Received April 6, 2006
Returned for revision June 16, 2006
Accepted July 21, 2006
Visualizing Plant Development and Gene Expression in Three Dimensions Using Optical Projection Tomography
Karen Lee 1, Jerome Avondo 2, Harris Morrison 3, Lilian Blot 2, Margaret Stark 4, James Sharpe 3, Andrew Bangham 2, and Enrico Coen 1*
1 Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH United Kingdom
2 School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ United Kingdom
3 Optical Projection Tomography Group, Medical Research Council Human Genetics Unit, Western General Hospital, Edinburgh, EH4 2XU United Kingdom
4 Edinburgh Mouse Atlas Group, Medical Research Council Human Genetics Unit, Western General Hospital, Edinburgh, EH4 2XU United Kingdom
* To whom correspondence should be addressed. E-mail: enrico.coen{at}bbsrc.ac.uk.
A deeper understanding of the mechanisms that underlie plant growth and development requires quantitative data on three-dimensional (3D) morphology and gene activity at a variety of stages and scales. To address this, we have explored the use of optical projection tomography (OPT) as a method for capturing 3D data from plant specimens. We show that OPT can be conveniently applied to a wide variety of plant material at a range of scales, 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. For naturally semitransparent structures, such as roots, live 3D imaging using OPT is also possible. 3D domains of gene expression can be visualized using either marker genes, such as 
-glucuronidase, or more directly by whole-mount in situ hybridization. We also describe tools and software that allow the 3D data to be readily quantified and visualized interactively in different ways.
