Cryo-EM and single-particle analysis with Scipion

Cryo-electron microscopy has become one of the most important tools in biological research to reveal the structural information of macromolecules at near-atomic resolution. In single-particle analysis, the vitrified sample is imaged by an electron beam and the detectors at the end of the microscope...

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Detalhes bibliográficos
Autores: Jiménez-Moreno, A., Del Caño, L., Martínez, M., Ramírez-Aportela, E., Cuervo, A., Melero, R., Sánchez-García, R., Strelak, D., Fernández-Giménez, E., de Isidro-Gómez, F. P., Herreros, D., Conesa, P., Fonseca, Y., Maluenda, D., Jiménez de la Morena, J., Macías, J. R., Losana, P., Marabini Ruiz, Roberto, Carazo, J. M., Sorzano, C. O.S.
Formato: artículo
Fecha de publicación:2021
País:España
Recursos:Universidad Autónoma de Madrid
Repositorio:Biblos-e Archivo. Repositorio Institucional de la UAM
Idioma:inglés
OAI Identifier:oai:repositorio.uam.es:10486/697520
Acesso em linha:http://hdl.handle.net/10486/697520
https://dx.doi.org/10.3791/62261
Access Level:acceso abierto
Palavra-chave:Cryo-electron microscop
macromolecul
near-atomic resolution
Scipion
Informática
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spelling Cryo-EM and single-particle analysis with ScipionJiménez-Moreno, A.Del Caño, L.Martínez, M.Ramírez-Aportela, E.Cuervo, A.Melero, R.Sánchez-García, R.Strelak, D.Fernández-Giménez, E.de Isidro-Gómez, F. P.Herreros, D.Conesa, P.Fonseca, Y.Maluenda, D.Jiménez de la Morena, J.Macías, J. R.Losana, P.Marabini Ruiz, RobertoCarazo, J. M.Sorzano, C. O.S.Cryo-electron microscopmacromoleculnear-atomic resolutionScipionInformáticaCryo-electron microscopy has become one of the most important tools in biological research to reveal the structural information of macromolecules at near-atomic resolution. In single-particle analysis, the vitrified sample is imaged by an electron beam and the detectors at the end of the microscope column produce movies of that sample. These movies contain thousands of images of identical particles in random orientations. The data need to go through an image processing workflow with multiple steps to obtain the final 3D reconstructed volume. The goal of the image processing workflow is to identify the acquisition parameters to be able to reconstruct the specimen under study. Scipion provides all the tools to create this workflow using several image processing packages in an integrative framework, also allowing the traceability of the results. In this article the whole image processing workflow in Scipion is presented and discussed with data coming from a real test case, giving all the details necessary to go from the movies obtained by the microscope to a high resolution final 3D reconstruction. Also, the power of using consensus tools that allow combining methods, and confirming results along every step of the workflow, improving the accuracy of the obtained results, is discussed.MYJoVE CorporationDepartamento de Ingeniería InformáticaEscuela Politécnica Superior20212021-05-29research articlehttp://purl.org/coar/resource_type/c_2df8fbb1VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10486/697520https://dx.doi.org/10.3791/62261reponame:Biblos-e Archivo. Repositorio Institucional de la UAMinstname:Universidad Autónoma de MadridInglésengopen accesshttp://purl.org/coar/access_right/c_abf2info:eu-repo/semantics/openAccessoai:repositorio.uam.es:10486/6975202026-06-23T12:46:27Z
dc.title.none.fl_str_mv Cryo-EM and single-particle analysis with Scipion
title Cryo-EM and single-particle analysis with Scipion
spellingShingle Cryo-EM and single-particle analysis with Scipion
Jiménez-Moreno, A.
Cryo-electron microscop
macromolecul
near-atomic resolution
Scipion
Informática
