Copick MCP Server

Example Use Cases

• 1

  Explore and query Copick project data in a read-only manner.

• 2

  Discover and validate Copick CLI commands to build processing pipelines.

• 3

  Integrate Copick tools with Claude Desktop or Claude Code environments.

Description

The Copick MCP Server offers read-only data exploration tools to browse and query Copick project contents such as runs, picks, segmentations, meshes, and tomograms. It also provides CLI introspection tools that enable dynamic discovery and validation of Copick CLI commands, facilitating building and validating processing pipelines. The server supports smart caching and easy setup with Claude Desktop and Claude Code, enhancing user experience and integration.