Enumerate Fiji/ImageJ commands from SciJava CommandService and legacy ij.Menus. Large installs return thousands of entries; lower limit for faster responses.

Search installed commands by substring on name/class, plus fuzzy title matching. Use before describe_plugin to find the exact menu label.

Resolve one command by name and return SciJava input metadata when available. Legacy ImageJ1-only plugins may omit inputs; use run_macro in that case.

List configured ImageJ update sites (name and URL) when the updater classes are present. May return an empty list on minimal installs; see note field.

List open image windows with id, title, dimensions, and ImageJ type constant.

Read dimensions, channel/frame/slice counts, bit depth, and ROI statistics for one image. Uses the front image when image_title is omitted.

Return runtime health: Fiji path, headless/GUI mode, ImageJ version, and configured operation timeout. Use before long jobs to confirm the bridge is alive.

Execute ImageJ1 macro text in the current Fiji session. Returns macro return value and a tail of the ImageJ log. Prefer small, focused macros; increase timeout for heavy I/O.

Open an image from disk in Fiji and show it as the active window. Verify the path exists on the MCP host before calling.

Save the currently active image to disk using ImageJ's saveAs. Requires an image window to be frontmost in Fiji.

Run several macros in sequence. On failure, behavior depends on continue_on_error: either stop or record the error and continue. Each successful step returns the same shape as run_macro.

Capture pixels for verification: full_screen (primary monitor via Robot), active_image (current ImagePlus), or results_table (render Measure/Results data). Use active_image or results_table when running headless without a display.

Turn macro return text or a pasted Results snippet into structured JSON: detected format, key/value map, tabular rows, and/or extracted numbers. Prefer macros that return a small JSON or key=value string for best results.

Compare two screenshot_fiji payloads (before/after). Returns mean absolute error and RMSE on aligned grayscale patches plus a side-by-side JPEG for quick visual diff.

List bundled macro snippets (filters, segmentation, Z-project, channels, optional Fiji plugins) with stable ids. Filter by category: filters, process, segment, analyze, image, annotate, channels, stack, plugins.

Fetch one bundled macro template by id (from list_macro_templates).

Return recent tool invocations (run_macro, open_image, …) in order plus optional live open-image list. Trace is in-process only (resets when the MCP server restarts).

Clear the in-process session trace (does not close Fiji images).

Run a scripted pipeline: each step runs a macro, optionally followed by a screenshot. Supports MCP progress when the client requests it. Use verify_each_step=false for faster runs.