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Stack Stitching Module
Join several stacks into one volume: z-concatenation, z-overlap, and side-by-side xy mosaics, all through a single placement model. Align once, then reuse the placements on sibling volumes.
Each stack after the first is placed by a declared slice pair, "these two slices are the same physical section", which fixes the z-offset, plus an in-plane transform (dx, dy, rotation) that you align in an overlay viewer. Whether a junction is a z-continuation or a side-by-side mosaic is inferred from how much the two footprints overlap, not asked as a separate question.
Key Features
One placement model for z-concatenation, z-overlap, and xy mosaics
Overlay alignment with automatic phase correlation plus manual nudge and rotate
Per-junction control over duplicated z sections: keep the upper stack, keep the lower stack, or merge (average)
Stitch recipes saved next to the output and reapplied to sibling volumes without re-aligning
Supported Input
Multi-page TIFF stacks (.tif, .tiff)
Two data modes, detected automatically and never mixed in one stitch: images (grayscale raw or denoised) and label maps (segmentations, annotations)
All stacks in a stitch share the same pixel grid
Workflow
Select Stacks: start a new stitch, or apply a saved recipe
Align & Compose: for each junction, pick the matching slice pair and align the overlay; then review the placement summary, set the output options, and compose the volume. When applying a saved recipe, the alignment part is skipped and the step shows composing only
The result is a stitched TIFF plus a recipe. Duplicated z sections are trimmed by default (one stack's slices are dropped); a junction set to merge keeps both and averages them (images only), recorded as z_merge in the recipe.