Flexible workflows for on-the-fly electronmicroscopy single-particle image processing using Scipion
Electron microscopy of macromolecular structures is an approach that is in increasing demand in the field of structural biology. The automation of image acquisition has greatly increased the potential throughput of electron microscopy. Here, the focus is on the possibilities in Scipion to implement...
| Autores: | , , , , , , , , , , , , , , , , , , , |
|---|---|
| Tipo de recurso: | artículo |
| Fecha de publicación: | 2019 |
| País: | España |
| Institución: | Universidad Autónoma de Madrid |
| Repositorio: | Biblos-e Archivo. Repositorio Institucional de la UAM |
| Idioma: | inglés |
| OAI Identifier: | oai:repositorio.uam.es:10486/690936 |
| Acceso en línea: | http://hdl.handle.net/10486/690936 https://dx.doi.org/10.1107/S2059798319011860 |
| Access Level: | acceso abierto |
| Palabra clave: | Scipion image processing electron microscopy single-particle analysis stream processing electron-microscopy facilities Biología y Biomedicina / Biología |
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Flexible workflows for on-the-fly electronmicroscopy single-particle image processing using ScipionMaluenda, D.Majtner, T.Horvath, P.Vilas, J.L.Jiménez-Moreno, A.Mota, J.Ramírez-Aportela, E.Sánchez-García, R.Conesa, P.Caño, L. delRancel, Y.Fonseca, Y.Martínez, M.Sharov, G.García, C.A.Strelak, D.Melero, R.Marabini Ruiz, RobertoCarazo, J.M.Sorzano, C.O.S.Scipionimage processingelectron microscopysingle-particle analysisstream processingelectron-microscopy facilitiesBiología y Biomedicina / BiologíaElectron microscopy of macromolecular structures is an approach that is in increasing demand in the field of structural biology. The automation of image acquisition has greatly increased the potential throughput of electron microscopy. Here, the focus is on the possibilities in Scipion to implement flexible and robust image-processing workflows that allow the electron-microscope operator and the user to monitor the quality of image acquisition, assessing very simple acquisition measures or obtaining a first estimate of the initial volume, or the data resolution and heterogeneity, without any need for programming skills. These workflows can implement intelligent automatic decisions and they can warn the user of possible acquisition failures. These concepts are illustrated by analysis of the well known 2.2 Å resolution β-galactosidase data setThe authors would like to acknowledge financial support from The Spanish Ministry of Economy and Competitiveness through the BIO2016-76400-R (AEI/FEDER, UE) grant, the Comunidad Auto´noma de Madrid through grant S2017/BMD3817, the Instituto de Salud Carlos III (PT17/0009/0010), the European Union (EU) and Horizon 2020 through the CORBEL grant (INFRADEV-1-2014-1, Proposal 654248), the ‘la Caixa’ Foundation (ID 100010434, Fellow LCF/BQ/ IN18/11660021), Elixir–EXCELERATE (INFRADEV-3- 2015, Proposal 676559), iNEXT (INFRAIA-1-2014-2015, Proposal 653706), EOSCpilot (INFRADEV-04-2016, Proposal 739563) and INSTRUCT–ULTRA (INFRADEV03-2016-2017, Proposal 731005)International Union of CrystallographyDepartamento de Ingeniería InformáticaEscuela Politécnica Superior20192019-01-01research articlehttp://purl.org/coar/resource_type/c_2df8fbb1VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10486/690936https://dx.doi.org/10.1107/S2059798319011860reponame: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:10486/6909362026-06-23T12:46:27Z |
| dc.title.none.fl_str_mv |
Flexible workflows for on-the-fly electronmicroscopy single-particle image processing using Scipion |
| title |
Flexible workflows for on-the-fly electronmicroscopy single-particle image processing using Scipion |
| spellingShingle |
Flexible workflows for on-the-fly electronmicroscopy single-particle image processing using Scipion Maluenda, D. Scipion image processing electron microscopy single-particle analysis stream processing electron-microscopy facilities Biología y Biomedicina / Biología |
| title_short |
Flexible workflows for on-the-fly electronmicroscopy single-particle image processing using Scipion |
| title_full |
Flexible workflows for on-the-fly electronmicroscopy single-particle image processing using Scipion |
| title_fullStr |
Flexible workflows for on-the-fly electronmicroscopy single-particle image processing using Scipion |
| title_full_unstemmed |
Flexible workflows for on-the-fly electronmicroscopy single-particle image processing using Scipion |
| title_sort |
Flexible workflows for on-the-fly electronmicroscopy single-particle image processing using Scipion |
| dc.creator.none.fl_str_mv |
Maluenda, D. Majtner, T. Horvath, P. Vilas, J.L. Jiménez-Moreno, A. Mota, J. Ramírez-Aportela, E. Sánchez-García, R. Conesa, P. Caño, L. del Rancel, Y. Fonseca, Y. Martínez, M. Sharov, G. García, C.A. Strelak, D. Melero, R. Marabini Ruiz, Roberto Carazo, J.M. Sorzano, C.O.S. |
| author |
Maluenda, D. |
| author_facet |
Maluenda, D. Majtner, T. Horvath, P. Vilas, J.L. Jiménez-Moreno, A. Mota, J. Ramírez-Aportela, E. Sánchez-García, R. Conesa, P. Caño, L. del Rancel, Y. Fonseca, Y. Martínez, M. Sharov, G. García, C.A. Strelak, D. Melero, R. Marabini Ruiz, Roberto Carazo, J.M. Sorzano, C.O.S. |
| author_role |
author |
| author2 |
Majtner, T. Horvath, P. Vilas, J.L. Jiménez-Moreno, A. Mota, J. Ramírez-Aportela, E. Sánchez-García, R. Conesa, P. Caño, L. del Rancel, Y. Fonseca, Y. Martínez, M. Sharov, G. García, C.A. Strelak, D. Melero, R. 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 |
Scipion image processing electron microscopy single-particle analysis stream processing electron-microscopy facilities Biología y Biomedicina / Biología |
| topic |
Scipion image processing electron microscopy single-particle analysis stream processing electron-microscopy facilities Biología y Biomedicina / Biología |
| description |
Electron microscopy of macromolecular structures is an approach that is in increasing demand in the field of structural biology. The automation of image acquisition has greatly increased the potential throughput of electron microscopy. Here, the focus is on the possibilities in Scipion to implement flexible and robust image-processing workflows that allow the electron-microscope operator and the user to monitor the quality of image acquisition, assessing very simple acquisition measures or obtaining a first estimate of the initial volume, or the data resolution and heterogeneity, without any need for programming skills. These workflows can implement intelligent automatic decisions and they can warn the user of possible acquisition failures. These concepts are illustrated by analysis of the well known 2.2 Å resolution β-galactosidase data set |
| publishDate |
2019 |
| dc.date.none.fl_str_mv |
2019 2019-01-01 |
| 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/10486/690936 https://dx.doi.org/10.1107/S2059798319011860 |
| url |
http://hdl.handle.net/10486/690936 https://dx.doi.org/10.1107/S2059798319011860 |
| 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 |
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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 |
International Union of Crystallography |
| publisher.none.fl_str_mv |
International Union of Crystallography |
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reponame:Biblos-e Archivo. Repositorio Institucional de la UAM instname:Universidad Autónoma de Madrid |
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Universidad Autónoma de Madrid |
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Biblos-e Archivo. Repositorio Institucional de la UAM |
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Biblos-e Archivo. Repositorio Institucional de la UAM |
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