README.md

SlicerMorph Tutorials

These tutorials show how to use SlicerMorph (and other relevant Slicer) modules in digital morphology and morphometrics related tasks.

Tutorial descriptions

1. SlicerMorph preferences: Explains what customizations can be done to Slicer as well as how to set download directory

2. Sample Data: Shows how to use the Slicer's Sample Data module to download and access sample data to be used in tutorials

3. ImageStacks: Tutorial on how to import non-DICOM imagestacks easily into Slicer.

4. SkyscanReconImport: How to import output from Bruker/Skyscan MicroCT

5. [MorphoSourceImport: How to quickly query and import open-access 3D models from MorphoSource]((https://github.com/SlicerMorph/Tutorials/tree/main/MorphoSourceImport)

6. ExportAs: How to quickly export data from SlicerMorph

7. Markups-I: Introduction markup types, UI, settings:

8. Markups-II: Resampling Semi-landmarks on curves

9. Patch-based Semi-Landmarking tutorial:

10. Creating a template of Pseudo-landmarks via PseudoLMGenerator:

11. MarkupEditor: How to subset/edit dense landmark sets

12. MergeMarkups: Merging fix and semiLMs or separate curve semiLMs for analysis

13. ALPACA: Automated Landmarking through Point cloud Alignment and Correspondence Analysis

14. GPA-I: Basics of GPA: Setting the analysis, exploring the morphospace

15. GPA-II: 3D interactive visualization of morphospace and exporting animations

16. GPA-III: Exporting data/results for R

17. Auto3Dgm: An automated procedure for placing landmarks

18. Animator: How to create keyframe-based animations of microCT scans

Additional Tutorials for some Slicer Modules used commonly for digital morphology tasks:

1. [DICOM]

2. [CropVolume]

3. [Transforms]

4. [Models]

5. [Volumes]

6. [Volume Rendering]

7. [Lighting]

8. [Overview of Segmentation and related data types]

9. [Segmentation tutorial]

10. [Surface Toolbox]