A novel way to validate UAS-based high-throughput phenotyping protocols using in silico experiments for plant breeding p
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ORIGINAL ARTICLE
A novel way to validate UAS‑based high‑throughput phenotyping protocols using in silico experiments for plant breeding purposes Giovanni Galli1 · Felipe Sabadin1 · Germano Martins Ferreira Costa‑Neto1 · Roberto Fritsche‑Neto1 Received: 28 February 2020 / Accepted: 6 November 2020 © Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract Key message It is possible to make inferences regarding the feasibility and applicability of plant high-throughput phenotyping via computer simulations. Abstract Protocol validation has been a key challenge to the establishment of high-throughput phenotyping (HTP) in breeding programs. We add to this matter by proposing an innovative way for designing and validating aerial imagery-based HTP approaches with in silico 3D experiments for plant breeding purposes. The algorithm is constructed following a pipeline composed of the simulation of phenotypic values, three-dimensional modeling of trials, and image rendering. Our tool is exemplified by testing a set of experimental setups that are of interest in the context of maize breeding using a comprehensive case study. We report on how the choice of (percentile of) points in dense clouds, the experimental repeatability (heritability), the treatment variance (genetic variability), and the flight altitude affect the accuracy of high-throughput plant height estimation based on conventional structure-from-motion (SfM) and multi-view stereo (MVS) pipelines. The evaluation of both the algorithm and the case study was driven by comparisons of the computer-simulated (ground truth) and the HTPestimated values using correlations, regressions, and similarity indices. Our results showed that the 3D experiments can be adequately reconstructed, enabling inference-making. Moreover, it suggests that treatment variance, repeatability, and the choice of the percentile of points are highly influential over the accuracy of HTP. Conversely, flight altitude influenced the quality of reconstruction but not the accuracy of plant height estimation. Therefore, we believe that our tool can be of high value, enabling the promotion of new insights and further understanding of the events underlying the practice of highthroughput phenotyping.
Introduction High-throughput phenotyping (HTP) has consistently drawn the attention of the scientific community due to its potential to improve the rates of genetic gain (White et al. 2012; Araus and Cairns 2014; Araus et al. 2018). A wide range of ground and aerial-based systems have been implemented to perform phenotyping, but the use of unmanned aerial systems (UAS) Communicated by Martin Boer. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00122-020-03726-6) contains supplementary material, which is available to authorized users. * Giovanni Galli [email protected] 1
Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
has stood out due to the relatively low c
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