Arabidopsis phenotyping through geometric morphometrics
- Autores
- Manacorda, Carlos Augusto; Asurmendi, Sebastian
- Año de publicación
- 2018
- Idioma
- inglés
- Tipo de recurso
- artículo
- Estado
- versión publicada
- Descripción
- Background: Recently, great technical progress has been achieved in the field of plant phenotyping. High-throughput platforms and the development of improved algorithms for rosette image segmentation make it possible to extract shape and size parameters for genetic, physiological, and environmental studies on a large scale. The development of low-cost phenotyping platforms and freeware resources make it possible to widely expand phenotypic analysis tools for Arabidopsis. However, objective descriptors of shape parameters that could be used independently of the platform and segmentation software used are still lacking, and shape descriptions still rely on ad hoc or even contradictory descriptors, which could make comparisons difficult and perhaps inaccurate. Modern geometric morphometrics is a family of methods in quantitative biology proposed to be the main source of data and analytical tools in the emerging field of phenomics studies. Based on the location of landmarks (corresponding points) over imaged specimens and by combining geometry, multivariate analysis, and powerful statistical techniques, these tools offer the possibility to reproducibly and accurately account for shape variations among groups and measure them in shape distance units. Results: Here, a particular scheme of landmark placement on Arabidopsis rosette images is proposed to study shape variation in viral infection processes. Shape differences between controls and infected plants are quantified throughout the infectious process and visualized. Quantitative comparisons between two unrelated ssRNA+ viruses are shown, and reproducibility issues are assessed. Conclusions: Combined with the newest automated platforms and plant segmentation procedures, geometric morphometric tools could boost phenotypic features extraction and processing in an objective, reproducible manner.
Fil: Manacorda, Carlos Augusto. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina
Fil: Asurmendi, Sebastian. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina - Materia
-
ARABIDOPSIS
GEOMETRIC MORPHOMETRICS
LANDMARKS
ORMV
PHENOTYPING
PROCRUSTES ANALYSIS
TUMV - Nivel de accesibilidad
- acceso abierto
- Condiciones de uso
- https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
- Repositorio
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/175942
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Arabidopsis phenotyping through geometric morphometricsManacorda, Carlos AugustoAsurmendi, SebastianARABIDOPSISGEOMETRIC MORPHOMETRICSLANDMARKSORMVPHENOTYPINGPROCRUSTES ANALYSISTUMVhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Background: Recently, great technical progress has been achieved in the field of plant phenotyping. High-throughput platforms and the development of improved algorithms for rosette image segmentation make it possible to extract shape and size parameters for genetic, physiological, and environmental studies on a large scale. The development of low-cost phenotyping platforms and freeware resources make it possible to widely expand phenotypic analysis tools for Arabidopsis. However, objective descriptors of shape parameters that could be used independently of the platform and segmentation software used are still lacking, and shape descriptions still rely on ad hoc or even contradictory descriptors, which could make comparisons difficult and perhaps inaccurate. Modern geometric morphometrics is a family of methods in quantitative biology proposed to be the main source of data and analytical tools in the emerging field of phenomics studies. Based on the location of landmarks (corresponding points) over imaged specimens and by combining geometry, multivariate analysis, and powerful statistical techniques, these tools offer the possibility to reproducibly and accurately account for shape variations among groups and measure them in shape distance units. Results: Here, a particular scheme of landmark placement on Arabidopsis rosette images is proposed to study shape variation in viral infection processes. Shape differences between controls and infected plants are quantified throughout the infectious process and visualized. Quantitative comparisons between two unrelated ssRNA+ viruses are shown, and reproducibility issues are assessed. Conclusions: Combined with the newest automated platforms and plant segmentation procedures, geometric morphometric tools could boost phenotypic features extraction and processing in an objective, reproducible manner.Fil: Manacorda, Carlos Augusto. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; ArgentinaFil: Asurmendi, Sebastian. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaOxford University Press2018-06info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/175942Manacorda, Carlos Augusto; Asurmendi, Sebastian; Arabidopsis phenotyping through geometric morphometrics; Oxford University Press; GigaScience; 7; 7; 6-2018; 1-202047-217XCONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giy073/5039702info:eu-repo/semantics/altIdentifier/doi/10.1093/gigascience/giy073info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T10:04:04Zoai:ri.conicet.gov.ar:11336/175942instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-03 10:04:05.167CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse |
dc.title.none.fl_str_mv |
Arabidopsis phenotyping through geometric morphometrics |
title |
Arabidopsis phenotyping through geometric morphometrics |
spellingShingle |
Arabidopsis phenotyping through geometric morphometrics Manacorda, Carlos Augusto ARABIDOPSIS GEOMETRIC MORPHOMETRICS LANDMARKS ORMV PHENOTYPING PROCRUSTES ANALYSIS TUMV |
title_short |
Arabidopsis phenotyping through geometric morphometrics |
title_full |
Arabidopsis phenotyping through geometric morphometrics |
title_fullStr |
Arabidopsis phenotyping through geometric morphometrics |
title_full_unstemmed |
Arabidopsis phenotyping through geometric morphometrics |
title_sort |
Arabidopsis phenotyping through geometric morphometrics |
dc.creator.none.fl_str_mv |
Manacorda, Carlos Augusto Asurmendi, Sebastian |
author |
Manacorda, Carlos Augusto |
