Stationary and germ layer-specific cellular flows shape the zebrafish gastrula

During gastrulation, a sequence of complex processes transforms the blastula into a multi-layered embryo. Fixed sample analysis has revealed much about how genetic signaling cascades determine the major body axes and organize cell fate patterns into the germ layers: ectoderm, mesoderm, and endoderm. In toto live imaging of vertebrate development highlights that embryogenesis is a dynamic process that involves on the order of ten thousand cells, but hurdles related to data handling have hampered quantitative analysis. Therefore, our understanding of the rich physical aspects of multilayered tissue reconfigurations remains incomplete. Here, we reveal that modules of stationary and germ-layer-specific tissue flows shape the zebrafish gastrula. We combine in toto live imaging with tissue-specific markers and image analysis to reveal the global shape of the enveloping layer (EVL), epiblast, and mesoderm over time. A user-friendly tissue cartography pipeline based on the Blender 3D software moves into the reference frame of individual tissue layers. We find distinct tissue flow patterns in the enveloping layer (EVL), epiblast, and mesoderm, respectively. The instantaneous tissue flow of these germ layers is organized in a temporal sequence of hours-long, constant flow patterns. This suggests that a sequence of stationary tissue flow modules transports cells to their destination during gastrulation. Mathematical decomposition suggests that epiblast flow is strongly influenced by a superposition of rotational flow in the mesoderm, and divergent flow in the EVL. Molecular and cellular complexity notwithstanding, these results hint at surprisingly, tractable physical processes that underlie vertebrate gastrulation, and set the stage for investigations of how morphogens orchestrate dynamics.