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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. 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. MorphoSourceImport: How to query and retrieve data from MorphoSource using SlicerMorph

  7. CropVolume

  8. Volumes

  9. Models

  10. Transforms

Visualization

  1. Volume Rendering

  2. Lights

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

  4. HiResScreenCapture: How to generate highDPI images

  5. Colorize Volume: Create Colored Volume Rendering from segmentations

  6. QuickAlign: Allows to approximately align two objects and sync their 3D renderings

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 (SlicerMorph & DeCA)

  1. Grid-based Semi-Landmarking:

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

  3. ProjectSemiLMs: allows you to transfer a semiLM template to new samples using fixed LMs and TPS

  4. MergeMarkups: Merging different kinds of LMs for analysis

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

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

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

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

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

  10. GPA-IV: Visualizing PCA results as heatmaps

  11. DeCaL: Automated semi and fixed landmarking tutorial

  12. DeCA-I: Dense Surface Correspondence Analysis

  13. DeCA-II: Symmetry Analysis

SlicerMorph Photogrammetry

  1. User Guide for the Photogrammetry Extension (This is for stable v5.10)

  2. PhotoMasking (This is for preview builds)

  3. VideoMasking (This is for preview builds)

  4. OpenDroneMap (This is for preview builds)

  5. ClusterPhotos (This is for preview builds)

  6. Photogrammetry module video tutorial

MorphoCloud

  1. MorphoCloud: Explains what MorphoCloud is and how you can get started with it

  2. NNInteractive: How to setup AI-assisted interactive segmentation on MorphoCloud

MorphoDepot

  1. MorphoDepot Overview: How does collabration segmentation workflows work in a nutshell

  2. Configuration: Sections 1-2

  3. Preparing Data for a MorphoDepot Repo: Sections 3-4

  4. Creating the Repository: Section 5

  5. Project Management: Section6, covers both student and repo owner tasks

  6. Review and Merging Submissions: Covers how repo owners review and send feedback to students?

  7. Search: How to find MorphoDepot repositories

Image and Surface Model Registration

  1. ANTsPy Volumetric Registration Tutorial

  2. FastModelAlign: Fast Model registration via point-clouds (for stable version)

  3. FastModelAlign: Fast Model registration with deformation (for preview version)

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

Others

  1. What is a microCT: A short review of what microCT imaging is, and how it compares to medical CT and some additional details

  2. ScriptEditor: An extension to write and embed python code in Slicer scenes

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

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

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

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

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