Overlapping Sections Keep

When two stacks were imaged across the same physical sections, those z positions are duplicated. The "Overlapping sections keep" control decides what happens to the duplicates at that junction. It is a three-way choice: upper, lower, or merge.

The Three Options

• Upper: keep the upper (previous) stack's slices across the duplicated range; the lower stack's copies are trimmed

• Lower: keep the lower (this) stack's slices; the upper stack's copies are trimmed

• Merge: keep both stacks and average the two images at each duplicated z position

Merge Is Images Only

• Merge averages pixel values, which is meaningful only for grayscale images

• In label maps mode the merge button is disabled; class IDs cannot be averaged, so duplicated sections fall back to keeping the upper stack

• The recipe records merge as a z_merge flag on the lower stack; when a label-map recipe carries that flag the composer ignores it and keeps the earlier stack, with a warning

When It Applies

• This control only affects continuation junctions, where the footprints overlap enough for the stacks to be reading the same sections in z

• For side-by-side mosaics (small footprint overlap) there are no duplicated z positions, so the setting is ignored and all slices are kept

• Composing reports how many duplicated sections were actually averaged