AIND Metadata access MCP server
About
Access and interact with Allen Institute for Neural Dynamics (AIND) metadata directly within your IDE.
Details
- Author
- AllenNeuralDynamics
- Downloads
- 265
- Categories
- Database, Other
Jump to
- Runs via uvx with minimal setup
- Configurable through JSON in MCP client settings
- Works with Claude Desktop App
- Works with Cline in VSCode
Setting up with Highlight
This MCP is not yet compatible with Highlight’s one-click setup. However, you can still use it with Highlight by following these steps:
- Download and install Highlight from highlightai.com/download
- Navigate to the plugins tab and select "Add Custom Plugin"
-
Configure the plugin with the settings below
Plugin Name
AIND Metadata access MCP serverCommand (node, npx, python, etc.)Please refer to the README for specific instructions on how to obtain API keys or other required environment variables.
- Enable "Start Automatically" if you want the plugin to start when Highlight launches
From the repository
Add the provided JSON configuration to your MCP client’s settings. The server is launched with the command uvx and the argument ["aind-metadata-mcp"]. Supported clients include Claude Desktop App and Cline in VSCode.
Claude Desktop / Cursor
Paste into your MCP client config file to install this server.
{
"mcpServers": {
"aind metadata access mcp server": {
"aind_data_access": {
"command": "uvx",
"args": [
"aind-metadata-mcp"
]
}
}
}
}McpServers
{
"aind_data_access": {
"command": "uvx",
"args": [
"aind-metadata-mcp"
]
}
}An MCP (Model Context Protocol) server that provides access to AIND (Allen Institute for Neural Dynamics) metadata and data assets through a comprehensive set of tools and resources.
[!WARNING] This MCP server is deprecated. You can continue using it to access V1 metadata.
For V2 metadata, please seeaind-data-mcp.
- Data Retrieval: Query MongoDB collections with filters and projections
- Aggregation: Execute complex MongoDB aggregation pipelines
- Schema Exploration: Access detailed schema examples and documentation
- NWB File Access: Load and explore NWB (Neurodata Without Borders) files
- Data Summaries: Generate AI-powered summaries of data assets
Install uv if you haven't already - followingthis documentation
In order to ensure that the MCP server runs in your preferred client, you will have to download theaind-metadata-mcppackage to your console. If space is an issue, please setUV_CACHE_DIRandUV_TOOL_DIRto locations that have capacity before proceeding with the next step.
-
Simpler version of install Runuv tool install aind-metadata-mcpon your terminal and proceed below to configuring your MCP clients.
Create virtual environment with python 3.11 in IDE
# Instructions for Conda conda create -n <my_env> python=3.11 conda activate <my_env> # Instructions for virtual environment py -3.11 -m venv .venv # Windows startup .venv\Scripts\Activate.ps1 # Mac/ Linux startup source .venv/bin/activate
Run the following commands in your IDE terminal.
If all goes well, and you see the following notice -Starting MCP server 'aind_data_access' with transport 'stdio'-, you should be good for the set up in your client of choice!
Create~/.cursor/mcp.jsonwith the following content:
{ "mcpServers": { "aind-data-access": { "command": "aind-metadata-mcp", "args": [], "env": {} } } }
Important: Replaceaind-metadata-mcpwith the full path if needed:
Use the full path (e.g.,/Users/username/.local/bin/aind-metadata-mcp) in thecommandfield.
Restart Cursor completely (Cmd+Q then reopen)
Note: Cursor uses a different MCP configuration system than VSCode. The configuration must be in~/.cursor/mcp.json, not in the main settings.json file.
JSON Config files to add MCP servers in clients should be structured like this
Insert the following lines into the mcpServers dictionary
"aind_data_access": { "disabled": false, "timeout": 300, "type": "stdio", "command": "aind-metadata-mcp" }
Note that after configuring the JSON files, it will take a few minutes for the serve to populate in the client.
- Click the three lines at the top left of the screen.
- File > Settings > Developer > Edit config
- Ensure that Cline is downloaded to VScode
- Click the three stacked rectangles at the top right of the Cline window
- Installed > Configure MCP Servers
- Close and reopen VSCode
- Command palette (ctr shift p)
- Search for MCP: Add server
- SelectManual Install/stdio
- When prompted for a command, inputuvx aind-data-access
- Name your server
- Close and reopen VSCode
- In Copilot chat -> Select agent mode -> Click the three stacked rectangles to configure tools
- In order to enable the agent to reply with context of the AIND API, you'll have to manually add the .txt files (under resources) in this repository
- Locate thefollowing capsule, to spin up Cline and Co-pilot with the aind-metadata-mcp pre-installed.
- Refer the thecode ocean MCP serverfor additional support
- Either pin version 4.2, or 4.5
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