MapTheMind

The Obsidian plugin for neuroscientists working on the mouse brain. MapTheMind 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.

Main features

• 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.

Getting started

1. Open Settings → Community plugins → Browse, search for MapTheMind, and click Install, then Enable.
2. Click the brain icon in the ribbon (or run the command Open MapTheMind view) to open the plugin pane.
3. 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.
4. Inside a region, pick a 2D atlas section to create a viewpoint, and add cell-type notes to the layers you care about.

Network usage

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.

Storage

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.

Platform

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.

License

GPL-3.0-only. See LICENSE.