Abstract
Recent advances in quantitative bioimage analysis have enabled detailed analyses of cellular and subcellular morphological features, enhancing our understanding of cellular functions. Here, we introduce an image-based phenotyping pipeline designed for the comprehensive analysis of dynamic organelle morphology, particularly the Golgi apparatus and cilia, during cell cycle progression. Our approach emphasizes interpretable feature extraction, enabling detection of both prominent and subtle morphological changes. By using well-characterized morphological dynamics of intracellular structures as benchmarks, we demonstrated that our method can reliably detect established phenotypic changes and serves as a valid tool for quantitative profiling. Further investigation of the G0/G1 transition revealed an unexplored link between Golgi dynamics and ciliary disassembly. Specifically, inhibition of the G0/G1 transition correlated with ciliary persistence and unique Golgi dispersion, involving Aurora kinase A (AURKA). Our results thus indicate an association of Golgi morphology with cell cycle reentry and ciliary dynamics, underscoring the value of our profiling method in studying cellular regulation in health and disease.