title: TIPS: a system for automated image-based phenotyping of maize tassels.
abstract: BACKGROUND
  The maize male inflorescence (tassel) produces pollen necessary for reproduction and commercial grain production of maize. The size of the tassel has been linked to factors affecting grain yield, so understanding the genetic control of tassel architecture is an important goal. Tassels are fragile and deform easily after removal from the plant, necessitating rapid measurement of any shape characteristics that cannot be retained during storage. Some morphological characteristics of tassels such as curvature and compactness are difficult to quantify using traditional methods, but can be quantified by image-based phenotyping tools. These constraints necessitate the development of an efficient method for capturing natural-state tassel morphology and complementary automated analytical methods that can quickly and reproducibly quantify traits of interest such as height, spread, and branch number.
  
  
  RESULTS
  This paper presents the Tassel Image-based Phenotyping System (TIPS), which provides a platform for imaging tassels in the field immediately following removal from the plant. TIPS consists of custom methods that can quantify morphological traits from profile images of freshly harvested tassels acquired with a standard digital camera in a field-deployable light shelter. Correlations between manually measured traits (tassel weight, tassel length, spike length, and branch number) and image-based measurements ranged from 0.66 to 0.89. Additional tassel characteristics quantified by image analysis included some that cannot be quantified manually, such as curvature, compactness, fractal dimension, skeleton length, and perimeter. TIPS was used to measure tassel phenotypes of 3530 individual tassels from 749 diverse inbred lines that represent the diversity of tassel morphology found in modern breeding and academic research programs. Repeatability ranged from 0.85 to 0.92 for manually measured phenotypes, from 0.77 to 0.83 for the same traits measured by image-based methods, and from 0.49 to 0.81 for traits that can only be measured by image analysis.
  
  
  CONCLUSIONS
  TIPS allows morphological features of maize tassels to be quantified automatically, with minimal disturbance, at a scale that supports population-level studies. TIPS is expected to accelerate the discovery of associations between genetic loci and tassel morphology characteristics, and can be applied to maize breeding programs to increase productivity with lower resource commitment.
authors.affiliation: Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706 USA.
authors.forename: Joseph L
authors.initials: JL
authors.lastname: Gage
authors.affiliation: Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706 USA.
authors.forename: Nathan D
authors.initials: ND
authors.lastname: Miller
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
authors.affiliation: Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Drive, 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.
authors.forename: Natalia
authors.initials: N
authors.lastname: de Leon
keywords: High-throughput; Image analysis; Inflorescence; Phenotyping; Tassel; Zea mays L.