High-throughput phenotyping of soybean maturity using time Series UAV imagery and convolutional neural networks.

TREVISAN, R. - PÉREZ, O. - SCHMITZ, N. - DIERS, B. - MARTIN, N

Resumen:

Abstract: Soybean maturity is a trait of critical importance for the development of new soybean cultivars, nevertheless, its characterization based on visual ratings has many challenges.Unmanned aerial vehicles (UAVs) imagery-based high-throughput phenotyping methodologieshave been proposed as an alternative to the traditional visual ratings of pod senescence. However, the lack of scalable and accurate methods to extract the desired information from the images remains a significant bottleneck in breeding programs. The objective of this study was to develop an image-based high-throughput phenotyping system for evaluating soybean maturity in breeding programs. Images were acquired twice a week, starting when the earlier lines began maturation until the latest ones were mature. Two complementary convolutional neural networks (CNN) weredeveloped to predict the maturity date. The first using a single date and the second using the five best image dates identified by the first model. The proposed CNN architecture was validated using more than 15,000 ground truth observations from five trials, including data from three growing seasons and two countries. The trained model showed good generalization capability with a root mean squared error lower than two days in four out of five trials. Four methods of estimating prediction uncertainty showed potential at identifying different sources of errors in the maturity date predictions. The architecture developed solves limitations of previous research and can be used at scale in commercial breeding programs.


