ViralPlaque: a Fiji macro for automated assessment of viral plaque statistics

Autores
Cacciabue, Marco Polo; Curra, Anabella Paola; Gismondi, Maria Ines
Año de publicación
2019
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
laque assay has been used for a long time to determine infectious titers and characterize prokaryotic and eukaryotic viruses forming plaques. Indeed, plaque morphology and dimensions can provide information regarding the replication kinetics and the virulence of a particular virus. In this work, we present ViralPlaque, a fast, open-source and versatile ImageJ macro for the automated determination of viral plaque dimensions from digital images. Also, a machine learning plugin is integrated in the analysis algorithm for adaptation of ViralPlaque to the user’s needs and experimental conditions. A high correlation between manual and automated measurements of plaque dimensions was demonstrated. This macro will facilitate reliable and reproducible characterization of cytolytic viruses with an increased processing speed.
Instituto de Biotecnología
Fil: Cacciabue, Marco Polo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Curra, Anabella Paola. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Gismondi, Maria Ines. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fuente
PeerJ 7: e7729. (Septiembre 2019)
Materia
Machine Learning
Bioinformatics
Automation
Virology
Aprendizaje Electrónico
Bioinformática
Automatización
Prokaryotae
Eukaryota
Virología
Plaque Assay
Plaque Size
Cytopathic Effect
Nivel de accesibilidad
acceso abierto
Condiciones de uso
http://creativecommons.org/licenses/by-nc-sa/4.0/
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
oai:localhost:20.500.12123/6233
Acceder
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oai_identifier_str oai:localhost:20.500.12123/6233
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network_name_str INTA Digital (INTA)
spelling ViralPlaque: a Fiji macro for automated assessment of viral plaque statisticsCacciabue, Marco PoloCurra, Anabella PaolaGismondi, Maria InesMachine LearningBioinformaticsAutomationVirologyAprendizaje ElectrónicoBioinformáticaAutomatizaciónProkaryotaeEukaryotaVirologíaPlaque AssayPlaque SizeCytopathic Effectlaque assay has been used for a long time to determine infectious titers and characterize prokaryotic and eukaryotic viruses forming plaques. Indeed, plaque morphology and dimensions can provide information regarding the replication kinetics and the virulence of a particular virus. In this work, we present ViralPlaque, a fast, open-source and versatile ImageJ macro for the automated determination of viral plaque dimensions from digital images. Also, a machine learning plugin is integrated in the analysis algorithm for adaptation of ViralPlaque to the user’s needs and experimental conditions. A high correlation between manual and automated measurements of plaque dimensions was demonstrated. This macro will facilitate reliable and reproducible characterization of cytolytic viruses with an increased processing speed.Instituto de BiotecnologíaFil: Cacciabue, Marco Polo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Curra, Anabella Paola. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Gismondi, Maria Ines. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaPeerJ2019-10-29T17:53:09Z2019-10-29T17:53:09Z2019-09info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttps://peerj.com/articles/7729/http://hdl.handle.net/20.500.12123/62332167-8359https://doi.org/10.7717/peerj.7729PeerJ 7: e7729. (Septiembre 2019)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by-nc-sa/4.0/Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)2025-10-16T09:29:40Zoai:localhost:20.500.12123/6233instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-10-16 09:29:41.139INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv ViralPlaque: a Fiji macro for automated assessment of viral plaque statistics
title ViralPlaque: a Fiji macro for automated assessment of viral plaque statistics
spellingShingle ViralPlaque: a Fiji macro for automated assessment of viral plaque statistics
Cacciabue, Marco Polo
Machine Learning
Bioinformatics
Automation
Virology
Aprendizaje Electrónico
Bioinformática
