An integrated calcium imaging processing toolbox for the analysis of neuronal population dynamics

Autores
Romano, Sebastián Alejo; Pérez Schuster, Verónica; Jouary, Adrien; Boulanger Weill, Jonathan; Candeo, Alessia; Pietri, Thomas; Sumbre, Germán
Año de publicación
2017
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
The development of new imaging and optogenetics techniques to study the dynamics of large neuronal circuits is generating datasets of unprecedented volume and complexity, demanding the development of appropriate analysis tools. We present a comprehensive computational workflow for the analysis of neuronal population calcium dynamics. The toolbox includes newly developed algorithms and interactive tools for image pre-processing and segmentation, estimation of significant single-neuron single-trial signals, mapping event-related neuronal responses, detection of activity-correlated neuronal clusters, exploration of population dynamics, and analysis of clusters' features against surrogate control datasets. The modules are integrated in a modular and versatile processing pipeline, adaptable to different needs. The clustering module is capable of detecting flexible, dynamically activated neuronal assemblies, consistent with the distributed population coding of the brain. We demonstrate the suitability of the toolbox for a variety of calcium imaging datasets. The toolbox open-source code, a step-by-step tutorial and a case study dataset are available at https://github.com/zebrain-lab/Toolbox-Romano-et-al.
Fil: Romano, Sebastián Alejo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigación en Biomedicina de Buenos Aires - Instituto Partner de la Sociedad Max Planck; Argentina. Ecole Normale Supérieure; Francia
Fil: Pérez Schuster, Verónica. Ecole Normale Supérieure; Francia. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Física; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina
Fil: Jouary, Adrien. Ecole Normale Supérieure; Francia
Fil: Boulanger Weill, Jonathan. Ecole Normale Supérieure; Francia
Fil: Candeo, Alessia. Ecole Normale Supérieure; Francia
Fil: Pietri, Thomas. Ecole Normale Supérieure; Francia
Fil: Sumbre, Germán. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina
Materia
calcium imaging
neuroscience
neuronal assemblies
data analysis
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/65326
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/65326
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling An integrated calcium imaging processing toolbox for the analysis of neuronal population dynamicsRomano, Sebastián AlejoPérez Schuster, VerónicaJouary, AdrienBoulanger Weill, JonathanCandeo, AlessiaPietri, ThomasSumbre, Germáncalcium imagingneuroscienceneuronal assembliesdata analysishttps://purl.org/becyt/ford/1.2https://purl.org/becyt/ford/1The development of new imaging and optogenetics techniques to study the dynamics of large neuronal circuits is generating datasets of unprecedented volume and complexity, demanding the development of appropriate analysis tools. We present a comprehensive computational workflow for the analysis of neuronal population calcium dynamics. The toolbox includes newly developed algorithms and interactive tools for image pre-processing and segmentation, estimation of significant single-neuron single-trial signals, mapping event-related neuronal responses, detection of activity-correlated neuronal clusters, exploration of population dynamics, and analysis of clusters' features against surrogate control datasets. The modules are integrated in a modular and versatile processing pipeline, adaptable to different needs. The clustering module is capable of detecting flexible, dynamically activated neuronal assemblies, consistent with the distributed population coding of the brain. We demonstrate the suitability of the toolbox for a variety of calcium imaging datasets. The toolbox open-source code, a step-by-step tutorial and a case study dataset are available at https://github.com/zebrain-lab/Toolbox-Romano-et-al.Fil: Romano, Sebastián Alejo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigación en Biomedicina de Buenos Aires - Instituto Partner de la Sociedad Max Planck; Argentina. Ecole Normale Supérieure; FranciaFil: Pérez Schuster, Verónica. Ecole Normale Supérieure; Francia. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Física; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; ArgentinaFil: Jouary, Adrien. Ecole Normale Supérieure; FranciaFil: Boulanger Weill, Jonathan. Ecole Normale Supérieure; FranciaFil: Candeo, Alessia. Ecole Normale Supérieure; FranciaFil: Pietri, Thomas. Ecole Normale Supérieure; FranciaFil: Sumbre, Germán. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; ArgentinaPublic Library of Science2017-06info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/65326Romano, Sebastián Alejo; Pérez Schuster, Verónica; Jouary, Adrien; Boulanger Weill, Jonathan; Candeo, Alessia; et al.; An integrated calcium imaging processing toolbox for the analysis of neuronal population dynamics; Public Library of Science; Plos Computational Biology; 13; 6; 6-2017; 1-23; e10055261553-734XCONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1371/journal.pcbi.1005526info:eu-repo/semantics/altIdentifier/url/https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005526info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-22T11:10:48Zoai:ri.conicet.gov.ar:11336/65326instacron: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:34982025-10-22 11:10:48.976CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv An integrated calcium imaging processing toolbox for the analysis of neuronal population dynamics
title An integrated calcium imaging processing toolbox for the analysis of neuronal population dynamics
spellingShingle An integrated calcium imaging processing toolbox for the analysis of neuronal population dynamics
Romano, Sebastián Alejo
