MCP server exposing 3 tools for allen-brain.
This URL is a JSON-RPC 2.0 endpoint over HTTP. Issue POST requests with a JSON-RPC body. Browsers and search crawlers land here on GET.
POST https://gateway.pipeworx.io/allen-brain/mcp
Content-Type: application/json
{"jsonrpc":"2.0","id":1,"method":"tools/list"}allen_search_genes — Look up genes in the Allen Brain Atlas gene catalog by symbol/acronym, name substring, or Entrez ID. AUTHORITATIVE for resolving a gene to the Allen internal gene id and organism that the atlas expression data is keyed on — note the atlas holds mouse and human as SEPARATE gene records with the same-but-differently-cased acronym (Gabra1 vs GABRA1), and the expression datasets attached to each differ. Use this before allen_expression_datasets.allen_structures — 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.allen_expression_datasets — 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.Code samples (curl / TypeScript / one-click client install), schemas, and the live playground are on the pack page:
https://pipeworx.io/packs/allen-brain/
Pipeworx is an open MCP gateway connecting AI agents to live data. pipeworx.io