Command-line interface

The SegSpy CLI segments an image file end-to-end and writes results to disk:

SegSpy run image.dm4 --backend traditional_cv --output ./out

This produces:

• out/image_particles.csv — one row per particle with all morphology metrics.

• out/image_labeled.png — the source-sized canvas with each particle’s mask drawn in a distinct colour.

Options

Option	Default	Purpose
file	(required)	Path to an EM image readable by HyperSpy (.dm4, .tif, …)
--backend	traditional_cv	Segmentation backend name (traditional_cv, sam)
--output	output	Output directory (created if missing)
--min-area	100	Minimum particle contour area in pixels
--no-grabcut	(flag)	Disable GrabCut refinement (traditional backend)

The CLI auto-detects TEM/SEM from the file’s metadata (same logic as from_signal). For anything beyond these flags — custom SAM thresholds, CLAHE tuning — use the library API from the quickstart.