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🪐🔧 Jupyter MCP Server

An MCP server developed for AI to connect and manage Jupyter Notebooks in real-time

Developed by Datalayer

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[!NOTE] We Need Your Feedback!

We're actively developing support for JupyterHub and Google Colab deployments. If you're using or planning to use Jupyter MCP Server with these platforms, we'd love to hear from you!

• 🏢 JupyterHub users: Share your deployment setup and requirements
• 🌐 Google Colab users: Help us understand your use cases and workflows

Join the conversation in our Community page - your feedback will help us prioritize features and ensure these integrations work seamlessly for your needs.

📖 Table of Contents

• Key Features
• MCP Overview
• Getting Started
• Best Practices
• Contributing
• Resources

🚀 Key Features

• ⚡ Real-time control: Instantly view notebook changes as they happen.
• 🔁 Smart execution: Automatically adjusts when a cell run fails thanks to cell output feedback.
• 🧠 Context-aware: Understands the entire notebook context for more relevant interactions.
• 📊 Multimodal support: Support different output types, including images, plots, and text.
• 📚 Multi-notebook support: Seamlessly switch between multiple notebooks.
• 🎨 JupyterLab integration: Enhanced UI integration like automatic notebook opening.
• 🤝 MCP-compatible: Works with any MCP client, such as Claude Desktop, Cursor, Windsurf, and more.

Compatible with any Jupyter deployment (local, JupyterHub, ...) and with Datalayer hosted Notebooks.

🔧 MCP Overview

🔧 Tools Overview

The server provides a rich set of tools for interacting with Jupyter notebooks, categorized as follows. For more details on each tool, their parameters, and return values, please refer to the official Tools documentation.

Server Management Tools

Name	Description
list_files	List files and directories in the Jupyter server's file system.
list_kernels	List all available and running kernel sessions on the Jupyter server.
connect_to_jupyter	Connect to a Jupyter server dynamically without restarting the MCP server. Not available when running as Jupyter extension. Useful for switching servers dynamically or avoiding hardcoded configuration. Read more

Multi-Notebook Management Tools

Name	Description
use_notebook	Connect to a notebook file, create a new one, or switch between notebooks.
list_notebooks	List all notebooks available on the Jupyter server and their status
restart_notebook	Restart the kernel for a specific managed notebook.
unuse_notebook	Disconnect from a specific notebook and release its resources.
read_notebook	Read notebook cells source content with brief or detailed format options.

Cell Operations and Execution Tools

Name	Description
read_cell	Read the full content (Metadata, Source and Outputs) of a single cell.
insert_cell	Insert a new code or markdown cell at a specified position.
delete_cell	Delete a cell at a specified index.
overwrite_cell_source	Overwrite the source code of an existing cell.
execute_cell	Execute a cell with timeout, supports multimodal output including images.
insert_execute_code_cell	Insert a new code cell and execute it in one step.
execute_code	Execute code directly in the kernel, supports magic commands and shell commands.

JupyterLab Integration

Available only when JupyterLab mode is enabled. It is enabled by default.

When running in JupyterLab mode, Jupyter MCP Server integrates with jupyter-mcp-tools to expose additional JupyterLab commands as MCP tools. By default, the following tools are enabled:

Name	Description
notebook_run-all-cells	Execute all cells in the current notebook sequentially
notebook_get-selected-cell	Get information about the currently selected cell

<details> <summary><strong>📚 Learn how to customize additional tools</strong></summary>

You can now customize which tools from jupyter-mcp-tools are available using the allowed_jupyter_mcp_tools configuration parameter. This allows you to enable additional notebook operations, console commands, file management tools, and more.

# Example: Enable additional tools via command-line
jupyter lab --port 4040 --IdentityProvider.token MY_TOKEN --JupyterMCPServerExtensionApp.allowed_jupyter_mcp_tools="notebook_run-all-cells,notebook_get-selected-cell,notebook_append-execute,console_create"

For the complete list of available tools and detailed configuration instructions, please refer to the Additional Tools documentation.

</details>

📝 Prompt Overview

The server also supports prompt feature of MCP, providing a easy way for user to interact with Jupyter notebooks.

Name	Description
jupyter-cite	Cite specific cells from specified notebook (like @ in Coding IDE or CLI)

For more details on each prompt, their input parameters, and return content, please refer to the official Prompt documentation.

🏁 Getting Started

For comprehensive setup instructions—including Streamable HTTP transport, running as a Jupyter Server extension and advanced configuration—check out our documentation. Or, get started quickly with JupyterLab and STDIO transport here below.

1. Set Up Your Environment

pip install jupyterlab==4.4.1 jupyter-collaboration==4.0.2 jupyter-mcp-tools>=0.1.4 ipykernel
pip uninstall -y pycrdt datalayer_pycrdt
pip install datalayer_pycrdt==0.12.17

[!TIP] To confirm your environment is correctly configured:

1. Open a notebook in JupyterLab
2. Type some content in any cell (code or markdown)
3. Observe the tab indicator: you should see an "×" appear next to the notebook name, indicating unsaved changes
4. Wait a few seconds—the "×" should automatically change to a "●" without manually saving

This automatic saving behavior confirms that the real-time collaboration features are working properly, which is essential for MCP server integration.

