High-throughput three-dimensional characterization of morphogenetic signals during the formation of the vertebrate retina

The precise differentiation of neural progenitors during development ensures the correct cognitive, sensory and motor functions of higher organisms. This balance between self-renewal and terminal differentiation is regulated by a complex interplay of signaling pathways, that set the spatial and temporal cues that ultimately shape and organize neurogenic tissues. The developing vertebrate retina is a widely used model to study how these key signaling cascades modulate the mode and rate of division of neural progenitors, despite its complex threedimensional architecture and the asymmetric differentiation dynamics. Here, we present a comprehensive multi-step framework that integrates in toto experiments with three dimensional image analysis and theoretical tools to provide a quantitative characterization of the dynamics of growth and differentiation of the developing vertebrate retina. Additionally, we use small molecule inhibitors to show that Hh and FGF activation promote differentiation and cell cycle progression, while Wnt and Notch activation respectively increase and decrease the average division rate. These results represent a detailed and accurate quantitative characterization of the development and regulation of the vertebrate retina. We propose that the same framework can be directly used to characterize other in vitro or in vivo tissues.