title: Image analysis of anatomical traits in stalk transections of maize and other grasses.
abstract: BACKGROUND
  Grass stalks architecturally support leaves and reproductive structures, functionally support the transport of water and nutrients, and are harvested for multiple agricultural uses. Research on these basic and applied aspects of grass stalks would benefit from improved capabilities for measuring internal anatomical features. In particular, methods suitable for phenotyping populations of plants are needed.
  
  
  RESULTS
  To meet the need for large-scale measurements of stalk anatomy features, we developed custom image processing software that utilized a variety of global thresholding, local filtering, and feature detection methods to measure rind thickness, pith area, vascular bundle counts, and individual vascular bundle size from digital images of hand-cut transections of stalks collected with a flatbed document scanner. The tool determined vascular bundle number with an average accuracy of 90% across maize genotypes that varied five-fold for this trait. The method is demonstrated on maize, sorghum, and Miscanthus stalks. The computer source code is staged for download.
  
  
  CONCLUSIONS
  Simplicity of sample preparation and semi-automated analyses enabled by this tool greatly increase measurement throughput relative to standard microscopy-based techniques while maintaining high accuracy. The tool is expected to be useful in genetic and physiological studies of the relationships between stalk anatomy and traits such as biofuel suitability, water use efficiency, or nutrient transport.
authors.affiliation: Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706 USA.
authors.forename: Sven
authors.initials: S
authors.lastname: Heckwolf
authors.affiliation: Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706 USA ; DOE Great Lakes Bioenergy Research Center, 1552 University Avenue, Madison, WI 53706 USA.
authors.forename: Marlies
authors.initials: M
authors.lastname: Heckwolf
authors.affiliation: Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706 USA ; DOE Great Lakes Bioenergy Research Center, 1552 University Avenue, Madison, WI 53706 USA.
authors.forename: Shawn M
authors.initials: SM
authors.lastname: Kaeppler
authors.affiliation: Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706 USA ; DOE Great Lakes Bioenergy Research Center, 1552 University Avenue, Madison, WI 53706 USA.
authors.forename: Natalia
authors.initials: N
authors.lastname: de Leon
authors.affiliation: Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706 USA.
authors.forename: Edgar P
authors.initials: EP
authors.lastname: Spalding