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 the complete typed schema, compact query paths, 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.

Call get_schema_context() for complete root fields, then request a dot-separated branch such as get_schema_context(path="Acquisition.data_streams", max_depth=1) when nested model fields are needed. Use detail="paths" for compact query paths or detail="example" for a synthetic 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 .

To refresh the bundled schema snapshot after updating the dev dependency:

uv run python scripts/generate_schema_tree_snapshot.py

Metadata

Release files for aind-data-mcp 0.4.19

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 0.4.19
File	Size	Uploaded
aind_data_mcp-0.4.19.tar.gz	63.9 kB	Sep 4, 2026	Details

Built distribution (wheel)

Table of built distributions (wheels) for aind-data-mcp 0.4.19
File	Interpreter	ABI	Platform	Reset
aind_data_mcp-0.4.19-py3-none-any.whl 61.7 kB Sep 4, 2026	Python 3	none	any	Details

Total release size: 125.6 kB

Release files / aind_data_mcp-0.4.19.tar.gz

Download URL	aind_data_mcp-0.4.19.tar.gz
Size	63.9 kB
Tags	Source
SHA-256 checksum How to use checksums	`d476f1c50a37d98d55963017449a247da7641a9ce4a42f1a3c0387214999d530`
BLAKE2b-256 checksum How to use checksums	`75ada382bfd317e3f283a345ffc21e5e6426b8c606df03f08ff8d485330a8c46`
Upload date	Sep 4, 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-0.4.19-py3-none-any.whl

Download URL	aind_data_mcp-0.4.19-py3-none-any.whl
Size	61.7 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`81286564fe1fe8b531ab52c5b91b920c60e1c35d82b6d6908d5c1592a82cf1fd`
BLAKE2b-256 checksum How to use checksums	`0d6f4b6c43bd5f7d670810a860d4b852b659e94470f34bfe561345909c7f8136`
Upload date	Sep 4, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/7.0.0 CPython/3.13.14`