First workflow

Start with an acquisition directory containing its raw OME-Zarr store. Commands also accept the store directly where described in their reference. Run from the repository checkout after completing installation.

Inspect and process

Check the recorded dimensions, channels, camera calibration, and scan geometry:

uv run inspect-opm "/path/to/acquisition"

Calibrate and deskew the camera data, applying deconvolution first:

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

Deconvolution requires a working CUDA GPU. Omit --deconvolve to calibrate and deskew without deconvolution. Processed images default to uint16. See the processing guide for output selection and resume.

Register and fuse

uv run fuse "/path/to/acquisition" --registration-channel 0

The channel index is zero-based. Choose a channel with signal in neighboring tile overlaps. Directory selection prefers deconvolved, deskewed data and prints the selected input. The result includes a registered fused volume and maximum-Z projection. See fusion for registration and depth gains.

View or export

View the registered projection without creating an ROI:

uv run display "/path/to/acquisition" --no-roi

Export the highest-resolution fused volume and maximum-Z projection:

uv run export-ome-tiff "/path/to/acquisition"

Open the OME-BigTIFF files through Fiji's Bio-Formats importer. See viewing and exports for larger datasets and presentation images.