fiji-mcp-server

fiji-mcp-server is an MCP server for Claude Code, Codex, Cursor, Gemini CLI, OpenCode from surajinacademia/Fiji_imageJ_mcp. Its token cost is not measured, scanned A, original, BSD-3-Clause.

A local MCP server that lets an AI control Fiji/ImageJ, an open-source tool for scientific image processing. It accepts commands and scripts and can work with images and results.

In plain words
What is it for?
It helps run Fiji/ImageJ commands, execute IJM or Groovy scripts, and handle images and processing results.
Why use it?
It removes the need to switch between the coding assistant and Fiji/ImageJ for supported image-processing tasks.

MCP server for Claude CodeCodexCursorGemini CLIOpenCode

Written for no agent in particular: it speaks MCP, so any client can run it.

Good fit It helps run Fiji/ImageJ commands, execute IJM or Groovy scripts, and handle images and processing results.

Compare 6 mcp servers from other repositories ↓
Install with agentmods
npx agentmods add mcp/surajinacademia/fiji_imagej_mcp/fiji-mcp-server
Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Clone the repo
git clone --depth 1 https://github.com/surajinacademia/Fiji_imageJ_mcp

Made for: Claude Code, Codex, Cursor, Gemini CLI, OpenCode.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for fiji-mcp-server

README.md
[![agentmods](https://agentmods.dev/badge/mcp/surajinacademia/fiji_imagej_mcp/fiji-mcp-server/github.svg)](https://agentmods.dev/mcp/surajinacademia/fiji_imagej_mcp/fiji-mcp-server)
Your own site
<a href="https://agentmods.dev/mcp/surajinacademia/fiji_imagej_mcp/fiji-mcp-server"><img src="https://agentmods.dev/badge/mcp/surajinacademia/fiji_imagej_mcp/fiji-mcp-server/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for fiji-mcp-server

Your own site · 80×15
<a href="https://agentmods.dev/mcp/surajinacademia/fiji_imagej_mcp/fiji-mcp-server"><img src="https://agentmods.dev/badge/mcp/surajinacademia/fiji_imagej_mcp/fiji-mcp-server.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session not measured What this adds to a session before it is invoked.
When invoked not measured Not applicable: nothing here is loaded into a session.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin original No closer match found in the catalogue.
Security

Grade A, and why

fiji-mcp-server scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 11d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

listed in the official MCP registry · 8 lines

What it actually says

{ "fiji-mcp-server": { "command": "uvx", "args": [ "fiji-mcp-server" ] } }

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 11d ago First seen · 8 lines scan A d23de1b02063

Subscribe to this mod's changes

fiji-mcp-server is an MCP server published in the GitHub repository surajinacademia/Fiji_imageJ_mcp (2 stars, last pushed 15d ago), licensed BSD-3-Clause. Its token cost is not measured: an MCP server costs its tool schemas, not its config file. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.