fiji-mcp-server 0.1.3

Model Context Protocol (MCP) server for Fiji/ImageJ: macros, discovery, screenshots, and workflows via PyImageJ

Fiji MCP Server

Talk to Fiji / ImageJ in plain English from Cursor, Claude, Gemini, Windsurf, and more.

Open images, run any ImageJ plugin, count cells, measure features, take screenshots to verify — without writing a single line of macro code yourself.

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See it in action

"Open the image, apply a Gaussian blur, show me before and after."

Before	After

"Threshold the bright spots, outline each object, report area and circularity."

Input	Outlined objects

#	Area	Circularity
1	1052	0.89
2	2840	0.72
3	641	0.91
4	1902	0.68

"Skeletonize the mask and summarize branches per tree."

Mask	Skeleton

Tree	Branches	Junctions
1	14	6
2	9	7

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Get started in 3 steps

1 — Install

pip install fiji-mcp-server

You need Python 3.10+, Fiji installed on your machine, and Java (required by PyImageJ). See quickstart if anything needs clarification.

2 — Connect to your AI app

Replace /Applications/Fiji with your actual Fiji folder (the one containing jars/ and plugins/).

App	One command
Claude Desktop	fiji-mcp-install install claude-desktop --fiji-path /Applications/Fiji
Cursor	fiji-mcp-install install cursor --fiji-path /Applications/Fiji
Claude Code	fiji-mcp-install install claude-code --fiji-path /Applications/Fiji
Gemini CLI	fiji-mcp-install install gemini --fiji-path /Applications/Fiji
Windsurf	fiji-mcp-install install windsurf --fiji-path /Applications/Fiji

Then restart the app.

3 — Verify it works

In chat, type:

Run the Fiji MCP health_check tool

You should get back the Fiji version and mode. First startup takes 30–90 seconds while the JVM loads — that's normal.

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What to ask

Once connected, just describe what you want:

"Open ./images/cells.tif and tell me the dimensions."

"Apply a Gaussian blur with sigma 4 and show me the result."

"Count the bright objects and give me their areas."

"Search for ImageJ commands related to 'threshold'."

"Open the image, subtract background, threshold, count particles — show me a screenshot after each step."

No macro knowledge needed. The assistant finds the right Fiji plugin, runs it, and can show you a screenshot to verify.

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Available tools (19 total)

Category	Tools
Run & I/O	health_check run_macro run_batch_macros open_image save_image
Screenshots	screenshot_fiji — full screen, active image, or results table
Discover plugins	list_all_commands search_commands describe_plugin list_extensions
Image info	list_open_images get_image_info
Workflows	run_workflow — chain steps with screenshot verification
Results	parse_macro_output compare_screenshots list_macro_templates get_macro_template
Session	get_session_trace clear_session_trace

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Documentation

Quick start	Install, configure, verify — step by step
All tools	What every tool does and when to use it
Configuration	Environment variables and troubleshooting
Architecture	How the pieces fit together

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Author: Suraj Sahu · UC Merced Physics · [e-mail]

Related: cellpose_mcp · PyImageJ · FastMCP

License: BSD-3-Clause