fuse¶
Register and blend processed tiles, saving fused OME-Zarr and maximum-Z images. Accepts an acquisition/output directory or processed store; directory selection prefers deconvolved, deskewed data.
| Option | Description |
|---|---|
--registration-channel VALUE |
Select the zero-based registration channel; default 0. |
--max-registration-shift-zyx Z Y X |
Override correction limits inferred from stage positions and scan geometry. |
--registration-threshold VALUE |
Minimum overlap similarity; default 0.7. |
--blend-pixels Z Y X |
Set edge blending widths; default 20 600 400. |
--downsample-factors Z Y X |
Set registration sampling factors; default 3 5 5. |
--ssim-window VALUE |
Set the overlap similarity window; default 15. |
--no-normalize-depth-intensity |
Disable brightness matching across depths; XY brightness differences are retained. |
--roi PATH |
Restrict fusion to a saved ROI. |
--regenerate-max-z |
Recreate maximum-Z images from existing fused data. |
--require-gpu |
Require CUDA registration. |
--chunk-shape-yx Y X |
Set fusion block dimensions; default 1024 1024. |
--fusion-ram-fraction VALUE |
Set available RAM fraction for fusion; default 0.4. |
--max-workers VALUE |
Set CPU fusion workers; default up to eight physical cores. |
--max-in-flight-writes VALUE |
Limit queued block writes; default 2. |
--optimization-rel-threshold VALUE |
Set the registration outlier multiplier; default 0.5. |
--optimization-abs-threshold VALUE |
Set the minimum registration residual cutoff; default 1.5. |
Append --help to list all options and defaults.