allenbrain-mcp

Community MCP server wrapping the Allen Brain Atlas API — cell types, mouse connectivity experiments, brain-structure ontologies, atlas images, and 3D expression grids.

   
Type MCP server
Supplier maflot (community; not officially endorsed by the Allen Institute)
Availability Alpha — created February 2026, “work in progress”
Pricing Free / OSS — no explicit license file in the repo; flag for legal review before redistributing
Capabilities Read-only

How to install 

git clone https://github.com/maflot/allenbrain-mcp
cd allenbrain-mcp
npm install
npm run build
npm start

Register with Claude Code (replace /path/to/allenbrain-mcp with the absolute path of the clone — e.g., $(pwd) if you’re still inside the directory from the previous step):

claude mcp add --transport stdio allenbrain -- node /path/to/allenbrain-mcp/build/index.js

What it does

  • execute_rma_query — raw RMA queries
  • get_cell_specimens
  • get_mouse_connectivity_experiments
  • get_atlases, get_structure_graphs, get_structures
  • get_atlas_images, get_section_images
  • get_grid_data_download_url — 3D expression grids (streamed to disk)
  • get_neuronal_models

Primary use cases: Query Allen Cell Types and Mouse Connectivity, resolve brain-structure ontologies, fetch atlas / section images and 3D expression grids.

Notes

TypeScript / Node, stdio transport. Calls the public Allen Brain Atlas API — no auth. Streams large downloads to disk. Alpha status and absent LICENSE file mean this is best used as an exploration tool, not a production dependency, until upstream clarifies licensing.

Sources

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