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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. Export File: This feature is now a core Slicer feature. Right click on any object in the Data module and choose "Export File".

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

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

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

  9. Markups-III: Landmark Template Creations

  10. Patch-based Semi-Landmarking tutorial:

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

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

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

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

  15. MALPACA: Multi-template ALPACA and Kmeans based template selection:

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

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

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

Deep-Learning based segmentation models

  1. MEMOS: A pre-trained segmentation model for E15 fetal mouse scans

  2. MonaiLabel: a server-client system that facilitates segmentation by using AI

  3. MonaiLabel: How to train new AI based segmentation models from scratch

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

  1. DICOM

  2. CropVolume

  3. Volumes

  4. Volume Rendering

  5. Lighting

  6. Overview of Segmentation and related data types

  7. Segmentation tutorial

  8. Transforms

  9. Models

  10. Mesh Editing via Surface Toolbox and Dynamic Modeler

  11. Discourse thread on how to reorient and resample in Slicer

  12. Discourse thread on rendering multi-channel (RGB) microscopy datasets in Slicer

  13. How to use sequences module to store rendering and orientation states to come back

  14. Dr. Jaimi Gray's Quick Guide for various 3D Slicer modules. Icons are clickable and will take you to her YT videos: