🚀 Jupyter MCP Server

🚀 Jupyter MCP Server

A comprehensive Model Context Protocol (MCP) server that bridges AI agents with Jupyter notebooks, enabling real-time code execution, visualization generation, and advanced image extraction capabilities.

🎯 About This Project

This project is a fork and enhancement of the original Jupyter MCP Server developed by Datalayer, Inc.. Special thanks to the Datalayer team for their foundational work on integrating Jupyter with the Model Context Protocol ecosystem.

Key Enhancements in This Fork:

• Improved documentation and setup process
• Enhanced error handling and robustness
• Additional example configurations
• Streamlined installation and configuration
• Updated dependencies and compatibility

🌟 Key Features

🎯 Real-Time Jupyter Integration

• Live Code Execution: Execute Python code in real-time through WebSocket connections
• Kernel Management: Automatic kernel creation, lifecycle management, and cleanup
• Session Persistence: Maintain state across multiple operations

🖼️ Advanced Image Extraction

• Multi-Format Support: Extract PNG and JPEG images from matplotlib, seaborn, plotly
• Base64 Encoding: Ready-to-use image data for AI processing
• Comprehensive Output Handling: Text, images, errors, and execution results

📚 Complete Notebook Management

• File Operations: Create, delete, switch between multiple notebooks
• Cell Manipulation: Add, modify, move, delete cells with full CRUD operations
• Content Management: Support for both markdown and code cells

🛡️ Enterprise-Ready Security

• Smart XSRF Handling: Automatic token detection and management
• Authentication Support: Compatible with tokenized Jupyter servers
• Error Recovery: Graceful fallbacks for connection issues

🏗️ Architecture

graph TD
    A[AI Agent/Claude] --> B[MCP Server]
    B --> C[Jupyter Server API]
    B --> D[WebSocket Channels]
    C --> E[Kernel Management]
    D --> F[Real-time Execution]
    F --> G[Output Capture]
    G --> H[Image Extraction]
    G --> I[Text Processing]
    B --> J[Notebook Files]

🛠️ 18 Comprehensive Tools

📝 Cell Content Management

• add_execute_code_cell - Execute Python code with real-time output
• add_markdown_cell - Add formatted documentation
• modify_cell - Edit existing cell content
• change_cell_type - Convert between markdown and code cells

🖼️ Output Extraction

• get_cell_image_output - Extract base64-encoded images (PNG/JPEG)
• get_cell_text_output - Get all text outputs including errors and tracebacks

🗂️ Notebook File Operations

• create_notebook - Create new notebook files
• delete_notebook - Remove notebook files safely
• switch_notebook - Change active notebook
• list_notebooks - Browse available notebooks

🔍 Data Discovery

• list_cells - Overview of all cells with preview
• read_cell - Full content of specific cells
• get_notebook_info - Comprehensive notebook metadata

View complete tool documentation →

🚀 Quick Start

Prerequisites

• Python 3.11+
• Jupyter Notebook
• Claude Desktop or compatible MCP client

Installation

1. Clone the repository

   git clone https://github.com/JosephLin11/jupyter-mcp-server.git
   cd jupyter-mcp-server
   

2. Install dependencies

   pip install -r requirements.txt
   

3. Start Jupyter Server

   ./scripts/start_jupyter.sh
   

4. Configure Claude Desktop Add to your claude_desktop_config.json:

   {
     "mcpServers": {
       "jupyter": {
         "command": "python",
         "args": ["/path/to/your/jupyter-mcp-server/src/jupyter_mcp_server.py"]
       }
     }
   }
   

   💡 Tip: Run python3 scripts/get_claude_config.py to generate the correct configuration with current paths!

💡 Example Use Cases

📊 Data Visualization Pipeline

# 1. Create and execute visualization code
add_execute_code_cell(cell_content="""
import matplotlib.pyplot as plt
import numpy as np
import seaborn as sns

# Generate sample data
data = np.random.normal(0, 1, 1000)

# Create beautiful visualization
plt.figure(figsize=(12, 8))
plt.subplot(2, 2, 1)
plt.hist(data, bins=50, alpha=0.7, color='skyblue')
plt.title('Distribution Analysis')

plt.subplot(2, 2, 2)
sns.boxplot(y=data)
plt.title('Box Plot Analysis')

plt.tight_layout()
plt.show()
""")

