Selecting and processing an ROI

First create a registered maximum-Z projection with fuse. ROI selection uses its calibrated world coordinates.

Draw a rectangle

uv run display "/path/to/processed"

Draw one rectangle in the napari processing ROI layer and close the viewer to save it. The default destination is <stem>_roi.json beside the data. --roi-output PATH selects another destination. ROI mode requires fused-max-z; use --no-roi for other display modes.

Process the selected raw region

uv run process-ROI "/path/to/processed"

The command resolves the raw acquisition through the processing journal, reads the saved ROI, processes its raw-data regions, and fuses the cropped tiles. Keep the source acquisition accessible. Deconvolution and resume are enabled by default; output goes to <stem>_roi in the input directory.

Supply the raw acquisition, ROI, and destination explicitly when needed:

uv run process-ROI "/path/to/raw.ome.zarr" "/path/to/selection_roi.json" --output "/path/to/roi-output"

Resume or restart

Rerun the same command after interruption. Compatible completed tile/channel checkpoints are reused; unfinished writes are processed again. Use --no-resume to overwrite the ROI output. --crop-after-deskew is inapplicable because this workflow already writes the selected physical crop.

To restrict fusion of existing processed tiles without reprocessing the raw data, use fuse --roi PATH. See the display and process-ROI references.