2. Start JupyterLab

# Start JupyterLab on port 8888, allowing access from any IP and setting a token
jupyter lab --port 8888 --IdentityProvider.token MY_TOKEN --ip 0.0.0.0

[!NOTE] If you are running notebooks through JupyterHub instead of JupyterLab as above, refer to our JupyterHub setup guide.

3. Configure Your Preferred MCP Client

Next, configure your MCP client to connect to the server. We offer two primary methods—choose the one that best fits your needs:

• 📦 Using uvx (Recommended for Quick Start): A lightweight and fast method using uv. Ideal for local development and first-time users.
• 🐳 Using Docker (Recommended for Production): A containerized approach that ensures a consistent and isolated environment, perfect for production or complex setups.

<details> <summary><b>📦 Using uvx (Quick Start)</b></summary>

First, install uv:

pip install uv
uv --version
# should be 0.6.14 or higher

See more details on uv installation.

Then, configure your client:

{
  "mcpServers": {
    "jupyter": {
      "command": "uvx",
      "args": ["jupyter-mcp-server@latest"],
      "env": {
        "JUPYTER_URL": "http://localhost:8888",
        "JUPYTER_TOKEN": "MY_TOKEN",
        "ALLOW_IMG_OUTPUT": "true"
      }
    }
  }
}

</details>

<details> <summary><b>🐳 Using Docker (Production)</b></summary>

On macOS and Windows:

{
  "mcpServers": {
    "jupyter": {
      "command": "docker",
      "args": [
        "run", "-i", "--rm",
        "-e", "JUPYTER_URL",
        "-e", "JUPYTER_TOKEN",
        "-e", "ALLOW_IMG_OUTPUT",
        "datalayer/jupyter-mcp-server:latest"
      ],
      "env": {
        "JUPYTER_URL": "http://host.docker.internal:8888",
        "JUPYTER_TOKEN": "MY_TOKEN",
        "ALLOW_IMG_OUTPUT": "true"
      }
    }
  }
}

On Linux:

{
  "mcpServers": {
    "jupyter": {
      "command": "docker",
      "args": [
        "run", "-i", "--rm",
        "-e", "JUPYTER_URL",
        "-e", "JUPYTER_TOKEN",
        "-e", "ALLOW_IMG_OUTPUT",
        "--network=host",
        "datalayer/jupyter-mcp-server:latest"
      ],
      "env": {
        "JUPYTER_URL": "http://localhost:8888",
        "JUPYTER_TOKEN": "MY_TOKEN",
        "ALLOW_IMG_OUTPUT": "true"
      }
    }
  }
}

</details>

[!TIP]

1. Port Configuration: Ensure the port in your Jupyter URLs matches the one used in the jupyter lab command. For simplified config, set this in JUPYTER_URL.
2. Server Separation: Use JUPYTER_URL when both services are on the same server, or set individual variables for advanced deployments. The different URL variables exist because some deployments separate notebook storage (DOCUMENT_URL) from kernel execution (RUNTIME_URL).
3. Authentication: In most cases, document and runtime services use the same authentication token. Use JUPYTER_TOKEN for simplified config or set DOCUMENT_TOKEN and RUNTIME_TOKEN individually for different credentials.
4. Notebook Path: The DOCUMENT_ID parameter specifies the path to the notebook the MCP client default to connect. It should be relative to the directory where JupyterLab was started. If you omit DOCUMENT_ID, the MCP client can automatically list all available notebooks on the Jupyter server, allowing you to select one interactively via your prompts.
5. Image Output: Set ALLOW_IMG_OUTPUT to false if your LLM does not support mutimodel understanding.

For detailed instructions on configuring various MCP clients—including Claude Desktop, VS Code, Cursor, Cline, and Windsurf — see the Clients documentation.

✅ Best Practices

• Interact with LLMs that supports multimodal input (like Gemini 2.5 Pro) to fully utilize advanced multimodal understanding capabilities.
• Use a MCP client that supports returning image data and can parse it (like Cursor, Gemini CLI, etc.), as some clients may not support this feature.
• Break down complex task (like the whole data science workflow) into multiple sub-tasks (like data cleaning, feature engineering, model training, model evaluation, etc.) and execute them step-by-step.
• Provide clearly structured prompts and rules (👉 Visit our Prompt Templates to get started)
• Provide as much context as possible (like already installed packages, field explanations for existing datasets, current working directory, detailed task requirements, etc.).

🤝 Contributing

We welcome contributions of all kinds! Here are some examples:

• 🐛 Bug fixes
• 📝 Improvements to existing features
• 🔧 New feature development
• 📚 Documentation improvements and prompt templates

For detailed instructions on how to get started with development and submit your contributions, please see our Contributing Guide.

Our Contributors

📚 Resources

Looking for blog posts, videos, or other materials about Jupyter MCP Server?

👉 Visit the Resources section in our documentation for more!

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If this project is helpful to you, please give us a ⭐️

Made with ❤️ by Datalayer

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