Imaging technologies have provided ways to measure complex plant traits at different scales. Such measurements allow us to understand how plants grow and how this growth is affected by the environment conditions. We have investigated image analysis techniques to understand how plant development occurs from stem cells in the shoot apical meristem using confocal microscopy images, and to phenotype plant panicle and root architecture using high resolution imagery. Those techniques have been used to support the research on Plant Biology of colleagues from Caltech and Cornell Univ., respectively.