RT Journal Article SR Electronic T1 PhenoImage: an open-source GUI for plant image analysis JF bioRxiv FD Cold Spring Harbor Laboratory SP 2020.09.01.278234 DO 10.1101/2020.09.01.278234 A1 Zhu, Feiyu A1 Saluja, Manny A1 Singh, Jaspinder A1 Paul, Puneet A1 Sattler, Scott E. A1 Staswick, Paul A1 Walia, Harkamal A1 Yu, Hongfeng YR 2020 UL http://biorxiv.org/content/early/2020/09/02/2020.09.01.278234.abstract AB High-throughput genotyping coupled with molecular breeding approaches has dramatically accelerated crop improvement programs. More recently, improved plant phenotyping methods have led to a shift from manual measurements to automated platforms with increased scalability and resolution. Considerable effort has also gone into the development of large-scale downstream processing of the imaging datasets derived from high-throughput phenotyping (HTP) platforms. However, most available tools require some programing skills. We developed PhenoImage – an open-source GUI based cross-platform solution for HTP image processing with the aim to make image analysis accessible to users with either little or no programming skills. The open-source nature provides the possibility to extend its usability to meet user-specific requirements. The availability of multiple functions and filtering parameters provides flexibility to analyze images from a wide variety of plant species and platforms. PhenoImage can be run on a personal computer as well as on high-performance computing clusters. To test the efficacy of the application, we analyzed the LemnaTec Imaging system derived RGB and fluorescence shoot images from two plant species: sorghum and wheat differing in their physical attributes. In the study, we discuss the development, implementation, and working of the PhenoImage.Highlight PhenoImage is an open-source application designed for analyzing images derived from high-throughput phenotyping.