Command reference

Run commands with uv run from the repository checkout. Each page gives the command's purpose, arguments, options, and an example. Append --help to any command for its installed options and defaults.

Indices are zero-based. Range arguments use an inclusive start and exclusive stop. Supply tuple options as separate values, such as --max-registration-shift-zyx 20 250 100.

Command	Purpose
inspect-opm	Print acquisition metadata.
process	Calibrate, deconvolve, and deskew an acquisition.
fuse	Register and blend processed tiles.
display	View processed images and select an ROI.
process-ROI	Process and fuse a selected raw-data region.
export-ome-tiff	Write fused images as compressed OME-BigTIFF.
export-projections	Write annotated projections and optional movies.
encode-projections	Encode existing projection TIFF sequences.
convert-timelapse	Export raw scan-plane timelapses.