Lucie Bracq, Romain Guiet, Sandra Offner, Béatrice Kunz, Gisou van der Goot, Nathalie Brandenberg
SWIFT (Single-organoid Workflow for quantitative Imaging classiFication and Tracking) is a fast and modular pipeline for quantitative, time-resolved organoid analysis from brightfield images. Requiring only minimal training annotations, SWIFT combines YOLOv8, SAM, and application-specific object classification to deliver accurate single-organoid segmentation, phenotyping, and tracking. The workflow is robust across organoid types and microscope systems. Applied to intestinal organoids, SWIFT uncovers dynamic Wnt-dependent morphological transitions, enabling scalable, high-throughput studies of epithelial plasticity.