Measuring plant phenotypes, a term used to describe the observable characteristics of an organism, is a critical aspect of studying and improving economically important crops. Phenotypes central to the breeding process include traits like kernel number in corn, seed size in wheat, or fruit color in grape. These features are visible to the naked human eye but are in fact driven by microscopic molecular and cellular processes in the plant. Using three-dimensional (3D) imaging is a recent innovation in the plant biology sector to capture phenotypes on the "whole-plant" scale: from miniscule cells and organelles in the roots, up to the leaves and flowers.