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Allen Brain Atlas MCP

The Allen Brain Atlas MCP server provides tools to query gene expression data and brain structure ontologies from the Allen Institute. It allows agents to search for genes by symbol or ID, resolve brain region names to structure IDs, and list in-situ hybridization experiments for specific genes.

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Package and access

Local package with source-attributed installation metadata. Koskamo does not execute packages during review.

Allen Brain Atlas MCP logo, by PipeworxCommunity listingLocal stdioSource reviewed; not executedPublished by Pipeworx
Vendor documentation

What you can do with it

  • Find genes in the Allen Brain Atlas by symbol, name or Entrez ID
  • Resolve a brain region name or acronym to its Allen structure id and containment path
  • List in-situ hybridization experiments for a gene with atlas product and plane of section

Source and maintenance

Community listingRegistry 0.2.1
mcp-registry: io.github.pipeworx-io/allen-brain@0.2.1Source repositoryProject website
Maintenance checked

Packages and installation

Source-provided package data. Koskamo has not executed or live-probed this package.

@pipeworx/mcp-allen-brain 0.2.1

npm
@pipeworx/mcp-allen-brain package definition
{
  "version": "0.2.1",
  "transport": "stdio",
  "identifier": "@pipeworx/mcp-allen-brain",
  "registryType": "npm",
  "environmentVariables": [
    {
      "name": "PIPEWORX_API_KEY",
      "description": "Optional Pipeworx API key. Without it calls are anonymous and capped daily; a free key raises the cap."
    }
  ]
}

Tools

Reported by the attributed source; not independently observed by Koskamo.

No tool definitions available.

Connect from your client

Each snippet configures the same source-provided package; replace placeholders before use.

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Cursor

Merge this local stdio configuration, replace every placeholder environment value, and restart Cursor. Koskamo has not executed this package.
Cursor configuration
{
  "mcpServers": {
    "allen-brain-atlas-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-allen-brain@0.2.1"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

Cline

Merge this local stdio configuration, replace every placeholder environment value, and restart Cline. Koskamo has not executed this package.
Cline configuration
{
  "mcpServers": {
    "allen-brain-atlas-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-allen-brain@0.2.1"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

VS Code

Merge this local stdio configuration, replace every placeholder environment value, and restart VS Code. Koskamo has not executed this package.
VS Code configuration
{
  "servers": {
    "allen-brain-atlas-mcp": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-allen-brain@0.2.1"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

Claude Desktop

Merge this local stdio configuration, replace every placeholder environment value, and restart Claude Desktop. Koskamo has not executed this package.
Claude Desktop configuration
{
  "mcpServers": {
    "allen-brain-atlas-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-allen-brain@0.2.1"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

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