MCP server that gives LLM agents a scripting interface into a running Fiji (ImageJ2) instance
Quick Install
Copy the config for your editor. Some servers may need additional setup — check the README.
Add to claude_desktop_config.json:
{
"mcpServers": {
"fiji-mcp": {
"command": "npx",
"args": [
"-y",
"SteffenPL/fiji-mcp"
]
}
}
}
Run in terminal:
claude mcp add fiji-mcp npx -y SteffenPL/fiji-mcp
Add to .cursor/mcp.json:
{
"mcpServers": {
"fiji-mcp": {
"command": "npx",
"args": [
"-y",
"SteffenPL/fiji-mcp"
]
}
}
}