# Fiji MCP Server

> Use this tool when you need to automate microscopy image analysis tasks, such as image processing and particle analysis, through natural language commands. The Fiji MCP Server enables AI agents to control Fiji/ImageJ, supporting operations like image opening and filtering, and automating workflows. It takes natural language inputs and outputs processed images and analysis results, ideal for streamlining image analysis pipelines and workflows.

Canonical page: https://skillsregistry.net/skills/surajinacademia-fiji-imagej-mcp  
JSON: https://api.skillsregistry.net/v1/skills/surajinacademia-fiji-imagej-mcp

## Description

Enables AI agents to control Fiji/ImageJ for microscopy image analysis through natural language commands, supporting operations like image opening, filtering, particle analysis, and automated workflows.

## Trust

- **Trust score (0–1):** 0.87
- **Verification tier:** verified
- **Last scanned:** 2026-09-19

## Facts

- **Version:** 1.0.0
- **Skill type:** atomic
- **Execution layer:** mcp-remote
- **Runtime environment:** api
- **Category:** media
- **Updated:** 2026-09-19

## Source

- **Source listing:** [Glama](https://glama.ai/mcp/servers/j60ivtoe01)
- **Repository:** <https://github.com/surajinacademia/Fiji_imageJ_mcp>

## Use it

Resolve this record through the SkillsRegistry MCP server (no auth, read-only):

```
claude mcp add --transport http --scope user skillsregistry https://api.skillsregistry.net/mcp
```

```json
{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "get_skill",
    "arguments": {
      "slug": "surajinacademia-fiji-imagej-mcp"
    }
  }
}
```

REST: `GET https://api.skillsregistry.net/v1/skills/surajinacademia-fiji-imagej-mcp` · pull for local use: `GET https://api.skillsregistry.net/v1/skills/surajinacademia-fiji-imagej-mcp/pull`

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SkillsRegistry indexes agent skills from public registries and GitHub. Skills we have analysed are scanned with Circle-IR and scored on six dimensions; each listing states its scan coverage. More: https://skillsregistry.net/llms.txt