How do I connect Fiji ImageJ MCP Server to Claude?

The listing records `/absolute/path/to/fiji-mcp-server` as its setup step. Run it, then follow the repository's instructions for the client configuration; the listing names Claude Desktop, Claude Code, ChatGPT as compatible clients.

Is Fiji ImageJ MCP Server free?

The listed licence is BSD-3-Clause. Check the upstream terms for permitted use and commercial requirements; a public repository does not by itself mean the software is free or open source. Connected APIs and hosted services may have separate charges.

What can Fiji ImageJ MCP Server do?

Fiji ImageJ MCP Server documents 9 tools to the agent, including compare_screenshots, get_results, get_state. The descriptions above come from project documentation. A live handshake does not test individual tool behavior.

Fiji ImageJ MCP

Unclaimed

by surajinacademia

Enable AI agents to use Fiji/ImageJ for microscopy image analysis

Install

$/absolute/path/to/fiji-mcp-server

Set up this server

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This server needs project-specific setup. Follow the project instructions; no reusable public launch command is available yet.

Project instructions

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Security profile

Claimed and verified servers get a weekly static scan that shows what the code can reach: external services, environment variables, shell commands, agent configuration folders, plus any dependencies with known advisories. Claim this listing to get one. How the security profile works

9 of 9 tools

Documented tools (9)

From project documentation. A server handshake does not verify each tool’s description or behavior.

compare_screenshots

Compare two saved raster paths visually and, when sizes match, numerically.

get_results

Read an ordered, paginated page from Fiji's live Results table.

get_state

Read Fiji lifecycle, active/open images, and Results-table state.

open_image

Open an existing local image and make it current.

run_command

Run one resolved installed command with supported parameters or options.

run_script

Run one trusted IJM or Groovy script.

save_image

Save the active image to a new exact lowercase supported path.

screenshot

Return and optionally save a PNG of the active plane or Results.

search_commands

Search registered SciJava and ImageJ1 commands and inspect their routes.

Tool change history

Compared across complete checks of the same configuration. Tools were listed, not invoked. Input-schema changes are not measured here.

No complete tool checks yet.

FAQ

Questions about Fiji ImageJ MCP Server

How do I connect Fiji ImageJ MCP Server to Claude?: The listing records `/absolute/path/to/fiji-mcp-server` as its setup step. Run it, then follow the repository's instructions for the client configuration; the listing names Claude Desktop, Claude Code, ChatGPT as compatible clients.
Is Fiji ImageJ MCP Server free?: The listed licence is BSD-3-Clause. Check the upstream terms for permitted use and commercial requirements; a public repository does not by itself mean the software is free or open source. Connected APIs and hosted services may have separate charges.
What can Fiji ImageJ MCP Server do?: Fiji ImageJ MCP Server documents 9 tools to the agent, including compare_screenshots, get_results, get_state. The descriptions above come from project documentation. A live handshake does not test individual tool behavior.