# 2. Extract the generated image
get_cell_image_output(cell_index=0)

🧪 Scientific Computing

# 3D surface visualization
add_execute_code_cell(cell_content="""
from mpl_toolkits.mplot3d import Axes3D
import numpy as np
import matplotlib.pyplot as plt

fig = plt.figure(figsize=(12, 9))
ax = fig.add_subplot(111, projection='3d')

# Create mesh
x = np.linspace(-5, 5, 100)
y = np.linspace(-5, 5, 100)
X, Y = np.meshgrid(x, y)
Z = np.sin(np.sqrt(X**2 + Y**2))

# Render surface
surface = ax.plot_surface(X, Y, Z, cmap='plasma', alpha=0.9)
ax.set_title('3D Mathematical Function')
plt.colorbar(surface)
plt.show()
""")

# Extract 3D visualization
get_cell_image_output(cell_index=1)

🏆 Technical Highlights

Advanced WebSocket Implementation

• Real-time bidirectional communication with Jupyter kernels
• Comprehensive message type handling (execute_result, display_data, stream, error)
• Automatic reconnection and fallback mechanisms

Smart Output Processing

• Multi-format image extraction (PNG, JPEG) with base64 encoding
• Structured output capture preserving metadata
• Error handling with full traceback support

Robust Security Model

• Automatic XSRF token detection and management
• Multiple authentication endpoint support
• Graceful degradation for different Jupyter configurations

Enterprise-Grade Error Handling

• Comprehensive logging with configurable levels
• Fallback execution modes for reliability
• Resource cleanup and connection management

📊 Comparison with Alternatives

Feature	This Implementation	jjsantos01 MCP	Cursor MCP
Tools Available	🏆 18 tools	10 tools	8-10 tools
Image Extraction	🏆 PNG + JPEG	PNG only	None
Setup Complexity	🏆 Automatic	Manual browser init	CLI args
Version Support	🏆 All Jupyter versions	Jupyter 6.x only	Version agnostic
Real-time Execution	🏆 WebSocket + HTTP	WebSocket bridge	File-only
Security Handling	🏆 Auto XSRF	Basic	Enhanced

🧪 Testing

Run the comprehensive test suite:

# Test image extraction capabilities
python tests/test_image_extraction.py

# Test notebook operations  
python tests/test_notebook_save.py

📁 Project Structure

jupyter-mcp-server/
├── src/
│   └── jupyter_mcp_server.py      # Main MCP server implementation
├── notebooks/                     # 📓 All Jupyter notebooks are created here
│   └── mcp_notebook.ipynb         # Default notebook for MCP operations
├── tests/
│   ├── test_image_extraction.py   # Image extraction tests
│   └── test_notebook_save.py      # Notebook operation tests
├── scripts/
│   ├── start_jupyter.sh           # Jupyter server startup script
│   └── get_claude_config.py       # Claude configuration generator
├── examples/
│   ├── claude_desktop_config.json # Example configuration
│   ├── mcp_notebook.ipynb         # Example notebook
│   └── new_notebook.ipynb         # Sample notebook
├── docs/
│   ├── MCP_TOOLS_SUMMARY.md       # Complete tool reference
│   ├── SETUP.md                   # Setup guide
│   └── IMAGE_EXTRACTION_README.md # Image extraction guide
├── requirements.txt               # Python dependencies
├── pyproject.toml                 # Project configuration
└── README.md                      # Project documentation

🤝 Contributing

Contributions are welcome! Please follow these steps:

1. Fork the repository
2. Create a feature branch (git checkout -b feature/amazing-feature)
3. Commit your changes (git commit -m 'Add amazing feature')
4. Push to the branch (git push origin feature/amazing-feature)
5. Open a Pull Request

📄 License

This project is licensed under the BSD 3-Clause License - see the LICENSE file for details.

🌟 Acknowledgments

• Original Development: Datalayer, Inc. for creating the foundational Jupyter MCP Server
• Inspired by the Model Context Protocol ecosystem
• Built upon the robust Jupyter Server API
• Enhanced with ideas from various MCP implementations
• Special thanks to the open-source community

📧 Contact

Joseph Lin - GitHub

Project Link: https://github.com/JosephLin11/jupyter-mcp-server

Original Project: https://github.com/datalayer/jupyter-mcp-server

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