@pipeworx/allen-brain

Connect: https://gateway.pipeworx.io/allen-brain/mcp · Install: one-click buttons

No MCP client? Skip the connection: POST https://gateway.pipeworx.io/v1/tools/search_packs {"query":"..."} to find a tool below, GET /v1/tools/<name> for its schema, POST the same URL with arguments for the data — see For AI agents.

Tools: 3

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.

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.

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.

Tools

• allen_search_genes — Finds genes in the Allen Brain Atlas by symbol, name or Entrez ID, with the organism each record belongs to.
• allen_structures — Resolves a brain region name or acronym to its Allen structure id, parent, and root-to-leaf containment path.
• allen_expression_datasets — Lists the Allen Brain Atlas in-situ hybridization experiments for a gene, with atlas product and plane of section.