Table 3.
Open source high-throughput plant phenotype image processing software or tools.
| Name | URL | Description |
|---|---|---|
| ImageJ | http://imagej.nih.gov/ij | A popular, powerful, and extensible application used to process and measure a large quantity of phenotypic traits captured by images. |
| IAP | http://iap.ipk-gatersleben.de | Large-scale plant phenotyping image analysis software for different species based on real-time imaging data obtained from various spectra (Klukas et al., 2014). |
| HTPheno | http://htpheno.ipk-gatersleben.de | A high-throughput (top and side view) plant phenotyping image analysis pipeline implemented as a plug-in for ImageJ (Hartmann et al., 2011). |
| Rosette tracker | http://telin.ugent.be/∼jdvylder/RosetteTracker | Time-lapse visual, chlorophyll fluorescence, or thermal sequence of image analysis tool for quantification genotype effects of Arabidopsis thaliana, implemented as a plug-in for ImageJ (De Vylder et al., 2012). |
| PANorama | http://ricediversity.org | Flexible software which simultaneously measures multiple architectural and branching phenotypes from images (Crowell et al., 2014). |
| HPGA | http://www.msu.edu/∼jincn/HPGA | A high-throughput phenotyping tool for plant growth modeling and functional analysis (Tessmer et al., 2013). |
| Phenophyte | https://vphenodbs.rnet.missouri.edu/PhenoPhyte/index.php | A web-based application which measures area-related phenotypic traits from imagery and multiple experimental setup (Green et al., 2012). |
| SmartGrain | http://www.nias.affrc.go.jp/qtl/Smart Grain | Image analysis software for high-throughput phenotyping measurements of seed shape (Tanabata et al., 2012). |
| HYPOTrac | http://phytomorph.wisc.edu/HYPOTrace/download/index.htm | Automated hypocotyl growth and shape measuring software from grayscale images of Arabidopsis seedlings (Wang et al., 2009). |
| LAMINA | http://lamina.sourceforge.net | Automated leaves image analysis tool which measures a variety of characteristics related to leaf shape and size (Bylesjo et al., 2008). |
| Leaf Analyzer | http://leafanalyser.openillusionist.org.uk/doku.php | An automated software for rapid and large-scale analyses of leaf shape variation (Weight et al., 2008). |
| Leaf Processor | http://gips.group.shef.ac.uk/resources.html | An application that semi-automatically stores a number of single-metric parameters and PCA analysis for leaf shape and size including contour bending energy (Backhaus et al., 2010). |