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Cline Integration

Setup guide for using napari MCP server with Cline - the powerful AI coding assistant available as extensions for both VS Code and Cursor IDE.

🚀 Quick Setup

For VS Code

# 1. Install napari-mcp
pip install napari-mcp

# 2. Auto-configure Cline in VS Code
napari-mcp-install cline-vscode

# 3. Restart VS Code (or reload window)

For Cursor IDE

# 1. Install napari-mcp
pip install napari-mcp

# 2. Auto-configure Cline in Cursor
napari-mcp-install cline-cursor

# 3. Restart Cursor

📍 Configuration Locations

Cline in VS Code

  • macOS: ~/Library/Application Support/Code/User/globalStorage/saoudrizwan.claude-dev/settings/cline_mcp_settings.json
  • Windows: %APPDATA%/Code/User/globalStorage/saoudrizwan.claude-dev/settings/cline_mcp_settings.json
  • Linux: ~/.config/Code/User/globalStorage/saoudrizwan.claude-dev/settings/cline_mcp_settings.json

VS Code Insiders

For VS Code Insiders, replace Code with Code - Insiders in the path.

Cline in Cursor IDE

  • macOS: ~/Library/Application Support/Cursor/User/globalStorage/saoudrizwan.claude-dev/settings/cline_mcp_settings.json
  • Windows: %APPDATA%/Cursor/User/globalStorage/saoudrizwan.claude-dev/settings/cline_mcp_settings.json
  • Linux: ~/.config/Cursor/User/globalStorage/saoudrizwan.claude-dev/settings/cline_mcp_settings.json

💡 Why Use Cline with napari?

  • Powerful AI Assistant: Advanced coding capabilities with full napari control
  • VS Code Integration: Leverages VS Code's powerful editing features
  • Tool Permissions: Fine-grained control over which tools to allow
  • Project Context: Understands your workspace and files
  • Live Visualization: See napari visualizations as you develop

🧪 Testing

After configuration, open the Cline extension and test:

Can you call session_information() to show the napari session?

Load images from ./data/ folder into napari

💻 Development Workflows

Image Processing Development

Create a Python script that applies Gaussian blur to images in ./input/ and saves to ./output/

Help me debug why this segmentation isn't working as expected

Napari Plugin Development

Help me create a napari widget for interactive thresholding

Test this plugin code and show the results in napari

Batch Processing

Process all TIFF files in this directory with the filter pipeline we discussed

Create visualizations for each processing step

🔧 Manual Configuration

The CLI installer creates configurations with these features:

Basic Configuration

{
  "mcpServers": {
    "napari-mcp": {
      "command": "uv",
      "args": ["run", "--with", "napari-mcp", "napari-mcp"],
      "alwaysAllow": [],
      "disabled": false
    }
  }
}

With Tool Permissions

You can pre-approve specific tools to skip confirmation prompts:

{
  "mcpServers": {
    "napari-mcp": {
      "command": "uv",
      "args": ["run", "--with", "napari-mcp", "napari-mcp"],
      "alwaysAllow": ["screenshot", "list_layers", "session_information"],
      "disabled": false
    }
  }
}

Using Persistent Environment

{
  "mcpServers": {
    "napari-mcp": {
      "command": "python",
      "args": ["-m", "napari_mcp.server"],
      "always Allow": [],
      "disabled": false
    }
  }
}

⚙️ Tool Permissions

Cline supports configuring which tools can be called without confirmation:

  • alwaysAllow: List of tool names that don't require confirmation
  • disabled: Set to true to temporarily disable the server

Recommended for alwaysAllow: - session_information - Safe read-only operation - list_layers - Safe read-only operation - screenshot - Safe read-only operation

Use caution with: - execute_code - Runs arbitrary Python code - install_packages - Installs packages via pip

🛠️ Management

# Check installation status
napari-mcp-install list

# Update VS Code configuration
napari-mcp-install cline-vscode --force

# Update Cursor configuration
napari-mcp-install cline-cursor --force

# Uninstall
napari-mcp-install uninstall cline-vscode
# or
napari-mcp-install uninstall cline-cursor

❌ Troubleshooting

Cline Doesn't See napari MCP

MCP server not appearing

Solutions:

  1. Verify Cline extension is installed:
  2. VS Code: Check Extensions panel

  3. Cursor: Check Extensions panel

  4. Check installation: 

    napari-mcp-install list

  5. Open Cline MCP settings:

  6. Click the MCP icon in Cline extension

  7. Verify napari-mcp appears in server list

  8. Restart editor:

  9. VS Code: Reload window (Cmd/Ctrl + Shift + P → "Reload Window")

  10. Cursor: Completely restart

  11. Reinstall: 

    napari-mcp-install cline-vscode --force
# or
napari-mcp-install cline-cursor --force

Wrong IDE Detected

Configured for wrong IDE

Problem: Accidentally used cline-vscode instead of cline-cursor (or vice versa)

Solution: Uninstall and reinstall for correct IDE:

# Uninstall wrong one
napari-mcp-install uninstall cline-vscode

# Install correct one
napari-mcp-install cline-cursor

VS Code Insiders

Config not found in VS Code Insiders

Solution: The path is different for Insiders. Manually create config at:

  • macOS: ~/Library/Application Support/Code - Insiders/User/globalStorage/saoudrizwan.claude-dev/settings/cline_mcp_settings.json
  • Windows: %APPDATA%/Code - Insiders/User/globalStorage/saoudrizwan.claude-dev/settings/cline_mcp_settings.json
  • Linux: ~/.config/Code - Insiders/User/globalStorage/saoudrizwan.claude-dev/settings/cline_mcp_settings.json

🔐 Security Considerations

  • Cline runs with your user permissions
  • The alwaysAllow list bypasses confirmation prompts - use carefully
  • Code execution tools (execute_code, install_packages) should require confirmation
  • Never add untrusted tools to alwaysAllow

📚 Next Steps

📖 Learn More About Cline

→ Back to Integrations Overview