Single-cell morphodynamics predict cell fate decisions during mucociliary epithelial differentiation

Abstract Cell state transitions underlie the emergence of diverse cell types and are traditionally defined by changes in gene expression. Yet these transitions also involve coordinated shifts in cell morphology and behaviour, which remain poorly characterized in densely packed epithelia. We developed a quantitative live-imaging and computational framework to track thousands of individual cells over time in the rapidly differentiating Xenopus mucociliary epithelium (MCE). From segmentations and trajectories, we extracted dynamic features-cell and nuclear shape, movement, position-to create a time-resolved morphodynamic dataset spanning the full course of differentiation. While single features showed high noise and low separability of ground-truth cell types, supervised machine learning revealed that integrating time-resolved features robustly predicts final cell fate. Gradient-boosted trees and multinomial logistic regression achieved moderate but consistent accuracy, especially for abundant epithelial lineages. Key discriminants included normalized Z-position, membrane-nucleus offset, and absolute experimental time, whereas movement contributed minimally to the results. Our results show that morphodynamic signatures encode predictive information about cell identity and provide a framework linking physical dynamics with molecular state. Competing Interest Statement V.K. is the founder of a not-for-profit company, Kapoorlabs, which was compensated for analysis work related to this study. The company operates on a not-for-profit basis and has no commercial interest in the outcomes of this research. All other authors declare no competing interests Footnotes Added missing ORCID numbers and funding agencies