# AIND Metadata MCP Server
[](LICENSE)
[](https://github.com/semantic-release/semantic-release)
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.
## Features
This MCP server provides tools for:
- **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
## Installation
Install uv if you haven't already - following [this documentation](https://docs.astral.sh/uv/getting-started/installation/)
Install the MCP server using uv:
```bash
uv tool install aind-metadata-mcp
```
Or using pip:
```bash
pip install aind-metadata-mcp
```
## Configuration
### For Cline (VSCode Extension)
In order to ensure that the MCP server runs in your preferred client, you will have to download the `aind-metadata-mcp` package to your console. If space is an issue, please set `UV_CACHE_DIR` and `UV_TOOL_DIR` to locations that have capacity before proceeding with the next step.
1. Simpler version of install
Run `uv tool install aind-metadata-mcp` on your terminal and proceed below to configuring your MCP clients.
2. If the above step didn't work:
Create virtual environment with python 3.11 in IDE
```bash
# 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.
```bash
pip install uv
uvx aind-metadata-mcp
```
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!
### Cursor IDE
1. Install the MCP server:
```bash
uv tool install aind-metadata-mcp
```
2. Create the MCP configuration file:
```bash
mkdir -p ~/.cursor
```
3. Create `~/.cursor/mcp.json` with the following content:
```json
{
"mcpServers": {
"aind-data-access": {
"command": "aind-metadata-mcp",
"args": [],
"env": {}
}
}
}
```
4. **Important**: Replace `aind-metadata-mcp` with the full path if needed:
```bash
which aind-metadata-mcp
```
Use the full path (e.g., `/Users/username/.local/bin/aind-metadata-mcp`) in the `command` field.
5. 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.
## Instructions for use in MCP clients
JSON Config files to add MCP servers in clients should be structured like this
```bash
{
"mcpServers": {
}
}
```
Insert the following lines into the mcpServers dictionary
```bash
"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.
### Claude Desktop App
- Click the three lines at the top left of the screen.
- File > Settings > Developer > Edit config
### Cline in VSCode
- 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
### Github Copilot in VSCode
- Command palette (ctr shift p)
- Search for MCP: Add server
- Select `Manual Install` / `stdio`
- When prompted for a command, input `uvx 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
### For use in Code Ocean
* Locate the [following capsule](https://codeocean.allenneuraldynamics.org/capsule/7008682/tree), to spin up Cline and Co-pilot with the aind-metadata-mcp pre-installed.
* Refer the the [code ocean MCP server](https://github.com/codeocean/codeocean-mcp-server) for additional support
* Either pin version 4.2, or 4.5
