Development and growth of plant organs is determined by a myriad of molecular processes that occur in each individual cell. As a direct consequence of these processes, cells alter in size and shape. They therefore serve as excellent parameters to thoroughly understand gene function. However, conventional single-plane analyses fail to accurately capture cell metrics. Here, we present a comprehensive illustrated guide that demonstrates how SCRI Renaissance 2200 staining of Arabidopsis thaliana embryos and roots can be combined with the open-source application MorphoGraphX to quantify cell parameters in 3D. We compare this staining method with other common staining techniques and provide examples of embryo and root tissue segmentation. With our novel approach, subtle single-cell phenotypes can be identified in their native context, providing new possibilities to dissect gene networks.