Embryogenesis, the process of forming a functioning organism from a fertilised egg, involves the precise and complex orchestration of hundreds to billions of cells dividing, changing their position, shape or size through hours, days or months. This orchestration often consists in a predefined set of instructions which implies that, within species, embryos follow the same developmental program and therefore are morphologically similar. Nonetheless, this reproducibility of the development can be observed at different scales between different species, from a reproducibility at the single cell scale to one at the tissue scale. To understand the functional and evolutionary basis of these differences in reproducibility scale, we developed methods to measure developmental variability across scales from single-cell molecular and morphological measurements to eventually build a Morpholecular atlas.