author_facet |
Manacorda, Carlos Augusto Asurmendi, Sebastian |
author_role |
author |
author2 |
Asurmendi, Sebastian |
author2_role |
author |
dc.subject.none.fl_str_mv |
ARABIDOPSIS GEOMETRIC MORPHOMETRICS LANDMARKS ORMV PHENOTYPING PROCRUSTES ANALYSIS TUMV |
topic |
ARABIDOPSIS GEOMETRIC MORPHOMETRICS LANDMARKS ORMV PHENOTYPING PROCRUSTES ANALYSIS TUMV |
purl_subject.fl_str_mv |
https://purl.org/becyt/ford/1.6 https://purl.org/becyt/ford/1 |
dc.description.none.fl_txt_mv |
Background: Recently, great technical progress has been achieved in the field of plant phenotyping. High-throughput platforms and the development of improved algorithms for rosette image segmentation make it possible to extract shape and size parameters for genetic, physiological, and environmental studies on a large scale. The development of low-cost phenotyping platforms and freeware resources make it possible to widely expand phenotypic analysis tools for Arabidopsis. However, objective descriptors of shape parameters that could be used independently of the platform and segmentation software used are still lacking, and shape descriptions still rely on ad hoc or even contradictory descriptors, which could make comparisons difficult and perhaps inaccurate. Modern geometric morphometrics is a family of methods in quantitative biology proposed to be the main source of data and analytical tools in the emerging field of phenomics studies. Based on the location of landmarks (corresponding points) over imaged specimens and by combining geometry, multivariate analysis, and powerful statistical techniques, these tools offer the possibility to reproducibly and accurately account for shape variations among groups and measure them in shape distance units. Results: Here, a particular scheme of landmark placement on Arabidopsis rosette images is proposed to study shape variation in viral infection processes. Shape differences between controls and infected plants are quantified throughout the infectious process and visualized. Quantitative comparisons between two unrelated ssRNA+ viruses are shown, and reproducibility issues are assessed. Conclusions: Combined with the newest automated platforms and plant segmentation procedures, geometric morphometric tools could boost phenotypic features extraction and processing in an objective, reproducible manner. Fil: Manacorda, Carlos Augusto. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina Fil: Asurmendi, Sebastian. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina |
description |
Background: Recently, great technical progress has been achieved in the field of plant phenotyping. High-throughput platforms and the development of improved algorithms for rosette image segmentation make it possible to extract shape and size parameters for genetic, physiological, and environmental studies on a large scale. The development of low-cost phenotyping platforms and freeware resources make it possible to widely expand phenotypic analysis tools for Arabidopsis. However, objective descriptors of shape parameters that could be used independently of the platform and segmentation software used are still lacking, and shape descriptions still rely on ad hoc or even contradictory descriptors, which could make comparisons difficult and perhaps inaccurate. Modern geometric morphometrics is a family of methods in quantitative biology proposed to be the main source of data and analytical tools in the emerging field of phenomics studies. Based on the location of landmarks (corresponding points) over imaged specimens and by combining geometry, multivariate analysis, and powerful statistical techniques, these tools offer the possibility to reproducibly and accurately account for shape variations among groups and measure them in shape distance units. Results: Here, a particular scheme of landmark placement on Arabidopsis rosette images is proposed to study shape variation in viral infection processes. Shape differences between controls and infected plants are quantified throughout the infectious process and visualized. Quantitative comparisons between two unrelated ssRNA+ viruses are shown, and reproducibility issues are assessed. Conclusions: Combined with the newest automated platforms and plant segmentation procedures, geometric morphometric tools could boost phenotypic features extraction and processing in an objective, reproducible manner. |
publishDate |
2018 |
dc.date.none.fl_str_mv |
2018-06 |
dc.type.none.fl_str_mv |
info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://purl.org/coar/resource_type/c_6501 info:ar-repo/semantics/articulo |
format |
article |
status_str |
publishedVersion |
dc.identifier.none.fl_str_mv |
http://hdl.handle.net/11336/175942 Manacorda, Carlos Augusto; Asurmendi, Sebastian; Arabidopsis phenotyping through geometric morphometrics; Oxford University Press; GigaScience; 7; 7; 6-2018; 1-20 2047-217X CONICET Digital CONICET |
url |
http://hdl.handle.net/11336/175942 |
identifier_str_mv |
Manacorda, Carlos Augusto; Asurmendi, Sebastian; Arabidopsis phenotyping through geometric morphometrics; Oxford University Press; GigaScience; 7; 7; 6-2018; 1-20 2047-217X CONICET Digital CONICET |
dc.language.none.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
info:eu-repo/semantics/altIdentifier/url/https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giy073/5039702 info:eu-repo/semantics/altIdentifier/doi/10.1093/gigascience/giy073 |
dc.rights.none.fl_str_mv |
info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by-nc-sa/2.5/ar/ |
eu_rights_str_mv |
openAccess |
rights_invalid_str_mv |
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/ |
dc.format.none.fl_str_mv |
application/pdf application/pdf |
dc.publisher.none.fl_str_mv |
Oxford University Press |
publisher.none.fl_str_mv |
Oxford University Press |
dc.source.none.fl_str_mv |
reponame:CONICET Digital (CONICET) instname:Consejo Nacional de Investigaciones Científicas y Técnicas |
reponame_str |
CONICET Digital (CONICET) |
collection |
CONICET Digital (CONICET) |
instname_str |
Consejo Nacional de Investigaciones Científicas y Técnicas |
repository.name.fl_str_mv |
CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas |
repository.mail.fl_str_mv |
dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar |
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