nwb-mcp-server 0.1.1

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

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 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 is used to run the server with the required dependencies, in an isolated virtual environment.

See the uv installation guide for platform-specific instructions for a system-wide installation.

Alternatively, install with pip in your system Python environment:

pip install uv

2. Copilot Chat extension

Available on the [VS Code extensions marketplace] (https://marketplace.visualstudio.com/items?itemName=GitHub.copilot-chat)

Similar extensions, such as Cline, may also work.

Add server to Copilot Chat in VS Code

• ensure MCP is enabled in settings
• the first startup may take a few seconds as it downloads packages

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", "units"]	null
infer_schema_length	Number of NWB files to scan to infer schema for all files	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