title: Visualizing plant development and gene expression in three dimensions using optical projection tomography.
abstract: 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 beta-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.
authors.affiliation: Department of Cell and Developmental Biology, John Ines Centre, Norwich Research Park, Norwich, NR4 7UH United Kingdom.
authors.forename: Karen
authors.initials: K
authors.lastname: Lee
authors.forename: Jerome
authors.initials: J
authors.lastname: Avondo
authors.forename: Harris
authors.initials: H
authors.lastname: Morrison
authors.forename: Lilian
authors.initials: L
authors.lastname: Blot
authors.forename: Margaret
authors.initials: M
authors.lastname: Stark
authors.forename: James
authors.initials: J
authors.lastname: Sharpe
authors.forename: Andrew
authors.initials: A
authors.lastname: Bangham
authors.forename: Enrico
authors.initials: E
authors.lastname: Coen
mesh_terms: D035264:Flowers / Q000033:anatomy & histology / Q000378:metabolism / Q000502:physiology; D015870:Gene Expression; D017930:Genes, Reporter; D005966:Glucuronidase / Q000032:analysis; D021621:Imaging, Three-Dimensional / Q000379:methods; D018519:Meristem / Q000033:anatomy & histology / Q000378:metabolism / Q000502:physiology; D063245:Plant Development; D018515:Plant Leaves / Q000033:anatomy & histology / Q000378:metabolism / Q000502:physiology; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D018517:Plant Roots / Q000033:anatomy & histology / Q000378:metabolism / Q000502:physiology; D010944:Plants / Q000033:anatomy & histology / Q000196:embryology*; D036226:Seedlings / Q000033:anatomy & histology / Q000378:metabolism / Q000502:physiology; D012639:Seeds / Q000033:anatomy & histology / Q000378:metabolism / Q000502:physiology; D012984:Software; D041622:Tomography, Optical / Q000379:methods*
chemical_list: D010940:Plant Proteins; D005966:Glucuronidase