README.md

Outline

SNT features several viewers for neuroanatomy:

• Reconstruction Viewer (the most versatile)
• Reconstruction Plotter
• Graph Viewer
• sciview integration
• Legacy 3D Viewer integration

In this section, students will learn about the different viewers, and their scripting capabilities.

Key Concepts

Tree, DirectWeightedGraph, Mesh, LUT-mapping, BrainAnnotation, Annotation Graph

Overview

1. Reconstruction Viewer:
   1. Overview
   2. Tips (Drag & drop, shortcuts, tags, 'recordable' commands)
   3. Handling groups of cells: Olfactory Projection Fibers: Group1 vs Group2
      1. "Import and compare groups" command
      2. Tags
      3. Analyses
   4. Interactive scripts: In Script EditorL run Script Templates: Neuroanatomy> Render> Reconstruction Viewer Demo then RecViewerScript.groovy

Exercises

• Script Templates: Neuroanatomy> Render>

Homework

Using snt.demoTrees() can you generate a montage of:

• Skeletonized images
• Viewer2D instances (MultiTreeViewer)
• Animated video (image sequence) in Viewer3D

Resources

SNT Manuscript | SNT Manuscript scripts | User Documentation | Forum | Source Code | API