tile-snake-pattern-stitching

SNAKE pattern tile ordering corrects the sequence of multiplex microscopy tiles acquired with alternating row directions. This Skill reorders tiles from acquisition order to grid positions, ensuring proper alignment before stitching in CODEX-like imaging workflows across arbitrary grid sizes.

A SNAKE pattern captures microscopy tiles by traversing rows in alternating directions—left-to-right, then right-to-left—to optimize stage movement during multiplex imaging. This acquisition method requires coordinate remapping during stitching to prevent misalignment.

Yes. This Skill handles both position-based filenames and acquisition-order renaming, mapping tiles from their original acquisition sequence to grid coordinates and producing stitch-ready tile sequences with corrected naming.

Yes. The Skill is CuPy-enabled for GPU acceleration when available, allowing faster tile reordering in Python-based pipelines processing large multiplex microscopy datasets.

Apply SNAKE pattern correction immediately after tile acquisition and before stitching, whenever multiplex microscopy tiles were captured with alternating row directions. It corrects coordinate mismatches that cause stitching failures.

SNAKE pattern coordinate sequences are generated for arbitrary grid sizes, accommodating variable dimensions in multiplex microscopy tile layouts without pre-defined size constraints.