mcp-slicer

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MCP-Slicer connects 3D Slicer with model clients like Claude Desktop or Cline through the Model Context Protocol (MCP), enabling direct interaction and control of 3D Slicer. This integration allows for medical image processing, scene creation, and manipulation using natural language.

1. list_nodes: List and filter Slicer MRML nodes and view their properties

2. execute_python_code: Execute Python code in the Slicer environment

• 3D Slicer 5.8 or newer
• Python 3.13 or newer
• uv package manager

If you're on Mac, please install uv as

brew install uv

On Windows

powershell -c "irm https://astral.sh/uv/install.ps1 | iex"

and then

set Path=C:\Users\nntra\.local\bin;%Path%

Otherwise installation instructions are on their website: Install uv

⚠️ Please install UV first

Go to Claude > Settings > Developer > Edit Config > claude_desktop_config.json to include the following:

{
  "mcpServers": {
    "slicer": {
      "command": "uvx",
      "args": ["mcp-slicer"]
    }
  }
}

{
  "mcpServers": {
    "slicer": {
      "command": "uvx",
      "args": ["mcp-slicer"]
    }
  }
}

1. Open the Slicer Web Server module,
2. ensure the required interfaces are checked,
3. then start the server

What Markups nodes are in the Slicer scene now, list their names, what is their length if it is a line, and what is its angle if it is an angle

Draw a translucent green cube of 8 cm in the Slicer scene, mark its vertices, and then draw a red sphere inscribed in it.

Utilizes existing Slicer Web Server interfaces. For technical details, please see Slicer web server user guide

• The execute_python_code tool allows running arbitrary Python code in 3D Slicer, which is powerful but potentially dangerous.

  ⚠️ Not recommended for production use.

• Complex operations may need to be broken down into smaller steps.

Contributions are welcome! Feel free to submit Pull Requests.

This is a third-party integration project, not developed by the 3D Slicer team.