3D Allen CCF Brain Atlas — DANDI Explorer

Interactive 3D viewer of the Allen Common Coordinate Framework (CCF) mouse brain atlas, highlighting regions that have associated datasets on the DANDI Archive.

Read the blog post for more details.

Features

• 3D brain visualization using Three.js with Allen CCF mesh data
• Region coloring by Allen CCF color scheme, opacity scaled by dataset count
• Click to isolate — selecting a region dims everything else, showing only the selected structure at full opacity
• Hierarchy tree — collapsible Allen CCF structure tree with search; badges show direct/total dandiset counts
• Dandiset panel — click a region to see associated DANDI datasets with direct links
• Orientation buttons — snap to dorsal, ventral, anterior, posterior, left, right views
• Resizable sidebar — drag to expand the hierarchy panel for deep navigation
• Mouse-only data — filters to Mus musculus datasets only (48 dandisets, 353 brain structures)

Quick Start

1. Generate data

python scripts/build_data.py

This downloads the Allen structure graph, matches DANDI locations to CCF terms, and downloads OBJ meshes (~190 MB) to data/meshes/.

Requires label_results_full.json from the DANDI location analysis. Set the path via:

LABEL_RESULTS_PATH=/path/to/label_results_full.json python scripts/build_data.py

2. Serve locally

python -m http.server 8000

3. Open

Navigate to http://localhost:8000

Project Structure

├── index.html                  # Main app
├── style.css                   # Styles
├── app.js                      # Three.js scene, hierarchy tree, dandiset panel
├── data/
│   ├── structure_graph.json    # Allen hierarchy tree (from Allen API)
│   ├── dandi_regions.json      # Structure data with direct + aggregate dandiset counts
│   ├── mesh_manifest.json      # Index of available meshes
│   └── meshes/                 # OBJ files by structure ID (generated, not in git)
└── scripts/
    └── build_data.py           # Generates all static data

Data Sources

• Allen Brain Atlas API — structure graph and OBJ meshes
• DANDI Archive — dataset-to-brain-region mappings from NWB file metadata