SlicerMorph Tutorials

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

Tutorial descriptions

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

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

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

4. GEVolImport: A utility module import 3D volumes from GE/Phoenix scanners with PCR/VOL combination

5. DICOM

6. CropVolume

7. Volumes

8. Models

9. Transforms

Visualization

1. Volume Rendering

2. Lights

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

4. HiResScreenCapture: How to generate highDPI still images

5. Colorize Volume:

Markups Related

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

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

3. Markups-III: Landmark Template Creations

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

Segmentations Related

1. Overview of Segmentation modules and related data types

2. Creating custom color tables with terminologies

3. Segmentation tutorial

4. Editing 3D Models via Surface Toolbox and Dynamic Modeler

5. Creating Solid Models from Segmentations

Geometric Morphometrics Related

1. Grid-based Semi-Landmarking:

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

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

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

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

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

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

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

9. DeCaL Automated semi and fixed landmarking tutorial

10. DeCA: Dense Surface Correspondence Analysis

Photogrammetry

1. User Guide for the Photogrammetry Extension

2. Photogrammetry module video tutorial

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

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

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

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

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

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

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