Allen Brain
NPM · @PIPEWORX/MCP-ALLEN-BRAIN · 2 COMPONENTS
Gene expression experiments and the brain structure ontology from the Allen Institute's Brain…
Available components
Last scanned (20 minutes ago)
Scores higher than 69% of npm servers
Category Health and Science
How this component scores in each security and reliability category. Every signal is checked automatically from public evidence about the published package, including repeated runs of it in an isolated sandbox, and we only credit what we can confirm. How we score → Why this is hard to score →
Supply Chain Security100
- No malware found by supply-chain analysis.Pass
- No known CVEs affecting this package version or its production dependencies.Pass
- No install/post-install scripts declared.Pass
- No production dependencies, so there is no dependency health to assess. View diagnostics → Pass
Provenance & Transparency97
- Source repository is publicly reachable at the declared URL. View diagnostics → Pass
- Cryptographically verified build provenance (signed, bound to pipeworx-io/mcp-allen-brain). View diagnostics → Pass
- Clear OSI-approved license (MIT).Pass
- Actively maintained (last published 5 days ago).Pass
- Security-disclosure policy not yet verified: we couldn't inspect the source repository.Unverified
Schema Quality & AI Usability60
- AI-judged instruction clarity (good).Pass
- Context-footprint check failed: tool/resource definitions use about 861 tokens (~287/item across 3 items; 3 tools + 0 resources), over budget; trim descriptions and params. See how to fix → Fail
- Usage-examples check failed: none of the tools include examples. See how to fix → Fail
Stability & Change Management23
- Stability observed for 7 of 30 days with no destabilising changes; credit accrues until the full window elapses.Partial
Tool Coverage100
- 100% of tools have a non-trivial description (not blank, and not just the tool's name).Pass
- 100% of tool parameters carry a description.Pass
Tool Safety100
- No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.Pass
- We read all 3 captured tool definition(s), and no name or description among them implies an irreversible operation.Pass
- An AI judge read all 4 captured unit(s) of tool text and found none that tries to manipulate the model reading it.Pass
Capabilities100
- Implements a supported MCP spec version (2025-11-25); the latest is 2026-07-28.Pass
Every change we have recorded for this component, newest first. Security-relevant changes are always shown. ▲ marks a change for the better, ▼ a change for the worse; unmarked changes are neutral.
- 5 Nov 26 0
- Security disclosure: fail → unverified ▼ functional
- 3 Nov 26 +1
No change was recorded against any check on this day. Stability & Change Management went from 13 to 17. That category is still filling its 30-day observation window: 4 days of observed history at the previous scan, 5 at this one. The score rises as the window fills, whether or not the server changes.
- 1 Nov 26 +1
No change was recorded against any check on this day. Stability & Change Management went from 7 to 10. That category is still filling its 30-day observation window: 2 days of observed history at the previous scan, 3 at this one. The score rises as the window fills, whether or not the server changes.
- 30 Oct 26 +1
- Security disclosure: unverified → fail ▼ functional
- Stability: unverified → 0.03 ▲ functional
- Package version: 0.2.0 → 0.2.1 functional
- 29 Oct 26 78
First indexed and scored.
Diagnostic detail from the automated scan of this channel: what the scanner observed at each step, so you can see exactly where a check passed or failed. It is informational only and never changes the trust score.
Captured 5 Nov 2026 · Analysed npm/@pipeworx/mcp-allen-brain@0.2.1
Provenance Verified
A signed build attestation was found and verified, binding this exact artifact to the source repository it claims to come from.
| Result | Verified |
|---|---|
| Ecosystem | npm |
| Reason | Verified |
| Discovered via | Registry attestation endpoint |
| Source repo | pipeworx-io/mcp-allen-brain |
| Certificate issuer | https://token.actions.githubusercontent.com |
| Certificate SAN | https://github.com/pipeworx-io/mcp-allen-brain/.github/workflows/publish.yml@refs/heads/main |
| Rekor log index | 3587916145 |
| Predicate type | SLSA build provenance https://slsa.dev/provenance/v1 |
| Subject digest | sha512:17fd2bf04f8d80314e4eb79aa4ffb4255e03f206ac4d38e81b98162be7aaee34a96fbaa25878e3139925a09dc9144e63baa4f3a5ffcde52a80e86cab5 |
Background: How many MCP packages publish verified provenance →
Dependencies 0 packages
| Packages resolved | 0 |
|---|---|
| Tree resolution | Complete |
Background: SBOMs and build attestations, explained →
The tools this component advertises to a client, with an estimated token cost for each. Expand a tool to see its parameters and schema. The per-tool counts are indicative and are not scored directly; the schema's total context footprint is one signal in Schema Quality & AI Usability. A tool's description is untrusted text the model reads on every call, which is what makes this list a security surface and not just an inventory: how tool poisoning works →
allen_expression_datasets ~292
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.