Detalles Bibliográficos
2020
MACHINE LEARNING
PHYSIOLOGICAL MATURITY
PLANT BREEDING
GLYCINE MAX (L.) MERR
SOYBEAN PHENOLOGY
SOJA
MEJORAMIENTO GENETICO DE PLANTAS
Inglés
Instituto Nacional de Investigación Agropecuaria
AINFO
http://www.ainfo.inia.uy/consulta/busca?b=pc&id=61456&biblioteca=vazio&busca=61456&qFacets=61456
Acceso abierto
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author TREVISAN, R.
author2 PÉREZ, O.
SCHMITZ, N.
DIERS, B.
MARTIN, N
author2_role author
author
author
author
author_facet TREVISAN, R.
PÉREZ, O.
SCHMITZ, N.
DIERS, B.
MARTIN, N
author_role author
bitstream.checksum.fl_str_mv 2e1ed13b2aab11e727137cb9eea5e4d3
bitstream.checksumAlgorithm.fl_str_mv MD5
bitstream.url.fl_str_mv https://redi.anii.org.uy/jspui/bitstream/20.500.12381/1519/1/sword-2022-10-20T22%3a42%3a09.original.xml
collection AINFO
dc.creator.none.fl_str_mv TREVISAN, R.
PÉREZ, O.
SCHMITZ, N.
DIERS, B.
MARTIN, N
dc.date.accessioned.none.fl_str_mv 2022-10-21T01:42:09Z
dc.date.available.none.fl_str_mv 2022-10-21T01:42:09Z
dc.date.issued.none.fl_str_mv 2020
dc.date.updated.none.fl_str_mv 2022-10-21T01:42:09Z
dc.description.abstract.none.fl_txt_mv Abstract: Soybean maturity is a trait of critical importance for the development of new soybean cultivars, nevertheless, its characterization based on visual ratings has many challenges.Unmanned aerial vehicles (UAVs) imagery-based high-throughput phenotyping methodologieshave been proposed as an alternative to the traditional visual ratings of pod senescence. However, the lack of scalable and accurate methods to extract the desired information from the images remains a significant bottleneck in breeding programs. The objective of this study was to develop an image-based high-throughput phenotyping system for evaluating soybean maturity in breeding programs. Images were acquired twice a week, starting when the earlier lines began maturation until the latest ones were mature. Two complementary convolutional neural networks (CNN) weredeveloped to predict the maturity date. The first using a single date and the second using the five best image dates identified by the first model. The proposed CNN architecture was validated using more than 15,000 ground truth observations from five trials, including data from three growing seasons and two countries. The trained model showed good generalization capability with a root mean squared error lower than two days in four out of five trials. Four methods of estimating prediction uncertainty showed potential at identifying different sources of errors in the maturity date predictions. The architecture developed solves limitations of previous research and can be used at scale in commercial breeding programs.
dc.identifier.none.fl_str_mv http://www.ainfo.inia.uy/consulta/busca?b=pc&id=61456&biblioteca=vazio&busca=61456&qFacets=61456
dc.language.iso.none.fl_str_mv en
eng
dc.rights.es.fl_str_mv Acceso abierto
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
dc.source.none.fl_str_mv reponame:AINFO
instname:Instituto Nacional de Investigación Agropecuaria
instacron:Instituto Nacional de Investigación Agropecuaria
dc.subject.none.fl_str_mv MACHINE LEARNING
PHYSIOLOGICAL MATURITY
PLANT BREEDING
GLYCINE MAX (L.) MERR
SOYBEAN PHENOLOGY
SOJA
MEJORAMIENTO GENETICO DE PLANTAS
dc.title.none.fl_str_mv High-throughput phenotyping of soybean maturity using time Series UAV imagery and convolutional neural networks.
dc.type.none.fl_str_mv Article
PublishedVersion
info:eu-repo/semantics/article
dc.type.version.none.fl_str_mv info:eu-repo/semantics/publishedVersion
description Abstract: Soybean maturity is a trait of critical importance for the development of new soybean cultivars, nevertheless, its characterization based on visual ratings has many challenges.Unmanned aerial vehicles (UAVs) imagery-based high-throughput phenotyping methodologieshave been proposed as an alternative to the traditional visual ratings of pod senescence. However, the lack of scalable and accurate methods to extract the desired information from the images remains a significant bottleneck in breeding programs. The objective of this study was to develop an image-based high-throughput phenotyping system for evaluating soybean maturity in breeding programs. Images were acquired twice a week, starting when the earlier lines began maturation until the latest ones were mature. Two complementary convolutional neural networks (CNN) weredeveloped to predict the maturity date. The first using a single date and the second using the five best image dates identified by the first model. The proposed CNN architecture was validated using more than 15,000 ground truth observations from five trials, including data from three growing seasons and two countries. The trained model showed good generalization capability with a root mean squared error lower than two days in four out of five trials. Four methods of estimating prediction uncertainty showed potential at identifying different sources of errors in the maturity date predictions. The architecture developed solves limitations of previous research and can be used at scale in commercial breeding programs.
eu_rights_str_mv openAccess
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repository.name.fl_str_mv AINFO - Instituto Nacional de Investigación Agropecuaria
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spelling 2022-10-21T01:42:09Z2022-10-21T01:42:09Z20202022-10-21T01:42:09Zhttp://www.ainfo.inia.uy/consulta/busca?b=pc&id=61456&biblioteca=vazio&busca=61456&qFacets=61456Abstract: Soybean maturity is a trait of critical importance for the development of new soybean cultivars, nevertheless, its characterization based on visual ratings has many challenges.Unmanned aerial vehicles (UAVs) imagery-based high-throughput phenotyping methodologieshave been proposed as an alternative to the traditional visual ratings of pod senescence. However, the lack of scalable and accurate methods to extract the desired information from the images remains a significant bottleneck in breeding programs. The objective of this study was to develop an image-based high-throughput phenotyping system for evaluating soybean maturity in breeding programs. Images were acquired twice a week, starting when the earlier lines began maturation until the latest ones were mature. Two complementary convolutional neural networks (CNN) weredeveloped to predict the maturity date. The first using a single date and the second using the five best image dates identified by the first model. The proposed CNN architecture was validated using more than 15,000 ground truth observations from five trials, including data from three growing seasons and two countries. The trained model showed good generalization capability with a root mean squared error lower than two days in four out of five trials. Four methods of estimating prediction uncertainty showed potential at identifying different sources of errors in the maturity date predictions. The architecture developed solves limitations of previous research and can be used at scale in commercial breeding programs.https://hdl.handle.net/20.500.12381/1519enenginfo:eu-repo/semantics/openAccessAcceso abiertoMACHINE LEARNINGPHYSIOLOGICAL MATURITYPLANT BREEDINGGLYCINE MAX (L.) MERRSOYBEAN PHENOLOGYSOJAMEJORAMIENTO GENETICO DE PLANTASHigh-throughput phenotyping of soybean maturity using time Series UAV imagery and convolutional neural networks.ArticlePublishedVersioninfo:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionreponame:AINFOinstname:Instituto Nacional de Investigación Agropecuariainstacron:Instituto Nacional de Investigación AgropecuariaTREVISAN, R.PÉREZ, O.SCHMITZ, N.DIERS, B.MARTIN, NSWORDsword-2022-10-20T22:42:09.original.xmlOriginal SWORD entry documentapplication/octet-stream2873https://redi.anii.org.uy/jspui/bitstream/20.500.12381/1519/1/sword-2022-10-20T22%3a42%3a09.original.xml2e1ed13b2aab11e727137cb9eea5e4d3MD5120.500.12381/15192022-10-20 22:42:09.975oai:redi.anii.org.uy:20.500.12381/1519Gobiernohttp://inia.uyhttps://redi.anii.org.uy/oai/requestlorrego@inia.org.uyUruguayopendoar:2022-10-21T01:42:09AINFO - Instituto Nacional de Investigación Agropecuariafalse
spellingShingle High-throughput phenotyping of soybean maturity using time Series UAV imagery and convolutional neural networks.
TREVISAN, R.
MACHINE LEARNING
PHYSIOLOGICAL MATURITY
PLANT BREEDING
GLYCINE MAX (L.) MERR
SOYBEAN PHENOLOGY
SOJA
MEJORAMIENTO GENETICO DE PLANTAS
status_str publishedVersion
title High-throughput phenotyping of soybean maturity using time Series UAV imagery and convolutional neural networks.
title_full High-throughput phenotyping of soybean maturity using time Series UAV imagery and convolutional neural networks.
title_fullStr High-throughput phenotyping of soybean maturity using time Series UAV imagery and convolutional neural networks.
title_full_unstemmed High-throughput phenotyping of soybean maturity using time Series UAV imagery and convolutional neural networks.
title_short High-throughput phenotyping of soybean maturity using time Series UAV imagery and convolutional neural networks.
title_sort High-throughput phenotyping of soybean maturity using time Series UAV imagery and convolutional neural networks.
topic MACHINE LEARNING
PHYSIOLOGICAL MATURITY
PLANT BREEDING
GLYCINE MAX (L.) MERR
SOYBEAN PHENOLOGY
SOJA
MEJORAMIENTO GENETICO DE PLANTAS
url http://www.ainfo.inia.uy/consulta/busca?b=pc&id=61456&biblioteca=vazio&busca=61456&qFacets=61456