Image Harvest: an open-source platform for high-throughput plant image processing and analysis

Journal of Experimental Botany
Avi C KnechtHarkamal Walia

Abstract

High-throughput plant phenotyping is an effective approach to bridge the genotype-to-phenotype gap in crops. Phenomics experiments typically result in large-scale image datasets, which are not amenable for processing on desktop computers, thus creating a bottleneck in the image-analysis pipeline. Here, we present an open-source, flexible image-analysis framework, called Image Harvest (IH), for processing images originating from high-throughput plant phenotyping platforms. Image Harvest is developed to perform parallel processing on computing grids and provides an integrated feature for metadata extraction from large-scale file organization. Moreover, the integration of IH with the Open Science Grid provides academic researchers with the computational resources required for processing large image datasets at no cost. Image Harvest also offers functionalities to extract digital traits from images to interpret plant architecture-related characteristics. To demonstrate the applications of these digital traits, a rice (Oryza sativa) diversity panel was phenotyped and genome-wide association mapping was performed using digital traits that are used to describe different plant ideotypes. Three major quantitative trait loci were identif...Continue Reading

References

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Citations

Dec 15, 2016·Frontiers in Plant Science·Pu HuangThomas P Brutnell
Dec 19, 2017·Frontiers in Plant Science·Zoé Joly-LopezThomas E Bureau
Aug 24, 2018·Journal of Experimental Botany·Tsu-Wei ChenFrançois Tardieu
Jun 12, 2020·Journal of Experimental Botany·Malachy T CampbellGota Morota
Jun 28, 2019·Plant Direct·Tara A EndersCory D Hirsch
Jun 1, 2018·BioMed Research International·Rita ArmonienéAakash Chawade
Apr 10, 2019·Horticulture Research·Yu JiangJamal Hunter
Jul 25, 2017·Frontiers in Plant Science·Jordan R Ubbens, Ian Stavness
Aug 22, 2017·Frontiers in Plant Science·Piyush PandeyJames C Schnable
Aug 9, 2018·Plant Methods·Sarah Taghavi NaminJustin O Borevitz
Jul 10, 2019·Frontiers in Plant Science·Christoph U Germeier, Stefan Unger
Dec 15, 2020·Plant Phenomics : a Science Partner Journal·Ronghao WangJames C Schnable
Mar 18, 2021·Plant Phenomics : a Science Partner Journal·Seyed Vahid MirnezamiBaskar Ganapathysubramanian
Apr 13, 2017·American Journal of Botany·Malia A Gehan, Elizabeth A Kellogg

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