Investigating plant morphogenesis using 3D digital organs

How plant organs acquire their three-dimensional (3D) size and shape remains a prominent question in plant biology. Central questions revolve around how differential gene activity influences the growth of individual cell assemblies and how such growth patterns affect organ form. However, our understanding of morphogenetic processes at the cellular and supracellular level remains underdeveloped because the necessary analyses are notoriously difficult to perform with classical methods, especially in three dimensions and in deeper tissues. In recent years, significant improvements in imaging, artificial intelligence-based image processing, and 3D cell segmentation have enabled the generation of 3D digital plant organs with single-cell resolution. This review first describes the experimental toolbox that enables the generation and analysis of 3D digital organs. It then highlights a number of studies that illustrate their value for understanding plant morphogenesis. Finally, the review explores how cross-species comparative analysis of 3D digital organs can reveal evolutionary shifts in cellular patterns and their contribution to the astonishing diversity of morphology observed throughout the plant kingdom. Overall, the review aims to demonstrate how the advent of 3D digital organs has significantly broadened the range of approaches and opened new frontiers for the study of the cellular basis of tissue morphogenesis.