Just as comprehensive datasets of genomic sequence have revolutionalized biological discovery, large-scale quantitative measurements of gene expression and morphology will certainly be of great assistance in enabling computational embryology in the future. Such datasets will form the essential basis for systems level, computational models of molecular pathways and how gene expression concentrations and interactions alter to drive changes in cell shape, movement, connection, and differentiation. In this review, we discuss the strategies and methods used to generate such datasets.