MyROOT 2.0: An automatic tool for high throughput and accurate primary root length measurement

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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Detalles Bibliográficos
Autores: González, Alejandro, Sevillano, Xavier, Betegon Putze, Isabel, Blasco-Escámez, David, Ferrer, Marc, Caño- Delgado, Ana I.
Tipo de recurso: artículo
Fecha de publicación:2020
País:España
Institución:Universitat Ramon Llull (URL)
Repositorio:DAU Arxiu Digital de la Universitat Ramon Llull
OAI Identifier:oai:dau.url.edu:20.500.14342/5381
Acceso en línea:http://hdl.handle.net/20.500.14342/5381
https://doi.org/10.1016/j.compag.2019.105125
Access Level:acceso abierto
Palabra clave:Plant phenotyping
Root length measurement
Imaging tools
Plant science
High throughput Root phenotyping
Fenotipificació de plantes
Mesura de la longitud de les arrels
Eines d'imatge
Ciència vegetal
Fenotipificació d'arrels d'alt rendiment
Biotecnologia vegetal
004
57
58
62
632
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oai_identifier_str oai:dau.url.edu:20.500.14342/5381
network_acronym_str ES
network_name_str España
repository_id_str
spelling MyROOT 2.0: An automatic tool for high throughput and accurate primary root length measurementGonzález, AlejandroSevillano, XavierBetegon Putze, IsabelBlasco-Escámez, DavidFerrer, MarcCaño- Delgado, Ana I.Plant phenotypingRoot length measurementImaging toolsPlant scienceHigh throughput Root phenotypingFenotipificació de plantesMesura de la longitud de les arrelsEines d'imatgeCiència vegetalFenotipificació d'arrels d'alt rendimentBiotecnologia vegetal004575862632The 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.info:eu-repo/semantics/acceptedVersionElsevierUniversitat Ramon Llull. La Salle202520252020info:eu-repo/semantics/article25 p.application/pdfhttp://hdl.handle.net/20.500.14342/5381https://doi.org/10.1016/j.compag.2019.105125reponame:DAU Arxiu Digital de la Universitat Ramon Llullinstname:Universitat Ramon Llull (URL)InglésComputers and Electronics in Agriculture, vol. 168, gener 2020© 2019 Elsevier . Tots els drets reservatsinfo:eu-repo/semantics/openAccessoai:dau.url.edu:20.500.14342/53812026-06-21T06:40:37Z
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: An automatic tool for high throughput and accurate primary root length measurement
spellingShingle MyROOT 2.0: An automatic tool for high throughput and accurate primary root length measurement
González, Alejandro
Plant phenotyping
Root length measurement
Imaging tools
Plant science
High throughput Root phenotyping
Fenotipificació de plantes
Mesura de la longitud de les arrels
Eines d'imatge
Ciència vegetal
Fenotipificació d'arrels d'alt rendiment
Biotecnologia vegetal
004
57
58
62
632
title_short MyROOT 2.0: An automatic tool for high throughput and accurate primary root length measurement
title_full MyROOT 2.0: An automatic tool for high throughput and accurate primary root length measurement
title_fullStr MyROOT 2.0: An automatic tool for high throughput and accurate primary root length measurement
title_full_unstemmed MyROOT 2.0: An automatic tool for high throughput and accurate primary root length measurement
title_sort MyROOT 2.0: An automatic tool for high throughput and accurate primary root length measurement
dc.creator.none.fl_str_mv González, Alejandro
Sevillano, Xavier
Betegon Putze, Isabel
Blasco-Escámez, David
Ferrer, Marc
Caño- Delgado, Ana I.
author González, Alejandro
author_facet González, Alejandro
Sevillano, Xavier
Betegon Putze, Isabel
Blasco-Escámez, David
Ferrer, Marc
Caño- Delgado, Ana I.
author_role author
author2 Sevillano, Xavier
Betegon Putze, Isabel
Blasco-Escámez, David
Ferrer, Marc
Caño- Delgado, Ana I.
author2_role author
author
author
author
author
dc.contributor.none.fl_str_mv Universitat Ramon Llull. La Salle
dc.subject.none.fl_str_mv Plant phenotyping
Root length measurement
Imaging tools
Plant science
High throughput Root phenotyping
Fenotipificació de plantes
Mesura de la longitud de les arrels
Eines d'imatge
Ciència vegetal
Fenotipificació d'arrels d'alt rendiment
Biotecnologia vegetal
004
57
58
62
632
topic Plant phenotyping
Root length measurement
Imaging tools
Plant science
High throughput Root phenotyping
Fenotipificació de plantes
Mesura de la longitud de les arrels
Eines d'imatge
Ciència vegetal
Fenotipificació d'arrels d'alt rendiment
Biotecnologia vegetal
004
57
58
62
632
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 2020
2025
2025
dc.type.none.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv http://hdl.handle.net/20.500.14342/5381
https://doi.org/10.1016/j.compag.2019.105125
url http://hdl.handle.net/20.500.14342/5381
https://doi.org/10.1016/j.compag.2019.105125
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Computers and Electronics in Agriculture, vol. 168, gener 2020
dc.rights.none.fl_str_mv © 2019 Elsevier . Tots els drets reservats
info:eu-repo/semantics/openAccess
rights_invalid_str_mv © 2019 Elsevier . Tots els drets reservats
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 25 p.
application/pdf
dc.publisher.none.fl_str_mv Elsevier
publisher.none.fl_str_mv Elsevier
dc.source.none.fl_str_mv reponame:DAU Arxiu Digital de la Universitat Ramon Llull
instname:Universitat Ramon Llull (URL)
instname_str Universitat Ramon Llull (URL)
reponame_str DAU Arxiu Digital de la Universitat Ramon Llull
collection DAU Arxiu Digital de la Universitat Ramon Llull
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,811543

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