How do I install the fiji mcp server?

Use a recorded configuration for your client, replace example credential values and paths, and verify the documented runtime. Restart or reconnect the client, then inspect the available tools.

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Fiji MCP Server

See how it can look here: https://bsky.app/profile/nkiaru.bsky.social/post/3lrvofh64n225

Local serverstdioPython

What is the Fiji MCP Server?

See how it can look here: https://bsky.app/profile/nkiaru.bsky.social/post/3lrvofh64n225

More MCP options

Compare MCP servers by category, or browse hosted MCP servers if you prefer an endpoint over a local process.

Maintainer setup documentation.

Recorded tools

Check the linked publisher documentation and your connected client's tool list. Names and availability can vary with the server version and account permissions.

Tool	What it does
fiji-tools	(Java) contains a few functions that facilitates the comminucation with a LLM. The GUI for coding (editor) is easily accessible to a user, but not to a bot
fiji_mcp	(Python) simple wrapper of Fiji functions, exposed as tools for the MCP server

How to install the Fiji MCP Server

{
  "mcpServers": {
    "fiji_mcp": {
      "command": "uv",
      "args": [
        "--directory",
        "C:/Users/Nicolas/PycharmProjects/fiji_mcp",
        "run",
        "main.py"
      ]
    }
  }
}

From the project documentation. Replace placeholders and example paths before connecting.

Example prompts to try

“Use Fiji MCP to fiji-tools.”
“Use Fiji MCP to fiji mcp.”

Frequently asked questions

See how it can look here: https://bsky.app/profile/nkiaru.bsky.social/post/3lrvofh64n225 Confirm the tools offered by your installed version in the connected client. Tool availability and permissions depend on the server and account configuration.