Allen Brain MCP server

@pipeworx/allen-brain

Genes, the brain structure ontology, and in-situ hybridization expression experiments from the Allen Institute's public Brain Atlas RMA API — where in the brain a gene is expressed, and the canonical region hierarchy that expression is annotated against.

Part of Pipeworx — an MCP gateway connecting AI agents to 1679+ live data sources.

Tools

— gene symbol / name / Entrez ID → the Allen internal gene id and organism.

• allensearchgenes(acronym?, namecontains?, entrezid?, organism?, numrows?, startrow?)

— brain region name or acronym → structure id, parent, and the root-to-leaf structureidpath that establishes containment.

• allenstructures(acronym?, namecontains?, structureid?, graphid?, numrows?, startrow?)

— the ISH experiments (SectionDataSets) for a gene: atlas product, plane of section, section thickness, and the dataset id behind an Allen figure.

• allenexpressiondatasets(geneacronym, planeofsection?, productid?, includefailed?, numrows?, start_row?)

Auth

Keyless.

Data sources

every tool here is one RMA expression against it (model::Gene, model::Structure, model::SectionDataSet).

• — the RMA query endpoint;

Traps

Gene acronyms are case-distinct across species and that is a data fact, not a formatting one. Gabra1 is the mouse gene, GABRA1 the human one; they are separate records with different experiments attached (14 vs 94 SectionDataSets at time of writing). An exact-match query with the wrong casing returns a clean empty array. Both gene tools retry case-insensitively and set casing_note saying so, rather than reporting a silent zero.

Over-filtering a SectionDataSet query empties it silently. Adding products[id$eq1] to a gene with no Mouse-Brain-ISH series returns total_rows: 0 with success: true — not an error. Product and plane filters here are optional, and when a filtered query comes back empty the pack re-runs it unfiltered and reports the unfiltered total, so a zero reads as "your filter excluded everything" rather than "this gene has no expression data".

Encode the whole criteria value. RMA criteria contain [, ], $ and '. encodeURIComponent over the entire expression works; passing brackets raw works from a browser but is eaten by a shell and by some HTTP clients, which produces an empty result that looks like an API outage. (That is exactly how this pack's first probe failed.)

success: true with msg: [] is the normal shape of "no rows". A rejected query is success: false with the error in msg — the pack raises on that, so the two are never conflated.

Structure graphs are per-species. graph_id 1 is adult mouse, 10 human, 17 developing mouse. A human region is not in the mouse graph; the default is 1, and an empty result says which graph was searched.

Quick Start

Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):

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

What this endpoint actually serves

tools/list at https://gateway.pipeworx.io/allen-brain/mcp returns the tools in the table above plus the shared Pipeworx meta-tools — askpipeworx, discovertools, search_within, remember/recall and the rest of the gateway-wide set. So the tool count you see is larger than this table: a single-pack endpoint currently lists roughly 30 shared tools alongside the pack's own. The connection's initialize response states its exact scope, and is the authoritative answer for a given day.

Shortened. The full README is on GitHub.