High-throughput phenotyping of soybean maturity using time Series UAV imagery and convolutional neural networks.
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.
2020 | |
MACHINE LEARNING PHYSIOLOGICAL MATURITY PLANT BREEDING GLYCINE MAX (L.) MERR SOYBEAN PHENOLOGY SOJA MEJORAMIENTO GENETICO DE PLANTAS |
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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 |
format | article |
id | INIAOAI_b1fbfb83f2077164bcbd7de16d45aac8 |
instacron_str | Instituto Nacional de Investigación Agropecuaria |
institution | Instituto Nacional de Investigación Agropecuaria |
instname_str | Instituto Nacional de Investigación Agropecuaria |
language | eng |
language_invalid_str_mv | en |
network_acronym_str | INIAOAI |
network_name_str | AINFO |
oai_identifier_str | oai:redi.anii.org.uy:20.500.12381/1519 |
publishDate | 2020 |
reponame_str | AINFO |
repository.mail.fl_str_mv | lorrego@inia.org.uy |
repository.name.fl_str_mv | AINFO - Instituto Nacional de Investigación Agropecuaria |
repository_id_str | |
rights_invalid_str_mv | Acceso abierto |
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 |