AIND Data MCP Server

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. This server targets the V2 aind-data-schema format.

Installation

Each IDE/client has its own configuration method, look at their documentation for instructions on MCP configuration/setup.

You can either use the command uvx aind-data-mcp to launch the server, or install it locally with uv tool install aind-data-mcp and then launch it with just aind-data-mcp.

For use in Code Ocean

• Refer to the code ocean MCP server for additional support

Features

This MCP server provides the following tools:

Data Retrieval & Querying

• get_records — Query MongoDB collections using filters and projections
• aggregation_retrieval — Execute complex MongoDB aggregation pipelines
• count_records — Count documents matching a filter
• flatten_records — Retrieve and flatten records into dot-notation for easier inspection
• get_project_names — List all project names in the database
• get_summary — Generate an AI-powered summary for a specific data asset

Schema Navigation

• get_top_level_nodes — Explore the top-level fields of the V2 metadata schema
• get_additional_schema_help — Query-writing guidance for V2 aggregations
• get_modality_types — List all available data modality names and abbreviations

Schema Examples (one tool per document type)

• get_acquisition_example, get_data_description_example, get_instrument_example, get_procedures_example, get_subject_example, get_processing_example, get_model_example, get_quality_control_example

NWB File Access

• identify_nwb_contents_in_code_ocean — Load an NWB file from the /data directory in a Code Ocean capsule
• identify_nwb_contents_with_s3_link — Load an NWB file from an S3 path

Resources (accessible via the MCP protocol)

• resource://aind_api — Context and usage patterns for the AIND data access API
• resource://load_nwbfile — Reference script for loading NWB files

Development

To develop the code, run

uv sync --extra dev

To run tests:

uv run coverage run -m unittest discover && uv run coverage report

To run linting:

uv run flake8 . && uv run interrogate --verbose .