Normal organogenesis cannot be recapitulated in vitro for mammalian organs, unlike in species including Drosophila and zebrafish. Available 3D data in the form of ex vivo images only provide discrete snapshots of the development of an organ morphology. Here, we propose a computer-based approach to recreate its continuous evolution in time and space from a set of 3D volumetric images. Our method is based on the remapping of shape data into the space of the coefficients of a spherical harmonics expansion where a smooth interpolation over time is simpler. We tested our approach on mouse limb buds and embryonic hearts. A key advantage of this method is that the resulting 4D trajectory can take advantage of all the available data while also being able to interpolate well through time intervals for which there are little or no data. This allows for a quantitative, data-driven 4D description of mouse limb morphogenesis. Display omitted •Computer-based method recreating a 3D plus time evolution of a set of volumetric images•Technique based on the interpolation of the coefficients of spherical harmonics•Data-driven quantitative 4D description of limb and heart morphogenesis•Quantitatively reliable baseline description of organ development Continuous time-lapse imaging of developing mammalian organs is not yet possible. Dalmasso et al. propose a computer-based approach to recreate a continuous evolution in time and space from a set of 3D volumetric images using spherical harmonics. The result allows for a data-driven quantitative 4D description of limb and heart morphogenesis.