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bioRxiv · 10.1101/2020.09.01.278234

PhenoImage: an open-source GUI for plant image analysis

Zhu, F.·Saluja, M.·Singh, J.·Paul, P.·Sattler, S. E.·Staswick, P.·Walia, H.·Yu, H.
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Abstract

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. HighlightPhenoImage is an open-source application designed for analyzing images derived from high-throughput phenotyping.

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Zhu, F., Saluja, M., Singh, J., Paul, P., Sattler, S. E., Staswick, P., Walia, H., Yu, H.. 2020-09-02. PhenoImage: an open-source GUI for plant image analysis. https://doi.org/10.1101/2020.09.01.278234

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