# mcp-allen-brain

> mcp-allen-brain — pipeworx-io-mcp-allen-brain. Use this tool when you need to analyze gene expression in the brain or identify brain regions associated with specific genes. It solves problems related to understanding the spatial distribution of gene expression in the brain, leveraging the Allen Institute's Brain Atlas. The tool takes gene queries as input and outputs corresponding brain regions and expression levels, facilitating research in neuroscience and genetics.

Canonical page: https://skillsregistry.net/skills/pipeworx-io-mcp-allen-brain  
JSON: https://api.skillsregistry.net/v1/skills/pipeworx-io-mcp-allen-brain

## Description

Gene expression experiments and the brain structure ontology from the Allen Institute's Brain Atlas — where in the brain a gene is expressed.

## Trust

- **Trust score (0–1):** 0.97
- **Verification tier:** verified
- **Last scanned:** 2026-09-28

## Facts

- **Version:** 1.0.0
- **Skill type:** atomic
- **Execution layer:** container
- **Runtime environment:** vm
- **License:** MIT
- **Updated:** 2026-09-28

## Source

- **Source listing:** [GitHub](https://github.com/pipeworx-io/mcp-allen-brain)

## Use it

Resolve this record through the SkillsRegistry MCP server (no auth, read-only):

```
claude mcp add --transport http --scope user skillsregistry https://api.skillsregistry.net/mcp
```

```json
{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "get_skill",
    "arguments": {
      "slug": "pipeworx-io-mcp-allen-brain"
    }
  }
}
```

REST: `GET https://api.skillsregistry.net/v1/skills/pipeworx-io-mcp-allen-brain` · pull for local use: `GET https://api.skillsregistry.net/v1/skills/pipeworx-io-mcp-allen-brain/pull`

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SkillsRegistry indexes agent skills from public registries and GitHub. Skills we have analysed are scanned with Circle-IR and scored on six dimensions; each listing states its scan coverage. More: https://skillsregistry.net/llms.txt