Where in the brain does DANDI have data? As the archive grows, this question becomes increasingly important for researchers planning experiments, searching for collaborators, or surveying available data for meta-analyses. Today, we’re excited to introduce DANDI Atlas Explorer—an interactive 3D brain viewer that lets you explore the DANDI Archive through the lens of the Allen Common Coordinate Framework (CCF) mouse brain atlas.
What is DANDI Atlas Explorer?
DANDI Atlas Explorer is a browser-based tool that renders an interactive 3D mouse brain and highlights which regions have associated neurophysiology datasets on DANDI. Regions with more datasets appear more opaque, giving you an immediate, intuitive sense of data coverage across the brain. Click any region to see the specific dandisets that recorded there, with direct links back to the DANDI Archive.
The tool currently covers 48 dandisets spanning 353 brain structures, with data automatically updated nightly from the archive.
Key Features
Interactive 3D brain visualization. Rotate, zoom, and pan a fully rendered mouse brain with 445 anatomical meshes from the Allen Institute. Orientation buttons let you snap to standard views—dorsal, ventral, anterior, posterior, left, and right.
Hierarchical brain region browser. A searchable, collapsible tree mirrors the Allen CCF structure hierarchy. Each region displays a badge with the number of associated dandisets, making it easy to identify regions with available data.
Region-to-dataset linking. Click any brain region to see all dandisets that recorded from that area. Each dandiset entry shows its title, subject count, and a direct link to the DANDI Archive. You can drill down further to see individual subjects and their recording locations.
3D electrode visualization. For electrophysiology datasets, DANDI Atlas Explorer extracts electrode coordinates from NWB files and renders them as 3D point clouds within the brain. Select a subject to see exactly where electrodes were placed, overlaid on the anatomical context.
Shareable URLs. The app encodes your current selection in the URL, so you can share a link that takes a colleague directly to a specific brain region or dandiset view.
How It Works
DANDI Atlas Explorer bridges two major neuroscience resources. Brain anatomy comes from the Allen Brain Atlas API, which provides the hierarchical structure graph and 3D mesh geometry for every brain region. Dataset metadata comes from the DANDI Archive, where NWB files store brain region annotations and electrode coordinates alongside the neurophysiology data.
A Python pipeline processes this data:
- It queries the DANDI API for all mouse (Mus musculus) dandisets.
- For each dandiset, it streams NWB files to extract brain region labels and electrode coordinates—without downloading the full files.
- It matches extracted region names to Allen CCF structure IDs.
- It aggregates statistics and generates static JSON files that power the frontend.
The frontend is built with Three.js for 3D rendering, with no framework dependencies. A GitHub Actions workflow runs the data pipeline nightly, so the atlas stays current as new datasets are published to DANDI.
Use Cases
- Planning experiments: Check what data already exists for your brain region of interest before starting a new study.
- Finding collaborators: Discover which labs have published data from the same brain areas you study.
- Meta-analysis: Quickly survey data availability across brain regions for cross-dataset analyses.
- Teaching: Use the interactive 3D brain to teach neuroanatomy in the context of real datasets.
- Data discovery: Browse the DANDI Archive spatially rather than by keyword search.
Try It Now
DANDI Atlas Explorer is open source and runs entirely in your browser—no installation required.
The source code is available on GitHub. Contributions, bug reports, and feature requests are welcome.
DANDI Atlas Explorer was developed by CatalystNeuro with support from the DANDI project.