Multi-scale mechanical interactions across layers drive folding morphogenesis in the gut*

Understanding how organs transform into their target shapes during development is a challenge at the interface between physics and biology. In visceral organs, multiple tissue layers interact to orchestrate complex shape changes. While there has been significant progress in identifying genetic and anatomical ingredients underlying organogenesis, tracing the dynamics of cell behavior and tissue deformation that drive organ shape change remains an outstanding and essential challenge. Here, leveraging the Drosophila midgut as a model system, we use light-sheet microscopy, genetics, computer vision, and tissue cartography to reconstruct in toto shape dynamics of a developing organ in vivo. We identify the kinematic mechanism driving shape change by linking out-of-plane motion to active contraction patterns. Optogenetic perturbations reveal that muscle activity induces endodermal cell shape change and organ constriction. This induction cascade relies on calcium pulses in the muscle layer that are downstream of hox genes, and calcium inhibition abolishes constrictions. Our multi-scale analysis traces how biology controls a physical process generating whole-organ shape change, offering a kinematic and mechanical mechanism for organogenesis in heterologous tissue layers.