title_short Cryo-EM and single-particle analysis with Scipion
title_full Cryo-EM and single-particle analysis with Scipion
title_fullStr Cryo-EM and single-particle analysis with Scipion
title_full_unstemmed Cryo-EM and single-particle analysis with Scipion
title_sort Cryo-EM and single-particle analysis with Scipion
dc.creator.none.fl_str_mv Jiménez-Moreno, A.
Del Caño, L.
Martínez, M.
Ramírez-Aportela, E.
Cuervo, A.
Melero, R.
Sánchez-García, R.
Strelak, D.
Fernández-Giménez, E.
de Isidro-Gómez, F. P.
Herreros, D.
Conesa, P.
Fonseca, Y.
Maluenda, D.
Jiménez de la Morena, J.
Macías, J. R.
Losana, P.
Marabini Ruiz, Roberto
Carazo, J. M.
Sorzano, C. O.S.
author Jiménez-Moreno, A.
author_facet Jiménez-Moreno, A.
Del Caño, L.
Martínez, M.
Ramírez-Aportela, E.
Cuervo, A.
Melero, R.
Sánchez-García, R.
Strelak, D.
Fernández-Giménez, E.
de Isidro-Gómez, F. P.
Herreros, D.
Conesa, P.
Fonseca, Y.
Maluenda, D.
Jiménez de la Morena, J.
Macías, J. R.
Losana, P.
Marabini Ruiz, Roberto
Carazo, J. M.
Sorzano, C. O.S.
author_role author
author2 Del Caño, L.
Martínez, M.
Ramírez-Aportela, E.
Cuervo, A.
Melero, R.
Sánchez-García, R.
Strelak, D.
Fernández-Giménez, E.
de Isidro-Gómez, F. P.
Herreros, D.
Conesa, P.
Fonseca, Y.
Maluenda, D.
Jiménez de la Morena, J.
Macías, J. R.
Losana, P.
Marabini Ruiz, Roberto
Carazo, J. M.
Sorzano, C. O.S.
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Departamento de Ingeniería Informática
Escuela Politécnica Superior
dc.subject.none.fl_str_mv Cryo-electron microscop
macromolecul
near-atomic resolution
Scipion
Informática
topic Cryo-electron microscop
macromolecul
near-atomic resolution
Scipion
Informática
description Cryo-electron microscopy has become one of the most important tools in biological research to reveal the structural information of macromolecules at near-atomic resolution. In single-particle analysis, the vitrified sample is imaged by an electron beam and the detectors at the end of the microscope column produce movies of that sample. These movies contain thousands of images of identical particles in random orientations. The data need to go through an image processing workflow with multiple steps to obtain the final 3D reconstructed volume. The goal of the image processing workflow is to identify the acquisition parameters to be able to reconstruct the specimen under study. Scipion provides all the tools to create this workflow using several image processing packages in an integrative framework, also allowing the traceability of the results. In this article the whole image processing workflow in Scipion is presented and discussed with data coming from a real test case, giving all the details necessary to go from the movies obtained by the microscope to a high resolution final 3D reconstruction. Also, the power of using consensus tools that allow combining methods, and confirming results along every step of the workflow, improving the accuracy of the obtained results, is discussed.
publishDate 2021
dc.date.none.fl_str_mv 2021
2021-05-29
dc.type.none.fl_str_mv research article
http://purl.org/coar/resource_type/c_2df8fbb1
VoR
http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv http://hdl.handle.net/10486/697520
https://dx.doi.org/10.3791/62261
url http://hdl.handle.net/10486/697520
https://dx.doi.org/10.3791/62261
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv MYJoVE Corporation
publisher.none.fl_str_mv MYJoVE Corporation
dc.source.none.fl_str_mv reponame:Biblos-e Archivo. Repositorio Institucional de la UAM
instname:Universidad Autónoma de Madrid
instname_str Universidad Autónoma de Madrid
reponame_str Biblos-e Archivo. Repositorio Institucional de la UAM
collection Biblos-e Archivo. Repositorio Institucional de la UAM
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,300724

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