ImageJ / Fiji
About
An MCP server for ImageJ/Fiji, implemented as a Python wrapper for Fiji functions.
Details
- Author
- nicokiaru
- Categories
- Developer Tools, Other
- Tags
- #bioinformatics
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Setup
Install ImageJ / Fiji in your MCP client (Claude Desktop, Cursor, Windsurf, and others).
Repository: https://github.com/nicokiaru/fiji_mcp
Follow the installation instructions in the repository README, then restart your MCP client.
Proof of concept - MCP server for ImageJ / Fiji
See how it can look here:https://bsky.app/profile/nkiaru.bsky.social/post/3lrvofh64n225
This repo contains a basic MCP server for ImageJ/Fiji. It consists of 2 repositories:
- 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
To get this server working with Claude Desktop, you can add this in the configuration:
{"mcpServers": { "fiji_mcp": { "command": "uv", "args": [ "--directory", "C:/Users/Nicolas/PycharmProjects/fiji_mcp", "run", "main.py" ] } } }
The jar from fiji-tools has to be built - it's only available as SNAPSHOT at the moment.
<groupId>ch.epfl.biop</groupId> <artifactId>fiji-tools</artifactId> <version>0.1.0-SNAPSHOT</version>
Note that the jvm path has to be hardcoded in the Pythonmain.pycode:
# Entry point to run the server if __name__ == "__main__": import os os.environ['JAVA_HOME'] = r'C:\Users\Nicolas\.jdks\corretto-11.0.24' os.environ['PATH'] = r'C:\Users\Nicolas\.jdks\corretto-11.0.24\bin;' + os.environ.get('PATH', '')
Otherwise in the context where Claude Desktop is executed, the jvm cannot be found.
This is a web browser that enables your coding agent, such as Claude Code, to visit websites on your behalf and assist you in identifying bugs or creating UI test cases.
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