calcium imaging
neuroscience
neuronal assemblies
data analysis
title_short An integrated calcium imaging processing toolbox for the analysis of neuronal population dynamics
title_full An integrated calcium imaging processing toolbox for the analysis of neuronal population dynamics
title_fullStr An integrated calcium imaging processing toolbox for the analysis of neuronal population dynamics
title_full_unstemmed An integrated calcium imaging processing toolbox for the analysis of neuronal population dynamics
title_sort An integrated calcium imaging processing toolbox for the analysis of neuronal population dynamics
dc.creator.none.fl_str_mv Romano, Sebastián Alejo
Pérez Schuster, Verónica
Jouary, Adrien
Boulanger Weill, Jonathan
Candeo, Alessia
Pietri, Thomas
Sumbre, Germán
author Romano, Sebastián Alejo
author_facet Romano, Sebastián Alejo
Pérez Schuster, Verónica
Jouary, Adrien
Boulanger Weill, Jonathan
Candeo, Alessia
Pietri, Thomas
Sumbre, Germán
author_role author
author2 Pérez Schuster, Verónica
Jouary, Adrien
Boulanger Weill, Jonathan
Candeo, Alessia
Pietri, Thomas
Sumbre, Germán
author2_role author
author
author
author
author
author
dc.subject.none.fl_str_mv calcium imaging
neuroscience
neuronal assemblies
data analysis
topic calcium imaging
neuroscience
neuronal assemblies
data analysis
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.2
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv The development of new imaging and optogenetics techniques to study the dynamics of large neuronal circuits is generating datasets of unprecedented volume and complexity, demanding the development of appropriate analysis tools. We present a comprehensive computational workflow for the analysis of neuronal population calcium dynamics. The toolbox includes newly developed algorithms and interactive tools for image pre-processing and segmentation, estimation of significant single-neuron single-trial signals, mapping event-related neuronal responses, detection of activity-correlated neuronal clusters, exploration of population dynamics, and analysis of clusters' features against surrogate control datasets. The modules are integrated in a modular and versatile processing pipeline, adaptable to different needs. The clustering module is capable of detecting flexible, dynamically activated neuronal assemblies, consistent with the distributed population coding of the brain. We demonstrate the suitability of the toolbox for a variety of calcium imaging datasets. The toolbox open-source code, a step-by-step tutorial and a case study dataset are available at https://github.com/zebrain-lab/Toolbox-Romano-et-al.
Fil: Romano, Sebastián Alejo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigación en Biomedicina de Buenos Aires - Instituto Partner de la Sociedad Max Planck; Argentina. Ecole Normale Supérieure; Francia
Fil: Pérez Schuster, Verónica. Ecole Normale Supérieure; Francia. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Física; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina
Fil: Jouary, Adrien. Ecole Normale Supérieure; Francia
Fil: Boulanger Weill, Jonathan. Ecole Normale Supérieure; Francia
Fil: Candeo, Alessia. Ecole Normale Supérieure; Francia
Fil: Pietri, Thomas. Ecole Normale Supérieure; Francia
Fil: Sumbre, Germán. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina
description The development of new imaging and optogenetics techniques to study the dynamics of large neuronal circuits is generating datasets of unprecedented volume and complexity, demanding the development of appropriate analysis tools. We present a comprehensive computational workflow for the analysis of neuronal population calcium dynamics. The toolbox includes newly developed algorithms and interactive tools for image pre-processing and segmentation, estimation of significant single-neuron single-trial signals, mapping event-related neuronal responses, detection of activity-correlated neuronal clusters, exploration of population dynamics, and analysis of clusters' features against surrogate control datasets. The modules are integrated in a modular and versatile processing pipeline, adaptable to different needs. The clustering module is capable of detecting flexible, dynamically activated neuronal assemblies, consistent with the distributed population coding of the brain. We demonstrate the suitability of the toolbox for a variety of calcium imaging datasets. The toolbox open-source code, a step-by-step tutorial and a case study dataset are available at https://github.com/zebrain-lab/Toolbox-Romano-et-al.
publishDate 2017
dc.date.none.fl_str_mv 2017-06
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/11336/65326
Romano, Sebastián Alejo; Pérez Schuster, Verónica; Jouary, Adrien; Boulanger Weill, Jonathan; Candeo, Alessia; et al.; An integrated calcium imaging processing toolbox for the analysis of neuronal population dynamics; Public Library of Science; Plos Computational Biology; 13; 6; 6-2017; 1-23; e1005526
1553-734X
CONICET Digital
CONICET
url http://hdl.handle.net/11336/65326
identifier_str_mv Romano, Sebastián Alejo; Pérez Schuster, Verónica; Jouary, Adrien; Boulanger Weill, Jonathan; Candeo, Alessia; et al.; An integrated calcium imaging processing toolbox for the analysis of neuronal population dynamics; Public Library of Science; Plos Computational Biology; 13; 6; 6-2017; 1-23; e1005526
1553-734X
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1371/journal.pcbi.1005526
info:eu-repo/semantics/altIdentifier/url/https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005526
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
application/pdf
dc.publisher.none.fl_str_mv Public Library of Science
publisher.none.fl_str_mv Public Library of Science
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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score 12.982451

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