MyROOT: a method and software for the semiautomatic measurement of primary root length in Arabidopsis seedlings

Root analysis is essential for both academic and agricultural research. Despite the great advances in root phenotyping and imaging, calculating root length is still performed manually and involves considerable amounts of labor and time. To overcome these limitations, we developed MyROOT, a software...

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Autores: Betegón-Putze, Isabel, González, Alejandro, Sevillano, Xavier, Blasco‐Escámez, David, Caño-Delgado, Ana I.
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2019
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/206519
Acceso en línea:http://hdl.handle.net/10261/206519
Access Level:acceso abierto
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spelling MyROOT: a method and software for the semiautomatic measurement of primary root length in Arabidopsis seedlingsBetegón-Putze, IsabelGonzález, AlejandroSevillano, XavierBlasco‐Escámez, DavidCaño-Delgado, Ana I.Root analysis is essential for both academic and agricultural research. Despite the great advances in root phenotyping and imaging, calculating root length is still performed manually and involves considerable amounts of labor and time. To overcome these limitations, we developed MyROOT, a software for the semiautomatic quantification of root growth of seedlings growing directly on agar plates. Our method automatically determines the scale from the image of the plate, and subsequently measures the root length of the individual plants. To this aim, MyROOT combines a bottom‐up root tracking approach with a hypocotyl detection algorithm. At the same time as providing accurate root measurements, MyROOT also significantly minimizes the user intervention required during the process. Using Arabidopsis, we tested MyROOT with seedlings from different growth stages and experimental conditions. When comparing the data obtained from this software with that of manual root measurements, we found a high correlation between both methods (R2 = 0.997). When compared with previous developed software with similar features (BRAT and EZ‐Rhizo), MyROOT offered an improved accuracy for root length measurements. Therefore, MyROOT will be of great use to the plant science community by permitting high‐throughput root length measurements while saving both labor and time.AIC‐D is a recipient of a BIO2016‐78150‐P grant funded by the Spanish Ministry of Economy and Competitiveness and Agencia Estatal de Investigación (MINECO/AEI) and Fondo Europeo de Desarrollo Regional (FEDER), and a European Research Council, ERC Consolidator Grant (ERC‐2015‐CoG – 683163). IB‐P is funded by the FPU15/02822 grant from the Spanish Ministry of Education, Culture and Sport. DB‐E is funded by the ERC‐2015‐CoG – 683163 granted to the AIC‐D laboratory. This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 Research and Innovation Programme (Grant Agreement No. 683163). This work was supported by the CERCA Programme from the Generalitat de Catalunya. We acknowledge financial support from the Spanish Ministry of Economy and Competitiveness (MINECO), through the ‘Severo Ochoa Programme for Centres of Excellence in R&D’ 2016–2019 (SEV‐2015‐0533)’.Peer reviewedJohn Wiley & SonsMinisterio de Economía y Competitividad (España)Generalitat de CatalunyaEuropean CommissionEuropean Research CouncilMinisterio de Educación, Cultura y Deporte (España)Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202020202019info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/206519reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/BIO2016-78150-Pinfo:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/SEV-2015-0533https://doi.org/10.1111/tpj.14297Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/2065192026-05-22T06:33:51Z
dc.title.none.fl_str_mv MyROOT: a method and software for the semiautomatic measurement of primary root length in Arabidopsis seedlings
title MyROOT: a method and software for the semiautomatic measurement of primary root length in Arabidopsis seedlings
spellingShingle MyROOT: a method and software for the semiautomatic measurement of primary root length in Arabidopsis seedlings
Betegón-Putze, Isabel
title_short MyROOT: a method and software for the semiautomatic measurement of primary root length in Arabidopsis seedlings
title_full MyROOT: a method and software for the semiautomatic measurement of primary root length in Arabidopsis seedlings
title_fullStr MyROOT: a method and software for the semiautomatic measurement of primary root length in Arabidopsis seedlings
title_full_unstemmed MyROOT: a method and software for the semiautomatic measurement of primary root length in Arabidopsis seedlings
title_sort MyROOT: a method and software for the semiautomatic measurement of primary root length in Arabidopsis seedlings
dc.creator.none.fl_str_mv Betegón-Putze, Isabel
González, Alejandro
Sevillano, Xavier
Blasco‐Escámez, David
Caño-Delgado, Ana I.
author Betegón-Putze, Isabel
author_facet Betegón-Putze, Isabel
González, Alejandro
Sevillano, Xavier
Blasco‐Escámez, David
Caño-Delgado, Ana I.
author_role author
author2 González, Alejandro
Sevillano, Xavier
Blasco‐Escámez, David
Caño-Delgado, Ana I.
author2_role author
author
author
author
dc.contributor.none.fl_str_mv Ministerio de Economía y Competitividad (España)
Generalitat de Catalunya
European Commission
European Research Council
Ministerio de Educación, Cultura y Deporte (España)
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
description Root analysis is essential for both academic and agricultural research. Despite the great advances in root phenotyping and imaging, calculating root length is still performed manually and involves considerable amounts of labor and time. To overcome these limitations, we developed MyROOT, a software for the semiautomatic quantification of root growth of seedlings growing directly on agar plates. Our method automatically determines the scale from the image of the plate, and subsequently measures the root length of the individual plants. To this aim, MyROOT combines a bottom‐up root tracking approach with a hypocotyl detection algorithm. At the same time as providing accurate root measurements, MyROOT also significantly minimizes the user intervention required during the process. Using Arabidopsis, we tested MyROOT with seedlings from different growth stages and experimental conditions. When comparing the data obtained from this software with that of manual root measurements, we found a high correlation between both methods (R2 = 0.997). When compared with previous developed software with similar features (BRAT and EZ‐Rhizo), MyROOT offered an improved accuracy for root length measurements. Therefore, MyROOT will be of great use to the plant science community by permitting high‐throughput root length measurements while saving both labor and time.
publishDate 2019
dc.date.none.fl_str_mv 2019
2020
2020
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/206519
url http://hdl.handle.net/10261/206519
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
#PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/BIO2016-78150-P
info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/SEV-2015-0533
https://doi.org/10.1111/tpj.14297
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv John Wiley & Sons
publisher.none.fl_str_mv John Wiley & Sons
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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