nwb-mcp-server 0.1.3
An MCP server for accessing NWB (Neurodata Without Borders) files, providing AI agents with easy access to neuroscience data.
Requires Python: >=3.10

# NWB Model Context Protocol (MCP) Server

An MCP server for accessing NWB (Neurodata Without Borders) files, providing AI agents easy access to neuroscience data.

## Features
- 🚀 Rapid exploration of new datasets
- 🗂️ Automatically-generated analysis reports
- 🧠 Prompt templates instruct agents to get the most from the tools
- 💡 "No Code" mode allows analysis without modifying the local filesystem
- ⚡️ Uses [lazynwb](https://github.com/NeurodataWithoutBorders/lazynwb) for efficient data access across multiple NWB files
- ☁️ Supports local and cloud data (e.g. on AWS S3)
- 🔒 Read-only access to NWB data
- 🛠️ Easy setup

## Requirements

### 1. uv
[`uv`](https://github.com/astral-sh/uv#readme) is used to run the server with the required dependencies, in an isolated virtual environment.

See the [uv installation guide](https://docs.astral.sh/uv/getting-started/installation/) for platform-specific instructions for a system-wide installation.

Alternatively, install with pip in your system Python environment:

```sh
pip install uv
```

> **🛈 Note**
>
> `uv`, like `pip`, is one of the few tools it makes sense to install "globally" to your system
> Python, rather than in a virtual environment, since it is used to manage new virtual environments
> and Python versions.

### 2. Copilot Chat extension 
Available on the [VS Code extensions
marketplace](https://marketplace.visualstudio.com/items?itemName=GitHub.copilot-chat) (in Code
Ocean, this [postInstall file](https://gist.github.com/tmchartrand/0c46bdec6a4205aa7ce7555fd8f4c3b5)
should be used).

> **🛈 Note**
>
> Similar agent extensions, such as Cline or Claude Code, should also be able to connect to the
> server.

## Add server to Copilot Chat in VS Code

![Adding MCP to Copilot Chat](docs/resources/vscode_mcp_json.gif)

- ensure MCP is enabled in the settings UI, or with JSON setting `"chat.mcp.enabled": true`
- the first startup may take a few seconds as it downloads packages

> **🛈 Note**
>
> You may be prompted to choose between adding the server to a "global" or "workspace" config. If you intend
> to switch between datasets it may be preferable to have the `mcp.json` config in your workspace, to
> be able to easily modify the path to your data. The global setting is convenient in that the
> server will be available in all VS Code instances.

### Example `mcp.json`

```json
{
    "servers": {
        "nwb": {
            "command": "uvx",
            "args": [
                "nwb-mcp-server",
                "--root_dir", "data",
                "--glob_pattern", "*.nwb"
            ]
        }
    }
}
```
### Server configuration parameters
| Parameter            | Description                                                                                      | Default        |
|----------------------|--------------------------------------------------------------------------------------------------|----------------|
| root_dir             | Root directory to search for NWB files (forward slash ok on Windows)                             | `"data"`        |
| glob_pattern         | A glob pattern to apply to `root_dir` to locate NWB files. Use `"**/*.nwb"` for sub-directories. | `"*.nwb"`    |
| tables               | Restrict the list of NWB tables to use, e.g. `["trials", "intervals/epochs"]`                            | `null`     |
| infer_schema_length  | Number of NWB files to scan to infer schema for all. Affects server startup time.                       | `1`             |
| unattended           | Run the server in unattended mode (no user prompts, for automation)                              | `false`          |
| table_element_limit  | Max elements (columns x rows) allowed in a table returned by a SQL query                         | `500`            |

### uvx parameters
Any of the following parameters can be added to the `args` list before `nwb-mcp-server` to customize
the environment the server runs in: [uvx
parameters](https://docs.astral.sh/uv/reference/cli/#uv-tool-run)

`--upgrade` is useful to ensure the latest versions of dependencies are used.

> **🛈 Note**
>
> `uvx` is an alias for `uv tool run`, where "tool" means any pip-installable Python package
> that provides a command-line interface.

## Usage

The server provides the tools for querying NWB files efficiently. Getting an agent to use them
effectively requires careful design of the prompt, instructions, and the availability of other
tools. This is a work in progress.

> **🛈 Note**
>
> The server creates a virtual, read-only SQL database from the NWB files, which the agent can
> query. Exploration of a dataset or basic analysis that can be expressed in SQL
> is possible entirely within the chat dialog, without the need for the agent to create and run
> Python scripts in the workspace.

### Prompt templates
Use the provided prompt templates to add preset instructions that specify how the server should be
used (just start typing `/` followed by the name you gave the server):
![Accessing prompt templates](docs/resources/prompt_templates.png)

Feel free to customize the instructions before submitting the prompt.

![Exploring data 0](docs/resources/data_exploration_0.gif)

![Exploring data 1](docs/resources/data_exploration_1.gif)

### Custom chat modes
✨ **Coming soon!** ✨

As an alternative to prompt templates, use custom chat modes provided for data exploration and
analysis:
![VS Code custom chat
modes](https://code.visualstudio.com/assets/docs/copilot/chat/chat-modes/chat-mode-dropdown.png)
See [VS Code docs on custom chat modes](https://code.visualstudio.com/docs/copilot/chat/chat-modes#_custom-chat-modes).

### Non-NWB file support
🚧 **Experimental** 🚧
There is limited support for working with non-NWB files. Any set of files in tabular format than can
be read lazily using a `pl.scan_<format>` function, including parquet and csv, can be used with the
server. The provided prompt templates and chat modes are designed with the NWB format and
the `lazynwb` package in mind, so the agent will receive confusing instructions (although it
usually figures out the correct behavior!)

See the [Polars I/O documentation](https://docs.pola.rs/api/python/stable/reference/io.html)
for a complete list of compatible file formats.