@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

• allen_search_genes(acronym?, name_contains?, entrez_id?, organism?, num_rows?, start_row?) — gene symbol / name / Entrez ID → the Allen internal gene id and organism.

• allen_structures(acronym?, name_contains?, structure_id?, graph_id?, num_rows?, start_row?) — brain region name or acronym → structure id, parent, and the root-to-leaf structure_id_path that establishes containment.

• allen_expression_datasets(gene_acronym, plane_of_section?, product_id?, include_failed?, num_rows?, start_row?) — the ISH experiments (SectionDataSets) for a gene: atlas product, plane of section, section thickness, and the dataset id behind an Allen figure.

Related MCP server: Allen Brain API MCP Server

Auth

Keyless.

Data sources

• https://api.brain-map.org/api/v2/data/query.json — the RMA query endpoint; every tool here is one RMA expression against it (model::Gene, model::Structure, model::SectionDataSet).

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 — ask_pipeworx, discover_tools, 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.

This is deliberate, not multiplexing by accident. The meta-tools are what let a scoped connection answer a question this pack does not cover — via ask_pipeworx, which routes across the whole catalog — without you adding a second MCP server. There is currently no way to mount a pack endpoint without them; if the extra schemas cost you more context than the routing is worth, connect to the full gateway once rather than to several pack endpoints.

Or connect to the full Pipeworx gateway to get every pack's tools listed directly, instead of just this one's:

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

Both URLs reach the same gateway and the same 1679+ data sources. The only difference is which pack's tools are listed directly; ask_pipeworx reaches all of them from either one.

No MCP client? Call it over HTTP

curl -X POST https://gateway.pipeworx.io/v1/tools/allen_search_genes \
  -H 'Content-Type: application/json' \
  -d '{"acronym":"Gabra1"}'

No account needed for the first calls. Inspect any tool: GET https://gateway.pipeworx.io/v1/tools/allen_search_genes. Find one: POST https://gateway.pipeworx.io/v1/tools/search_packs with {"query":"..."}.

Standalone (no gateway account)

This package also runs as a local stdio MCP server — no Pipeworx account, no gateway round-trip:

{
  "mcpServers": {
    "allen-brain": {
      "command": "npx",
      "args": ["-y", "@pipeworx/mcp-allen-brain"]
    }
  }
}

Or run it directly to confirm it starts:

npx -y @pipeworx/mcp-allen-brain

It speaks MCP over stdin/stdout and answers initialize/tools/list/tools/call for only this pack's tools — none of the shared meta-tools the gateway connection above adds. Same source, same tools, no ask_pipeworx routing.

Using with ask_pipeworx

Instead of calling tools directly, you can ask questions in plain English — this works on the pack endpoint above as well as on the full gateway:

ask_pipeworx({ question: "your question about Allen Brain data" })

The gateway picks the right tool and fills the arguments automatically.

More

• Docs and guides

• pipeworx.io

License

MIT