Table 2.
Selected image analysis software programs and phenotyping platforms available for high-throughput phenotyping
| Tissue | Software | Purpose and design | Reference |
|---|---|---|---|
| Roots | WinRhizo Tron | Morphological descriptions of root area, volume, length, etc | http://www.regent.qc.ca/products/rhizo/RHIZOTron.html |
| KineRoot | 2D analysis of root growth and curvature | Basu et al. (2007) | |
| PlaRoM | Platform for measuring root extension and growth traits | Yazdanbakhsh and Fisahn (2009) | |
| EZ-Rhizo | 2D analysis of root system architecture | Armengaud et al. (2009) | |
| RootTrace | Counting and measuring root morphology | Naeem et al. (2011), French et al. (2009) | |
| DART | 2D analysis of root system architecture | Le Bot et al. (2010) | |
| SmartRoot | ImageJ plugin for the quantification of growth and architecture | Lobet et al. (2011) | |
| RootReader3D | 3D analysis of root system architecture | Clark et al. (2011) | |
| RootReader2D | 2D analysis of root system architecture | Clark et al. (2012) | |
| Gia-Roots | 2D analysis of root system architecture | Galkovskyi et al. (2012) | |
| Shoots/leaves | WinFolia | Morphological measurements of broad leaves | http://www.regent.qc.ca/products/folia/WinFOLIA.html |
| TraitMill | Platform for measuring various agronomic characteristics | Reuzeau et al. (2006) | |
| PHENOPSIS | Automated measurement of water deficit-related traits | Granier et al. (2006) | |
| LeafAnalyser | Rapid analysis of leaf shape variation | Weight et al. (2007) | |
| LAMINA | Quantification of leaf size and shape | Bylesjö et al. (2008) | |
| HYPOTrace | Analysis if hypocotyl growth and shape | Wang et al. (2009) | |
| LEAFPROCESSOR | Analysis of leaf shape | Backhaus et al. (2010) | |
| Lamina2Shape | Analysis of lamina shape | Dornbusch and Andrieu (2010) | |
| HTPheno | ImageJ plugin for morphological shoot measurements | Hartmann et al. (2011) | |
| LEAF-GUI | Analysis of leaf vein structure | Price et al. (2011) | |
| LemnaTec 3D Scanalyzer | Comprehensive platform for analysis of color, shape, size, and architecture | Golzarian et al. (2011), http://www.lemnatec.com/ | |
| Seeds/grain | WinSEEDLE | Volume and surface area measurements of seeds and needles | http://www.regent.qc.ca/products/needle/WinSEEDLE.html |
| SHAPE | Quantitative evaluation of shape parameters | Iwata and Ukai (2002), Iwata et al. (2010) | |
| ImageJ | General image analysis software for area, size, and shape; applied to grain | Herridge et al. (2011), http://rsb.info.nih.gov/ij/ | |
| GROWSCREEN-Rhizo | Simultaneous analysis of growth rate, leaf area, and root growth | Nagel et al. (2012) | |
| SmartGrain | High-throughput measurement of seed shape | Tanabata et al. (2012) |