Morphogenesis is a complex process that integrates several mechanisms from the molecular to the organ scales. In plants, division and growth are the two fundamental cellular mechanisms that drive morphogenesis. However, little is known about how these mechanisms are coordinated to establish functional tissue structure. A fundamental bottleneck is the current lack of techniques to systematically quantify the spatio-temporal evolution of 3D cell morphology during organ growth. Using leaf development as a relevant and challenging model to study morphogenesis, we developed a computational framework for cell analysis and quantification from 3D images and for the generation of 3D cell shape atlas. A remarkable feature of leaf morphogenesis being the formation of a laminar-like structure, we propose to automatically separate the cells corresponding to the leaf sides in the segmented leaves, by applying a clustering algorithm. The performance of the proposed pipeline was experimentally assessed on a dataset of 46 leaves in an early developmental state.