process-ROI¶
Process the raw region selected by display, then fuse its tiles. Accepts a raw
acquisition or processed-output directory, followed by an optional ROI JSON path.
Defaults to <stem>_roi.json, deconvolution enabled, and <stem>_roi output.
| Option | Description |
|---|---|
--no-deconvolve |
Disable deconvolution. |
--no-resume |
Overwrite ROI output; completed tiles/channels are resumed by default. |
--output PATH |
Set the ROI output directory. |
--registration-channel VALUE |
Select the zero-based registration channel; default 0. |
--crop-after-deskew |
Unsupported for ROI processing, which already writes a physical crop. |
Also accepts the process options --flatfield-correction, --save-float32,
--z-downsample-level, --decon-crop-scan, --decon-gpu-id, --decon-verbose,
and --decon-psf-paths.
uv run process-ROI "/path/to/acquisition" "/path/to/selection_roi.json" --output "/path/to/roi-output"
Append --help to list all options and defaults.