process

Calibrate and deskew an acquisition, optionally deconvolving it. Saves uint16 output beside the acquisition by default.

Option	Description
--deconvolve	Apply RLGC deconvolution before deskewing.
--flatfield-correction	Correct uneven illumination.
--save-float32	Preserve fractional intensities in float32 output.
--skip-empty-below VALUE	Zero channel tiles with insufficient signal above this intensity.
--skip-empty-min-signal-fraction VALUE	Required fraction above the cutoff; default 0.01.
--resume	Continue compatible completed tiles; otherwise overwrite output.
--output PATH	Set the output directory.
--live PATH	Process during acquisition using a supplied CYX illumination TIFF; pass the acquisition directory.
--time-range START STOP	Select timepoints.
--pos-range START STOP	Select positions.
--z-downsample-level VALUE	Deskewed Z reduction factor; default 2.
--crop-after-deskew	Crop Y to the region supported across all Z planes.
--no-max-projection	Disable per-tile and stage-placed maximum-Z images.
--no-create-fused-max-projection	Disable the stage-placed maximum-Z mosaic.
--write-fused-max-projection-tiff	Also save that mosaic as OME-TIFF.
--decon-crop-scan VALUE	Set scan planes per deconvolution chunk; default automatic.
--decon-gpu-id VALUE	Select the CUDA device; default 0.
--decon-verbose VALUE	Set solver verbosity; 0 suppresses iteration reports.
--decon-fallback-step-scan VALUE	Set chunk reduction after GPU allocation failure.
--decon-psf-paths PATH	Supply channel-ordered PSFs; repeat for each channel.
--decon-scan-upsample VALUE	Experimental 3D scan upsampling; requires deconvolution and full-volume GPU memory.
--eager-mode	Enable eager stopping for planar deconvolution.

uv run process "/path/to/acquisition" --deconvolve --flatfield-correction

Append --help to list all options and defaults.