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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

Data Import/Export, Downsampling, Transformations

  1. Sample Data: Shows how to use the Slicer's Sample Data module 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. Export File: This feature is now a core Slicer feature. Right click on any object in the Data module and choose "Export File".

  5. DICOM

  6. CropVolume

  7. Volumes

  8. Models

  9. Transforms

Visualization

  1. Volume Rendering

  2. Lighting

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

  4. HiResScreenCapture: How to generate highDPI still images

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 and related data types

  2. Segmentation tutorial

  3. Mesh Editing via Surface Toolbox and Dynamic Modeler

  4. 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

Photogrammetry

  1. User Guide for the Photogrammetry Extension

  2. Photogrammetry module video tutorial

Others

  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