Cryo-EM and Single-Particle Analysis with Scipion

J 2021

Cryo-EM and Single-Particle Analysis with Scipion

JIMÉNEZ-MORENO, Amaya, Laura DEL CAÑO, Marta MARTÍNEZ, Erney RAMÍREZ-APORTELA, Ana CUERVO et. al.

Základní údaje

Originální název

Cryo-EM and Single-Particle Analysis with Scipion

Autoři

JIMÉNEZ-MORENO, Amaya, Laura DEL CAÑO, Marta MARTÍNEZ, Erney RAMÍREZ-APORTELA, Ana CUERVO, Roberto MELERO, Ruben SÁNCHEZ-GARCÍA, David STŘELÁK (203 Česká republika, domácí), Estrella FERNÁNDEZ-GIMÉNEZ, Federico DE ISIDRO-GÓMEZ, David HERREROS, Pablo CONESA, Yunior FONSECA, David MALUENDA, Jorge JIMÉNEZ DE LA MORENA, Jose Ramon MACÍAS, Patricia LOSANA, Roberto MARABINI, Jose Maria CARAZO a Carlos SORZANO

Vydání

Jove-Journal of Visualized Experiments, Cambridge, JOURNAL OF VISUALIZED EXPERIMENTS, 2021, 1940-087X

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10609 Biochemical research methods

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 1.424

Kód RIV

RIV/00216224:14330/21:00129812

Organizační jednotka

Fakulta informatiky

DOI

http://dx.doi.org/10.3791/62261

UT WoS

000658340400045

Klíčová slova anglicky

cryo-electron microscopy; single-particle analysis

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 17. 8. 2023 07:24, RNDr. Pavel Šmerk, Ph.D.

Anotace

V originále

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.

Návaznosti

MUNI/A/1411/2019, interní kód MU

Název: Aplikovaný výzkum: softwarové architektury kritických infrastruktur, bezpečnost počítačových systémů, zpracování přirozeného jazyka a jazykové inženýrství, vizualizaci velkých dat a rozšířená realita.

Investor: Masarykova univerzita, Aplikovaný výzkum: softwarové architektury kritických infrastruktur, bezpečnost počítačových systémů, zpracování přirozeného jazyka a jazykové inženýrství, vizualizaci velkých dat a rozšířená realita., DO R. 2020_Kategorie A - Specifický výzkum - Studentské výzkumné projekty

Citovat

JIMÉNEZ-MORENO, Amaya, Laura DEL CAÑO, Marta MARTÍNEZ, Erney RAMÍREZ-APORTELA, Ana CUERVO, Roberto MELERO, Ruben SÁNCHEZ-GARCÍA, David STŘELÁK, Estrella FERNÁNDEZ-GIMÉNEZ, Federico DE ISIDRO-GÓMEZ, David HERREROS, Pablo CONESA, Yunior FONSECA, David MALUENDA, Jorge JIMÉNEZ DE LA MORENA, Jose Ramon MACÍAS, Patricia LOSANA, Roberto MARABINI, Jose Maria CARAZO a Carlos SORZANO. Cryo-EM and Single-Particle Analysis with Scipion. Jove-Journal of Visualized Experiments. Cambridge: JOURNAL OF VISUALIZED EXPERIMENTS, 2021, roč. 2021, č. 171, s. 1-27. ISSN 1940-087X. Dostupné z: https://dx.doi.org/10.3791/62261.

@article{1772603,
   author = {JiménezandMoreno, Amaya and del Caño, Laura and Martínez, Marta and RamírezandAportela, Erney and Cuervo, Ana and Melero, Roberto and SánchezandGarcía, Ruben and Střelák, David and FernándezandGiménez, Estrella and de IsidroandGómez, Federico and Herreros, David and Conesa, Pablo and Fonseca, Yunior and Maluenda, David and Jiménez de la Morena, Jorge and Macías, Jose Ramon and Losana, Patricia and Marabini, Roberto and Carazo, Jose Maria and Sorzano, Carlos},
   article_location = {Cambridge},
   article_number = {171},
   doi = {http://dx.doi.org/10.3791/62261},
   keywords = {cryo-electron microscopy; single-particle analysis},
   language = {eng},
   issn = {1940-087X},
   journal = {Jove-Journal of Visualized Experiments},
   title = {Cryo-EM and Single-Particle Analysis with Scipion},
   url = {http://dx.doi.org/10.3791/62261},
   volume = {2021},
   year = {2021}
}

TY  - JOUR
ID  - 1772603
AU  - Jiménez-Moreno, Amaya - del Caño, Laura - Martínez, Marta - Ramírez-Aportela, Erney - Cuervo, Ana - Melero, Roberto - Sánchez-García, Ruben - Střelák, David - Fernández-Giménez, Estrella - de Isidro-Gómez, Federico - Herreros, David - Conesa, Pablo - Fonseca, Yunior - Maluenda, David - Jiménez de la Morena, Jorge - Macías, Jose Ramon - Losana, Patricia - Marabini, Roberto - Carazo, Jose Maria - Sorzano, Carlos
PY  - 2021
TI  - Cryo-EM and Single-Particle Analysis with Scipion
JF  - Jove-Journal of Visualized Experiments
VL  - 2021
IS  - 171
SP  - 1-27
EP  - 1-27
PB  - JOURNAL OF VISUALIZED EXPERIMENTS
SN  - 1940087X
KW  - cryo-electron microscopy
KW  - single-particle analysis
UR  - http://dx.doi.org/10.3791/62261
N2  - 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.
ER  -

JIMÉNEZ-MORENO, Amaya, Laura DEL CAÑO, Marta MARTÍNEZ, Erney RAMÍREZ-APORTELA, Ana CUERVO, Roberto MELERO, Ruben SÁNCHEZ-GARCÍA, David STŘELÁK, Estrella FERNÁNDEZ-GIMÉNEZ, Federico DE ISIDRO-GÓMEZ, David HERREROS, Pablo CONESA, Yunior FONSECA, David MALUENDA, Jorge JIMÉNEZ DE LA MORENA, Jose Ramon MACÍAS, Patricia LOSANA, Roberto MARABINI, Jose Maria CARAZO a Carlos SORZANO. Cryo-EM and Single-Particle Analysis with Scipion. \textit{Jove-Journal of Visualized Experiments}. Cambridge: JOURNAL OF VISUALIZED EXPERIMENTS, 2021, roč.~2021, č.~171, s.~1-27. ISSN~1940-087X. Dostupné z: https://dx.doi.org/10.3791/62261.

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