Understanding organ morphogenesis requires a precise and complete geometrical description of the tissues that compose the organ of interest. In particular, early heart morphogenesis in mammals is challenging, due to the drastic tissue shape reorganization and the limitations in imaging approaches. We are studying the process heart tube formation in the mouse model using live imaging and high-resolution confocal microscopy. By analysing a temporally dense collection of 3D images from fixed specimens, we have generated a complete morphological description of heart tube formation from the early cardiac crescent (E7.5) to the heart looping stage (E8.5). This description includes the differentiating myocardium, the surrounding tissues in the pericardiac cavity, the endoderm and the incipient circulatory system as independently segmented tissues. We developed a new approach for morphometric staging of the specimens and generated a 3D+T virtual atlas of heart tube formation by surface interpolation between stages. The analysis of the results obtained show intra-specimen heterochrony in features of heart morphogenesis and identify specific hotspots of regional variability. These findings are being correlated with tissue dynamics deduced from the live imaging approach, which shows that the developing cardiac tube behaves as an elastic material. The atlas generated provides a suitable framework for co-representation of data from different experiments or labs and for the biophysical modelling of heart formation. Currently, we are upgrading this virtual heart development model by segmenting individual cells and nuclei in all the tissues involved in cardiogenesis.