Does this skill support GPU acceleration?

Yes, the provided logic is designed for Python 3.10+ environments and is optimized for use with CuPy for GPU-accelerated image processing.

How do I handle tiles named by grid position instead of acquisition order?

This skill includes a specific reordering workflow that maps position-indexed tiles (1, 2, 3, 4) back to their physical acquisition order to ensure the stitch model aligns correctly.

Why does standard raster stitching fail for CODEX images?

Standard raster stitching assumes all rows are scanned in the same direction. If applied to a snake pattern, the tiles in every other row will be out of sequence, resulting in a scrambled image.

What is a snake pattern in microscopy?

A snake (or serpentine) pattern alternates scanning direction on each row—moving left-to-right then right-to-left—to minimize microscope stage movement and acquisition time.

Tile Snake Pattern Stitching

Name: Tile Snake Pattern Stitching
Author: smith6jt-cop

bysmith6jt-cop

0•

Data Science & ML

Reconstructs multiplex microscopy images by correctly ordering tiles acquired via snake or serpentine stage patterns.

This skill provides standardized logic and Python implementations for stitching microscopy tiles acquired in a snake (boustrophedon) pattern, which is the default for systems like CODEX. It prevents common alignment failures by ensuring that odd-numbered rows are correctly reversed to match physical acquisition order. By providing validated coordinate generation formulas and tile reordering scripts, it allows researchers to accurately reconstruct high-resolution images from raw multiplex data within the KINTSUGI pipeline or similar image processing environments.

Key Features

010 GitHub stars

02Integration-ready code for Python 3.10+ and CuPy GPU environments

03Support for arbitrary grid sizes including 2x2, 3x3, and larger mosaics

04Automated coordinate generation for snake/serpentine tile patterns

05Standardized implementation for CODEX and PhenoCycler imaging workflows

06Logic for reordering position-named test tiles to match acquisition sequences

Use Cases

01Developing high-throughput image processing pipelines for biological research

02Stitching CODEX multiplex microscopy image tiles into a single mosaic

03Correcting scrambled image reconstructions caused by stage scanning patterns

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add smith6jt-cop/skills_registry tile-snake-pattern-stitching

For use in Claude.ai and ChatGPT

Download Skill