AIND Data MCP Server

Code Style Interrogate Coverage Python

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

{
    "servers": {
        "aind-data-mcp": {
            "url": "https://metadata-portal.allenneuraldynamics.org/mcp/",
            "type": "http"
        }
    },
    "inputs": []
}

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 .

Metadata

Release files for aind-data-mcp 0.4.14

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for aind-data-mcp 0.4.14
File	Size	Uploaded
aind_data_mcp-0.4.14.tar.gz	28.5 kB	Sep 1, 2026	Details

Built distribution (wheel)

Table of built distributions (wheels) for aind-data-mcp 0.4.14
File	Interpreter	ABI	Platform	Reset
aind_data_mcp-0.4.14-py3-none-any.whl 27.2 kB Sep 1, 2026	Python 3	none	any	Details

Total release size: 55.7 kB

Release files / aind_data_mcp-0.4.14.tar.gz

Download URL	aind_data_mcp-0.4.14.tar.gz
Size	28.5 kB
Tags	Source
SHA-256 checksum How to use checksums	`6bc85ef0002a5cbe3147bfd0bab01355dcff38fb8e649f4e318ff0651d719b33`
BLAKE2b-256 checksum How to use checksums	`5aaebaac4294290a6ada6fd5a68b77066c6acd35b204a56d9f3d2d3f1bcd70fb`
Upload date	Sep 1, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/7.0.0 CPython/3.13.14`

Release files / aind_data_mcp-0.4.14-py3-none-any.whl

Download URL	aind_data_mcp-0.4.14-py3-none-any.whl
Size	27.2 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`63d81000e5ab8d9ba0e84d15d33764b1353f082dafb4472a8686d3792f0e675a`
BLAKE2b-256 checksum How to use checksums	`9436b55776ac0e02ccfb1da93228a158677e9c67311287f7f1cda64cd7a376b9`
Upload date	Sep 1, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/7.0.0 CPython/3.13.14`