We have explored the use of optical projection tomography (OPT) as a method for capturing 3D morphology and gene activity at a variety of developmental stages and scales from plant specimens, in collaboration with the Medical Research Council, James Sharpe and Bioptonics. OPT can be conveniently applied to a wide variety of plant material including seedlings, leaves, flowers, roots, seeds, embryos and meristems. At the highest resolution large individual cells can be seen in the context of the surrounding plant structure. 3D domains of gene expression can be visualised using either marker genes such as ß-glucuronidase, or more directly by whole-mount in situ hybridization. To interactively analyse and quantify 3D OPT data we are developing software using haptics to accurately place points on volumes in 3D space. These tools will enable us to create 3D statistical shape models to analyse phenotypic variation in Arabidopsis leaves. For naturally semi-transparent structures, such as roots, live 3D imaging using OPT is possible. 3D gene expression patterns in living transgenic plants expressing fluorescent GFP markers can also be visualised by OPT. We are using GFP marked trichomes to track leaf growth in 4D, by obtaining OPT time-course data for Arabidopsis plants growing in the OPT device. Computer vision techniques are being developed to analyse sequential OPT datasets. The combination of 4D time-course data, 3D point-placing, trichome tracking and modelling will allow us to understand mechanisms controlling growth and shape from earliest stages of leaf growth to maturity.