# Allen Brain (npm · @pipeworx/mcp-allen-brain)

Gene expression experiments and the brain structure ontology from the Allen Institute's Brain…

- Trust score: 81/100 (high trust)
- Change this week: +3
- Registry status: active
- Liveness: live
- Owner verified: no
- Last scored: 2026-11-05

## Components

- remote · `gateway.pipeworx.io`: 65/100, [markdown](https://verifymcp.io/servers/pipeworx-io-allen-brain/allen-brain-mcp.md), [page](https://verifymcp.io/servers/pipeworx-io-allen-brain/allen-brain-mcp)
- npm · `@pipeworx/mcp-allen-brain`: 81/100 (this document), [markdown](https://verifymcp.io/servers/pipeworx-io-allen-brain/pipeworx-mcp-allen-brain.md), [page](https://verifymcp.io/servers/pipeworx-io-allen-brain/pipeworx-mcp-allen-brain)

## Channel facts

- Registry: `npm`
- Package: `@pipeworx/mcp-allen-brain`
- Version: `0.2.1`
- Transport: `stdio`

## Trust breakdown

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. Scores are 0–100 per category. Scoring method: https://verifymcp.io/docs/scoring (what has changed: https://verifymcp.io/docs/scoring/changelog)

Scored 2026-11-05.

- **Supply Chain Security**: 100/100
  - No malware found by supply-chain analysis.
  - No known CVEs affecting this package version or its production dependencies.
  - No install/post-install scripts declared.
  - No production dependencies, so there is no dependency health to assess.
- **Provenance & Transparency**: 97/100
  - Source repository is publicly reachable at the declared URL.
  - Cryptographically verified build provenance (signed, bound to pipeworx-io/mcp-allen-brain).
  - Clear OSI-approved license (MIT).
  - Actively maintained (last published 5 days ago).
  - Security-disclosure policy not yet verified: we couldn't inspect the source repository.
- **Schema Quality & AI Usability**: 60/100
  - AI-judged instruction clarity (good).
  - 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.
  - Usage-examples check failed: none of the tools include examples.
- **Stability & Change Management**: 23/100
  - Stability observed for 7 of 30 days with no destabilising changes; credit accrues until the full window elapses.
- **Tool Coverage**: 100/100
  - 100% of tools have a non-trivial description (not blank, and not just the tool's name).
  - 100% of tool parameters carry a description.
- **Tool Safety**: 100/100
  - No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.
  - We read all 3 captured tool definition(s), and no name or description among them implies an irreversible operation.
  - An AI judge read all 4 captured unit(s) of tool text and found none that tries to manipulate the model reading it.
- **Capabilities**: 100/100
  - Implements a supported MCP spec version (2025-11-25); the latest is 2026-07-28.

## Install

### 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.

### Claude

```bash
claude mcp add pipeworx-io-allen-brain -- npx -y @pipeworx/mcp-allen-brain
```

### Cursor

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

### VS Code

```json
{
  "servers": {
    "pipeworx-io-allen-brain": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-allen-brain"
      ]
    }
  }
}
```

### Codex

```bash
codex mcp add pipeworx-io-allen-brain -- npx -y @pipeworx/mcp-allen-brain
```

### opencode

```json
{
  "$schema": "https://opencode.ai/config.json",
  "mcp": {
    "pipeworx-io-allen-brain": {
      "type": "local",
      "command": [
        "npx",
        "-y",
        "@pipeworx/mcp-allen-brain"
      ],
      "enabled": true
    }
  }
}
```

### OpenClaw

```bash
openclaw mcp add pipeworx-io-allen-brain --command npx --arg -y --arg @pipeworx/mcp-allen-brain
```

### Hermes

```yaml
mcp_servers:
  pipeworx-io-allen-brain:
    command: "npx"
    args: ["-y", "@pipeworx/mcp-allen-brain"]
```

### Netclaw

```json
{
  "McpServers": {
    "pipeworx-io-allen-brain": {
      "Transport": "stdio",
      "Command": "npx",
      "Arguments": [
        "-y",
        "@pipeworx/mcp-allen-brain"
      ]
    }
  }
}
```

### Vellum

```bash
assistant mcp add pipeworx-io-allen-brain -t stdio -c npx -a -y @pipeworx/mcp-allen-brain
```

### Other

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

## Changelog

Every change recorded for this component, newest first. Days that predate change tracking, or that we cannot explain, say so: "we were watching and nothing happened" and "we were not watching" are different claims.

### 2026-11-05 (score 81, 0)

- [functional regression] Security disclosure: fail → unverified

### 2026-11-03 (score 81, +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.

### 2026-11-01 (score 80, +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.

### 2026-10-30 (score 79, +1)

- [functional regression] Security disclosure: unverified → fail
- [functional improvement] Stability: unverified → 0.03
- [functional] Package version: 0.2.0 → 0.2.1

### 2026-10-29 (score 78)

First indexed and scored.

## MCP tools (3)

### `allen_search_genes` (~270 tokens)

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.

Input parameters:

- `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).

### `allen_structures` (~244 tokens)

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.

Input parameters:

- `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).

### `allen_expression_datasets` (~292 tokens)

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.

Input parameters:

- `gene_acronym` (string, required): 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).

## Diagnostics

Captured diagnostic sections: Provenance, Dependencies. The full working is on the page: https://verifymcp.io/servers/pipeworx-io-allen-brain/pipeworx-mcp-allen-brain#diagnostics

## Score history

- 2026-11-05: 81
- 2026-11-04: 81
- 2026-11-03: 81
- 2026-11-02: 80
- 2026-11-01: 80
- 2026-10-31: 79
- 2026-10-30: 79
- 2026-10-29: 78

## Common questions

### 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.

## Links

- npm package: https://www.npmjs.com/package/@pipeworx/mcp-allen-brain
- Socket report: https://socket.dev/npm/package/@pipeworx/mcp-allen-brain
- Repository: https://github.com/pipeworx-io/mcp-allen-brain
- Website: https://pipeworx.io/packs/allen-brain
- Changelog RSS feed: https://verifymcp.io/servers/pipeworx-io-allen-brain/pipeworx-mcp-allen-brain.xml
- Changelog JSON feed: https://verifymcp.io/servers/pipeworx-io-allen-brain/pipeworx-mcp-allen-brain.json
- HTML version of this page: https://verifymcp.io/servers/pipeworx-io-allen-brain/pipeworx-mcp-allen-brain