The Obsidian plugin for neuroscientists working on the mouse brain. Neuro Mindmap turns your vault into a visual note-taking tool anchored to the Allen Mouse Brain Atlas (CCFv3): browse the whole brain in 3D, drill into Allen reference sections, and attach markdown notes to any region, viewpoint, or cell.
- Visually guided note-taking across scales. Start in a 3D whole-brain view, zoom into a region, pick a 2D Allen reference section, and place individual cell morphologies — every level is one click deep, and every level can hold notes.
- True to anatomy. All structures load from public atlases — the Allen Mouse Brain Atlas (CCFv3) for regions and reference sections, and NeuroMorpho.org for neuron morphologies.
- Flexible note creation. Whatever level you are looking at, create a markdown note from inside the plugin. Notes automatically capture the visual-anatomical context they were taken in and can link to other regions.
- Holistic visual search. A search bar at the bottom of the view surfaces notes from every nested context, so you can find what you wrote without remembering where you wrote it.
- Open Settings → Community plugins → Browse, search for Neuro Mindmap (Mouse), and click Install, then Enable.
- Click the brain icon in the ribbon (or run the command Open MapTheMind view) to open the plugin pane.
- The 3D whole-brain view loads on first open. Click a region to drill in; right-click a region to create a brain-region note for it.
- Inside a region, pick a 2D atlas section to create a viewpoint, and add cell-type notes to the layers you care about.
The plugin fetches atlas data on demand from these public APIs:
api.brain-map.org— Allen Brain Atlas structure tree and section metadata.download.alleninstitute.org— CCFv3 structure mesh OBJs (used by the 3D viewer).neuromorpho.org— neuron morphologies (SWC files) for cell-type notes.
No telemetry is collected and no third-party analytics are loaded. Downloads happen only when you open a region, section, or cell type that has not yet been cached.
Fetched atlas data and meshes are cached on disk inside the plugin folder so subsequent loads are instant and work offline:
<vault>/.obsidian/plugins/neuro-mindmap-mouse/mesh-cache/
<vault>/.obsidian/plugins/neuro-mindmap-mouse/atlas-cache/
After extensive use the cache can grow to ~200 MB. It can be safely deleted at any time to reclaim space — the plugin will refetch the files it needs on next use.
Desktop Obsidian only (v1.4.0+). Mobile support is not currently available; the 3D viewer relies on patterns that have not yet been adapted for touch input.
GPL-3.0-only. See LICENSE.