| Name | Type | Req | 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. |
| include_failed | boolean | – | Include experiments Allen flagged as failed QC (default false). |
| num_rows | number | – | Rows to return, 1-200 (default 25). |
| plane_of_section | string | – | Optional filter: "coronal" or "sagittal". Omit for both — filtering can empty an otherwise non-empty result. |
| product_id | number | – | 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. |
| start_row | number | – | 0-based offset for paging (default 0). |
No output schema declared.
No examples provided.
allen_search_genes ~270
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.
| Name | Type | Req | Description |
|---|---|---|---|
| acronym | string | – | Exact gene symbol, e.g. "Gabra1" (mouse) or "GABRA1" (human). Case matters for the exact match; matching is retried case-insensitively and the response says which casing hit. |
| entrez_id | number | – | NCBI Entrez Gene ID, e.g. 14394. |
| name_contains | string | – | Substring of the gene name, e.g. "dopamine receptor". Case-insensitive. |
| num_rows | number | – | Rows to return, 1-200 (default 25). |
| organism | string | – | Filter results to "mouse", "human", or omit for both. |
| start_row | number | – | 0-based offset for paging (default 0). |
No output schema declared.
No examples provided.
allen_structures ~244
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.
| Name | Type | Req | Description |
|---|---|---|---|
| acronym | string | – | Exact structure acronym, e.g. "CA1", "VISp", "SNr". |
| graph_id | number | – | Structure graph to search. 1 = adult mouse brain (default), 10 = human brain, 17 = developing mouse. |
| name_contains | string | – | Substring of the structure name, e.g. "hippocamp", "visual area". Case-insensitive. |
| num_rows | number | – | Rows to return, 1-200 (default 25). |
| start_row | number | – | 0-based offset for paging (default 0). |
| structure_id | number | – | Allen structure id, e.g. 382 (Field CA1). |
No output schema declared.
No examples provided.
How do I install the Allen Brain MCP server?
Allen Brain runs locally as an npm package, launched with npx -y @pipeworx/mcp-allen-brain. Ready-made configuration for Claude, Cursor, VS Code, Codex and 5 more is on this page, copied from each client's own documentation.
npm · @pipeworx/mcp-allen-brain
claude mcp add pipeworx-io-allen-brain -- npx -y @pipeworx/mcp-allen-brain
What is the Allen Brain MCP server?
Allen Brain is an MCP server listed in the public MCP registry as io.github.pipeworx-io/allen-brain. Gene expression experiments and the brain structure ontology from the Allen Institute's Brain… This page covers its npm package (@pipeworx/mcp-allen-brain).
Is the Allen Brain MCP server safe to use?
Allen Brain scores 81 out of 100 on VerifyMCP. We found no known CVEs affecting it as of 5 November 2026. It declares no install or post-install scripts. Its build provenance is signed and verified. That is a record of what we were able to check automatically, not an endorsement. The category breakdown on this page shows every signal behind the number, including the ones we could not confirm.
What tools does the Allen Brain MCP server expose?
Allen Brain exposes 3 tools: allen_search_genes, allen_structures, allen_expression_datasets. Their descriptions and schemas cost roughly 806 tokens of context every time the server is loaded.
Is the Allen Brain MCP server still maintained?
Allen Brain is still listed as active in the MCP registry. We last reached this channel on 5 November 2026. Those dates come from our own scans of the registry and the channel itself, not from anything the publisher announced.
What licence is the Allen Brain MCP server under?
Allen Brain declares the MIT licence, which is OSI-approved. That covers the source only, and says nothing about the cost of any service it calls.