Registration and fusion¶
Run fusion on completed processed tiles:
Select the input¶
Directory selection prefers *_decon_deskewed.ome.zarr when available and
prints the selected store. Supply the processed store itself to select it
explicitly. Fusion writes a registered multiscale volume and its maximum-Z
projection beside the processed data.
Register neighboring tiles¶
Choose a channel with shared tissue signal in tile overlaps. Stage positions, tile shapes, spacing, and scan geometry determine initial placement and automatic search limits. Registration downsampling adapts to each overlap. The similarity threshold defaults to 0.7.
Override the automatic correction limits when the acquisition needs a specific search envelope, using processed-image pixels in ZYX order:
Inspect connectivity warnings before accepting a mosaic. They describe links retained after global optimization. Unconnected groups lack a measured relative alignment. Review input choice, overlap signal, and registration limits when a dataset expected to be connected produces disconnected groups.
Match brightness across depths¶
Depth normalization is enabled by default. Registered overlaps at the same
stage XY supply one gain per depth, timepoint, and channel, shared across that
depth's XY tiles. Differences between XY fields are retained. Fitted gains are
saved in <stem>_depth_intensity_gains.json; source tiles remain unchanged.
Use --no-normalize-depth-intensity to omit these gains. The
method page explains gain fitting and geometric coverage.
Recreate the registered projection¶
This projects every resolution of the existing registered fused image without registering and blending the tiles again. See the fuse reference for all options.