`allen_expression_datasets`

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_expression_datasets for the schema, then POST the same URL with its arguments for the data.

Lists the Allen Brain Atlas in-situ hybridization experiments for a gene, with atlas product and plane of section.

Tool description as the model sees it

List the Allen Brain Atlas in-situ hybridization expression experiments (SectionDataSets) for a gene — which atlas product they belong to (Mouse Brain, Developing Mouse, Human Brain, Mouse Spinal Cord), plane of section (coronal/sagittal), section thickness, and the dataset id used to fetch images and per-structure expression. AUTHORITATIVE for “where in the brain is gene X expressed” and for finding the experiment ids behind an Allen expression figure.

Parameters

Name	Type	Required	Description
`gene_acronym`	string	yes	Gene symbol, e.g. “Gabra1” (mouse) or “GABRA1” (human). Casing selects the species record; both are tried and the response says which matched.
`plane_of_section`	string	no	Optional filter: “coronal” or “sagittal”. Omit for both — filtering can empty an otherwise non-empty result.
`product_id`	number	no	Optional Allen product id filter (1 = Mouse Brain ISH, 3 = Developing Mouse Brain). Omit unless you need one product; the response always reports the unfiltered total.
`include_failed`	boolean	no	Include experiments Allen flagged as failed QC (default false).
`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

{
  "gene_acronym": "Gabra1"
}

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_expression_datasets","arguments":{"gene_acronym":"Gabra1"}}}'

TypeScript (@pipeworx/sdk)

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

const result = await pipeworx.call('allen_expression_datasets', {
  "gene_acronym": "Gabra1"
});

More examples

{
  "gene_acronym": "Gabra1",
  "plane_of_section": "coronal"
}

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_expression_datasets