During organ development, morphological and topological changes jointly occur at the cellular and tissue levels. Hence, the systematic and integrative quantification of cellular parameters during growth is essential to better understand organogenesis. We developed an atlasing strategy to quantitatively map cellular parameters during organ growth. Our approach is based on the computation of prototypical shapes, which are average shapes of individual organs at successive developmental stages, whereupon statistical descriptors of cellular parameters measured from individual organs are projected. We describe here the algorithmic pipeline we developed for 3D organ shape registration, based on the establishment of an organ-centered coordinate system and on the automatic parameterization of organ surface. Using our framework, dynamic developmental trajectories can be readily reconstructed using point-to-point interpolation between parameterized organ surfaces at different time points. We illustrate and validate our pipeline using 3D confocal images of developing plant leaves.