MyROOT 2.0

The automatic measurement of external physical traits (i.e. phenotyping) of plant organs, such as root length -which is highly correlated with plant viability- is one of the current bottlenecks in academic and agricultural research. Although many root length measurement software tools are available...

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Autores: González, Alejandro, Sevillano, Xavier, Betegón Putze, Isabel|||0000-0002-5456-5205, Blasco Escámez, David|||0000-0002-7891-8706, Ferrer Massot, Marc|||0000-0003-0046-1301, Caño Delgado, Ana I.|||0000-0002-8071-6724
Formato: artículo
Fecha de publicación:2020
País:España
Recursos:Universitat Autònoma de Barcelona
Repositorio:Dipòsit Digital de Documents de la UAB
Idioma:inglés
OAI Identifier:oai:ddd.uab.cat:218482
Acesso em linha:https://ddd.uab.cat/record/218482
https://dx.doi.org/urn:doi:10.1016/j.compag.2019.105125
Access Level:acceso abierto
Palavra-chave:Plant phenotyping
Root length measurement
Imaging tools
Plant science
High throughput Root phenotyping
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spelling MyROOT 2.0An automatic tool for high throughput and accurate primary root length measurementGonzález, AlejandroSevillano, XavierBetegón Putze, Isabel|||0000-0002-5456-5205Blasco Escámez, David|||0000-0002-7891-8706Ferrer Massot, Marc|||0000-0003-0046-1301Caño Delgado, Ana I.|||0000-0002-8071-6724Plant phenotypingRoot length measurementImaging toolsPlant scienceHigh throughput Root phenotypingThe automatic measurement of external physical traits (i.e. phenotyping) of plant organs, such as root length -which is highly correlated with plant viability- is one of the current bottlenecks in academic and agricultural research. Although many root length measurement software tools are available to the community, plant scientists often find their usability is limited, the measurements they provide are not accurate enough or they are too limited to specific image characteristics. In response to that, this work describes MyROOT 2.0, an automatic software tool jointly developed by plant scientists and computer vision engineers to create a high throughput root length measurement tool that reduces user intervention to a minimum. Using Arabidopsis thaliana seedlings grown on agar plates as a case study, MyROOT 2.0 is capable of detecting the root regions of interest in a fully automatic manner with an accuracy of 98%. Furthermore, this work also presents previously unreported experiments to evaluate several constituting modules of MyROOT 2.0, such as the ability to determine image scale automatically with subpixel accuracy, or the influence of training the hypocotyl detector using wildtype or mutant samples. Finally, when compared to state-of-the-art root length measurement software tools, MyROOT 2.0 achieves the highest root detection rate, obtaining measurements which are four times more accurate than its competitors. This makes MyROOT 2.0 an attractive tool for high throughput root phenotyping. 22020-01-0120202020-01-01Articlehttp://purl.org/coar/resource_type/c_6501AMhttp://purl.org/coar/version/c_ab4af688f83e57aainfo:eu-repo/semantics/articleapplication/pdfhttps://ddd.uab.cat/record/218482https://dx.doi.org/urn:doi:10.1016/j.compag.2019.105125reponame:Dipòsit Digital de Documents de la UABinstname:Universitat Autònoma de BarcelonaInglésengMinisterio de Economía y Competitividad https://doi.org/10.13039/501100003329 BIO2016-78955European Commission https://doi.org/10.13039/501100000780 683163Ministerio de Educación, Cultura y Deporte https://doi.org/10.13039/501100003176 FPU15/0282Ministerio de Economía y Competitividad https://doi.org/10.13039/501100003329 SEV-2015-4850533open accesshttp://purl.org/coar/access_right/c_abf2Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, i la comunicació pública de l'obra, sempre que no sigui amb finalitats comercials, i sempre que es reconegui l'autoria de l'obra original. No es permet la creació d'obres derivades.https://creativecommons.org/licenses/by-nc-nd/4.0/info:eu-repo/semantics/openAccessoai:ddd.uab.cat:2184822026-06-06T12:50:31Z
dc.title.none.fl_str_mv MyROOT 2.0
An automatic tool for high throughput and accurate primary root length measurement