Automatización
Prokaryotae
Eukaryota
Virología
Plaque Assay
Plaque Size
Cytopathic Effect
title_short ViralPlaque: a Fiji macro for automated assessment of viral plaque statistics
title_full ViralPlaque: a Fiji macro for automated assessment of viral plaque statistics
title_fullStr ViralPlaque: a Fiji macro for automated assessment of viral plaque statistics
title_full_unstemmed ViralPlaque: a Fiji macro for automated assessment of viral plaque statistics
title_sort ViralPlaque: a Fiji macro for automated assessment of viral plaque statistics
dc.creator.none.fl_str_mv Cacciabue, Marco Polo
Curra, Anabella Paola
Gismondi, Maria Ines
author Cacciabue, Marco Polo
author_facet Cacciabue, Marco Polo
Curra, Anabella Paola
Gismondi, Maria Ines
author_role author
author2 Curra, Anabella Paola
Gismondi, Maria Ines
author2_role author
author
dc.subject.none.fl_str_mv Machine Learning
Bioinformatics
Automation
Virology
Aprendizaje Electrónico
Bioinformática
Automatización
Prokaryotae
Eukaryota
Virología
Plaque Assay
Plaque Size
Cytopathic Effect
topic Machine Learning
Bioinformatics
Automation
Virology
Aprendizaje Electrónico
Bioinformática
Automatización
Prokaryotae
Eukaryota
Virología
Plaque Assay
Plaque Size
Cytopathic Effect
dc.description.none.fl_txt_mv laque assay has been used for a long time to determine infectious titers and characterize prokaryotic and eukaryotic viruses forming plaques. Indeed, plaque morphology and dimensions can provide information regarding the replication kinetics and the virulence of a particular virus. In this work, we present ViralPlaque, a fast, open-source and versatile ImageJ macro for the automated determination of viral plaque dimensions from digital images. Also, a machine learning plugin is integrated in the analysis algorithm for adaptation of ViralPlaque to the user’s needs and experimental conditions. A high correlation between manual and automated measurements of plaque dimensions was demonstrated. This macro will facilitate reliable and reproducible characterization of cytolytic viruses with an increased processing speed.
Instituto de Biotecnología
Fil: Cacciabue, Marco Polo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Curra, Anabella Paola. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Gismondi, Maria Ines. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
description laque assay has been used for a long time to determine infectious titers and characterize prokaryotic and eukaryotic viruses forming plaques. Indeed, plaque morphology and dimensions can provide information regarding the replication kinetics and the virulence of a particular virus. In this work, we present ViralPlaque, a fast, open-source and versatile ImageJ macro for the automated determination of viral plaque dimensions from digital images. Also, a machine learning plugin is integrated in the analysis algorithm for adaptation of ViralPlaque to the user’s needs and experimental conditions. A high correlation between manual and automated measurements of plaque dimensions was demonstrated. This macro will facilitate reliable and reproducible characterization of cytolytic viruses with an increased processing speed.
publishDate 2019
dc.date.none.fl_str_mv 2019-10-29T17:53:09Z
2019-10-29T17:53:09Z
2019-09
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 https://peerj.com/articles/7729/
http://hdl.handle.net/20.500.12123/6233
2167-8359
https://doi.org/10.7717/peerj.7729
url https://peerj.com/articles/7729/
http://hdl.handle.net/20.500.12123/6233
https://doi.org/10.7717/peerj.7729
identifier_str_mv 2167-8359
dc.language.none.fl_str_mv eng
language eng
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
eu_rights_str_mv openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv PeerJ
publisher.none.fl_str_mv PeerJ
dc.source.none.fl_str_mv PeerJ 7: e7729. (Septiembre 2019)
reponame:INTA Digital (INTA)
instname:Instituto Nacional de Tecnología Agropecuaria
reponame_str INTA Digital (INTA)
collection INTA Digital (INTA)
instname_str Instituto Nacional de Tecnología Agropecuaria
repository.name.fl_str_mv INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuaria
repository.mail.fl_str_mv tripaldi.nicolas@inta.gob.ar
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