run_command

MCP tool from Fiji ImageJ MCP by surajinacademia

Run one resolved installed command with supported parameters or options.

How to use it

Project documentation lists run_command for the Fiji ImageJ MCP MCP server. Add the server to your MCP client (Claude Desktop, Cursor, Windsurf and others), then check which tools your installed version makes available. Tool availability can depend on configuration and credentials. A server handshake does not verify this tool’s behavior. See the full listing for setup details.

Install Fiji ImageJ MCP

$/absolute/path/to/fiji-mcp-server
FULL FIJI IMAGEJ MCP LISTING

Other tools in Fiji ImageJ MCP (8)

compare_screenshots

Compare two saved raster paths visually and, when sizes match, numerically.

get_results

Read an ordered, paginated page from Fiji's live Results table.

get_state

Read Fiji lifecycle, active/open images, and Results-table state.

open_image

Open an existing local image and make it current.

run_script

Run one trusted IJM or Groovy script.

save_image

Save the active image to a new exact lowercase supported path.

screenshot

Return and optionally save a PNG of the active plane or Results.

search_commands

Search registered SciJava and ImageJ1 commands and inspect their routes.