ImageBreed: Open-access plant breeding web–database for image-based phenotyping

Abstract

High-throughput image-phenotyping promises to accelerate the rate of genetic improvement in plant breeding through varietal selections informed by longitudinal growth models. To facilitate routine analyses and to drive breeding decisions, data integration is critical for effective management of germplasm, field experiment design, phenotyping, tissue sampling, genotyping, aerial-phenotyping campaigns, image files, and geo-spatial information. To this end, ImageBreed provides a software solution for end-to-end image-based phenotyping integrated into the Breedbase plant breeding system. ImageBreed provides open-source orthophotomosaic construction for raw image captures from standard color cameras and from the MicaSense RedEdge multispectral camera. Additionally, previously assembled orthophotomosaic raster images can be uploaded. Orthophotomosaic images allow for streamlined extraction of plot-polygon images; however, ImageBreed plot-polygon images can also be extracted directly from raw aerial image captures. A web–database interface streamlines assignment of plot-polygon images from the orthophotomosaic or raw aerial-captures to the field experiment design. Image processes spanning Fourier-transform filtering, thresholding, and vegetation index masking are applied to reduce noise in extracted phenotypes. Summary-statistic phenotypic values are extracted for every observed plot-polygon image using a structured ontology. Plot-polygon images are queryable against genotypic, phenotypic, and experimental design information for training of machine learning models and for driving breeding decisions in varietal advancement. ImageBreed is publicly available at http://imagebreed.org and built on the open-source Breedbase system (https://github.com/solgenomics/sgn); all image-processing scripts are available at https://github.com/solgenomics/DroneImageScripts and via a Docker image. All data deposited in http://imagebreed.org are publicly available for longitudinal model training and for driving future breeding decisions.