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
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/65326
Ver los metadatos del registro completo
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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 Técnicas2025-09-29T09:42:10Zoai: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:34982025-09-29 09:42:10.285CONICET 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) |
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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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13.070432 |