Quantifying cellular behavior during early mammalian development

In this thesis we study cell behaviours such as cellular decision making and self-organization using the developing mouse embryo as the system of study. To be able to extract the most needed cellular dynamics from experimental data, we developed a package for the segmentation, tracking, annotation and manual correction of errors in 3d multichannel live- imaged biological samples. Then, we apply these single cell analysis together with mathematical modeling and statistical methods to four distinc problems in the context of the mouse early embryonic development. First we study the differentiatioin of ICM progenitors into epiblast and primitive endoderm. Then, focus on the generation of pulsatil dynamics in the ERK signaling pathway. In the next two chapters we focus on post-implantation development. In one of them, we characterise cell competition in the context of gastrulation. Finally, we study the differentiation of the visceral endoderm into anterior visceral endoderm. In this Thesis, We show that the spatio-temporal analysis of cellular dynamics is a key approach in the study of develping systems