Fiji_imageJ_mcp

Runs reproducible Fiji/ImageJ batch analysis via the Fiji MCP server—either the bundled MCP-stdio report script or the same tool sequence through an MCP client. Use when generating the comprehensive image analysis report, batch-processing demo_images, driving health_check/open_image/run_macro/search_commands, or when the user mentions Fiji MCP image workflows, microscopy batch reports, or stdio-safe ImageJ macros.

Run Fiji/ImageJ analysis through the Fiji MCP stdio server—env vars (FIJI_PATH, FIJI_MODE, FIJI_MCP_PYTHON, FIJI_DATA_ROOTS), headless MCP, stdio-safe macros without print(), health_check and tool sequencing, optional batch report script from a fiji-mcp-server checkout. Use for Fiji MCP workflows, microscopy batch reports, or MCP/macro config.