`allen_structures`

Pack: allen-brain · Endpoint: https://gateway.pipeworx.io/allen-brain/mcp

No MCP client? Call it directly: GET https://gateway.pipeworx.io/v1/tools/allen_structures for the schema, then POST the same URL with its arguments for the data.

Resolves a brain region name or acronym to its Allen structure id, parent, and root-to-leaf containment path.

Tool description as the model sees it

Query the Allen Brain Atlas structure ontology — the canonical hierarchy of named brain regions (Field CA1, Primary visual area, Substantia nigra) with their acronyms, colors, parent structure, and full root-to-leaf structure_id_path. AUTHORITATIVE for resolving a brain-region name or acronym to the structure ID that Allen expression, connectivity and reference-space data are annotated against, and for establishing whether one region contains another.

Parameters

Name	Type	Required	Description
`acronym`	string	no	Exact structure acronym, e.g. “CA1”, “VISp”, “SNr”.
`name_contains`	string	no	Substring of the structure name, e.g. “hippocamp”, “visual area”. Case-insensitive.
`structure_id`	number	no	Allen structure id, e.g. 382 (Field CA1).
`graph_id`	number	no	Structure graph to search. 1 = adult mouse brain (default), 10 = human brain, 17 = developing mouse.
`num_rows`	number	no	Rows to return, 1-200 (default 25).
`start_row`	number	no	0-based offset for paging (default 0).

Example call

Arguments

{
  "acronym": "CA1"
}

curl

curl -X POST https://gateway.pipeworx.io/allen-brain/mcp \
  -H 'Content-Type: application/json' \
  -d '{"jsonrpc":"2.0","id":1,"method":"tools/call","params":{"name":"allen_structures","arguments":{"acronym":"CA1"}}}'

TypeScript (@pipeworx/sdk)

import { Pipeworx } from '@pipeworx/sdk';
const pipeworx = new Pipeworx();

const result = await pipeworx.call('allen_structures', {
  "acronym": "CA1"
});

More examples

{
  "name_contains": "visual area",
  "graph_id": 1
}

Connect

Add this to your MCP client config, or use one-click install buttons:

{
  "mcpServers": {
    "allen-brain": {
      "url": "https://gateway.pipeworx.io/allen-brain/mcp"
    }
  }
}

See Getting Started for client-specific install steps.

allen_structures