DICOM-MCP

Instructions

Implementation Reference

• src/dicom_mcp/server.py:367-405 (handler)

  MCP tool handler for 'crop-dicom-image'. Retrieves cached DICOM image by series_uid, crops it using crop_image helper with boundary_percentage, caches the result, and returns shape information.

  elif name == "crop-dicom-image":
      series_uid = arguments.get("series_uid")
      boundary_percentage = float(arguments.get("boundary_percentage", 0.2))
      
      if not series_uid or series_uid not in dicom_cache:
          raise ValueError(f"Invalid or not loaded series UID: {series_uid}. Use load-dicom-series first.")
          
      if boundary_percentage <= 0 or boundary_percentage >= 0.5:
          raise ValueError("Boundary percentage must be between 0 and 0.5")
          
      # Get the cached image
      cached_data = dicom_cache[series_uid]
      original_image = cached_data["image"]
      
      # Crop the image
      cropped_image = crop_image(original_image, boundary_percentage)
      
      # Cache the cropped image with a new ID
      cropped_uid = f"{series_uid}_cropped_{int(boundary_percentage*100)}"
      dicom_cache[cropped_uid] = {
          "image": cropped_image,
          "metadata": cached_data["metadata"],
          "original": series_uid,
          "crop_percentage": boundary_percentage
      }
      
      # Return summary information
      original_shape = original_image.shape
      cropped_shape = cropped_image.shape
      
      return [
          types.TextContent(
              type="text",
              text=f"Cropped DICOM image {series_uid} to {cropped_uid}\n" +
                   f"Original shape: {original_shape}\n" +
                   f"Cropped shape: {cropped_shape}\n" +
                   f"Boundary percentage: {boundary_percentage}"
          )
      ]

• src/dicom_mcp/server.py:211-222 (registration)

  Registration of the 'crop-dicom-image' tool in the MCP server's list_tools handler, including name, description, and input schema.

  types.Tool(
      name="crop-dicom-image",
      description="Crop a loaded DICOM image by removing boundary percentage",
      inputSchema={
          "type": "object",
          "properties": {
              "series_uid": {"type": "string", "description": "Series UID of the loaded DICOM image"},
              "boundary_percentage": {"type": "number", "description": "Percentage of image to crop from each boundary (0.0-0.5)"},
          },
          "required": ["series_uid"],
      },
  )

• src/dicom_mcp/dicom_tools.py:255-267 (helper)

  Helper function crop_image that performs the actual image cropping by slicing the numpy array based on boundary percentage.

  def crop_image(image: np.ndarray, boundary_percentage: float = 0.2) -> np.ndarray:
      """Crop an image by removing the specified percentage from each boundary"""
      if boundary_percentage <= 0 or boundary_percentage >= 0.5:
          raise ValueError("Boundary percentage must be between 0 and 0.5")
      
      shape = image.shape
      boundary = [int(s * boundary_percentage) for s in shape]
      
      # Calculate slice indices
      slices = tuple(slice(b, s - b) for b, s in zip(boundary, shape))
      
      # Return cropped image
      return image[slices]