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 exact leaf-path projections; optionally return a reproducible result marker
aggregation_retrieval — Execute complex MongoDB aggregation pipelines, including logical aliases for legacy field paths
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_schema_context — Explore compact V2 field paths by node and opt-in small examples
get_modality_types — List all available data modality names and abbreviations

The MCP initialize response includes a ready tool manifest. Use get_schema_context(node="subject", detail="example") only when a compact synthetic example is needed; ordinary path discovery does not load bulky schema examples.

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 0.4.18

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 0.4.18
File	Size	Uploaded
aind_data_mcp-0.4.18.tar.gz	32.1 kB	Sep 3, 2026	Details

Built distribution (wheel)

Table of built distributions (wheels) for aind-data-mcp 0.4.18
File	Interpreter	ABI	Platform	Reset
aind_data_mcp-0.4.18-py3-none-any.whl 29.7 kB Sep 3, 2026	Python 3	none	any	Details

Total release size: 61.8 kB

Release files / aind_data_mcp-0.4.18.tar.gz

Download URL	aind_data_mcp-0.4.18.tar.gz
Size	32.1 kB
Tags	Source
SHA-256 checksum How to use checksums	`c54c414f7a1be403fc6525a520356f785e9a00e1749a3d6044d04ac7c33a1311`
BLAKE2b-256 checksum How to use checksums	`31ec7eecc28c7cc54dd0c18180fc0373f5b65799258c42d0e0ea3586ca5c3e04`
Upload date	Sep 3, 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-0.4.18-py3-none-any.whl

Download URL	aind_data_mcp-0.4.18-py3-none-any.whl
Size	29.7 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`bc513d498a9841ef114718e66b88a0db4b7026c1966d9ed18f52d0b4dd904d94`
BLAKE2b-256 checksum How to use checksums	`d79c7d39a7861e24523e2724e20352c5d2295aba9eb1dad5e1b7940d197db765`
Upload date	Sep 3, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/7.0.0 CPython/3.13.14`