title MyROOT 2.0
spellingShingle MyROOT 2.0
González, Alejandro
Plant phenotyping
Root length measurement
Imaging tools
Plant science
High throughput Root phenotyping
title_short MyROOT 2.0
title_full MyROOT 2.0
title_fullStr MyROOT 2.0
title_full_unstemmed MyROOT 2.0
title_sort MyROOT 2.0
dc.creator.none.fl_str_mv González, Alejandro
Sevillano, Xavier
Betegón Putze, Isabel|||0000-0002-5456-5205
Blasco Escámez, David|||0000-0002-7891-8706
Ferrer Massot, Marc|||0000-0003-0046-1301
Caño Delgado, Ana I.|||0000-0002-8071-6724
author González, Alejandro
author_facet González, Alejandro
Sevillano, Xavier
Betegón Putze, Isabel|||0000-0002-5456-5205
Blasco Escámez, David|||0000-0002-7891-8706
Ferrer Massot, Marc|||0000-0003-0046-1301
Caño Delgado, Ana I.|||0000-0002-8071-6724
author_role author
author2 Sevillano, Xavier
Betegón Putze, Isabel|||0000-0002-5456-5205
Blasco Escámez, David|||0000-0002-7891-8706
Ferrer Massot, Marc|||0000-0003-0046-1301
Caño Delgado, Ana I.|||0000-0002-8071-6724
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv Plant phenotyping
Root length measurement
Imaging tools
Plant science
High throughput Root phenotyping
topic Plant phenotyping
Root length measurement
Imaging tools
Plant science
High throughput Root phenotyping
description The automatic measurement of external physical traits (i.e. phenotyping) of plant organs, such as root length -which is highly correlated with plant viability- is one of the current bottlenecks in academic and agricultural research. Although many root length measurement software tools are available to the community, plant scientists often find their usability is limited, the measurements they provide are not accurate enough or they are too limited to specific image characteristics. In response to that, this work describes MyROOT 2.0, an automatic software tool jointly developed by plant scientists and computer vision engineers to create a high throughput root length measurement tool that reduces user intervention to a minimum. Using Arabidopsis thaliana seedlings grown on agar plates as a case study, MyROOT 2.0 is capable of detecting the root regions of interest in a fully automatic manner with an accuracy of 98%. Furthermore, this work also presents previously unreported experiments to evaluate several constituting modules of MyROOT 2.0, such as the ability to determine image scale automatically with subpixel accuracy, or the influence of training the hypocotyl detector using wildtype or mutant samples. Finally, when compared to state-of-the-art root length measurement software tools, MyROOT 2.0 achieves the highest root detection rate, obtaining measurements which are four times more accurate than its competitors. This makes MyROOT 2.0 an attractive tool for high throughput root phenotyping.
publishDate 2020
dc.date.none.fl_str_mv 2
2020-01-01
2020
2020-01-01
dc.type.none.fl_str_mv Article
http://purl.org/coar/resource_type/c_6501
AM
http://purl.org/coar/version/c_ab4af688f83e57aa
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://ddd.uab.cat/record/218482
https://dx.doi.org/urn:doi:10.1016/j.compag.2019.105125
url https://ddd.uab.cat/record/218482
https://dx.doi.org/urn:doi:10.1016/j.compag.2019.105125
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.relation.none.fl_str_mv Ministerio de Economía y Competitividad https://doi.org/10.13039/501100003329 BIO2016-78955
European Commission https://doi.org/10.13039/501100000780 683163
Ministerio de Educación, Cultura y Deporte https://doi.org/10.13039/501100003176 FPU15/0282
Ministerio de Economía y Competitividad https://doi.org/10.13039/501100003329 SEV-2015-4850533
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
https://creativecommons.org/licenses/by-nc-nd/4.0/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
https://creativecommons.org/licenses/by-nc-nd/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv reponame:Dipòsit Digital de Documents de la UAB
instname:Universitat Autònoma de Barcelona
instname_str Universitat Autònoma de Barcelona
reponame_str Dipòsit Digital de Documents de la UAB
collection Dipòsit Digital de Documents de la UAB
repository.name.fl_str_mv
repository.mail.fl_str_mv
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