](https://github.com/SlicerMorph/Tutorials/blob/main/microCT/README.md)
0. #### [**What is photogrammetry:** Background on Structure-from-Motion photogrammetry for biological specimens — how it works, capture/scaling, and what it is good at](https://github.com/SlicerMorph/Tutorials/blob/main/photogrammetry/README.md)
0. #### [**What is surface 3D scanning:** Background on structured-light and laser surface scanning of specimens — how they work, capture considerations, and outputs](https://github.com/SlicerMorph/Tutorials/blob/main/surfaceScanning/README.md)
1. #### [**ScriptEditor:** An extension to write and embed python code in Slicer scenes](https://github.com/SlicerMorph/Tutorials/blob/main/ScriptEditor/README.MD)
1. #### [**SlicerMorph preferences:** Explains what customizations can be done to Slicer as well as how to set download directory](https://github.com/SlicerMorph/Tutorials/tree/main/MorphPrefs)
11. #### [Discourse thread on how to reorient and resample in Slicer](https://discourse.slicer.org/t/how-to-properly-use-the-segment-editor-with-transformed-volumes/21861/11?u=muratmaga)
12. #### [Discourse thread on rendering multi-channel (RGB) microscopy datasets in Slicer](https://discourse.slicer.org/t/best-data-import-practices-for-microscopy/22056/4?u=muratmaga)
13. #### [How to use sequences module to store rendering and orientation states to come back](https://discourse.slicer.org/t/new-feature-basic-support-for-physically-based-rendering-pbr/21725/17)
14. #### [Dr. Jaimi Gray's Quick Guide for various 3D Slicer modules. Icons are clickable and will take you to her YT videos:](http://www.graysvertebrateanatomy.com/__static/c0e61a322fc1f771762f9a4d60fbf7ee/gray-3d-slicer-quick-guide.pdf)


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