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Maluenda D, Majtner T, Horvath P, Vilas JL, Jiménez-Moreno A, Mota J, Ramírez-Aportela E, Sánchez-García R, Conesa P, del Caño L, Rancel Y, Fonseca Y, Martínez M, Sharov G, García C, Strelak D, Melero R, Marabini R, Carazo JM, Sorzano COS. Flexible workflows for on-the-fly electron-microscopy single-particle image processing using Scipion. Acta Crystallogr D Struct Biol 2019; 75:882-894. [PMID: 31588920 PMCID: PMC6778851 DOI: 10.1107/s2059798319011860] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 08/28/2019] [Indexed: 01/18/2023] Open
Abstract
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.
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Affiliation(s)
- D. Maluenda
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - T. Majtner
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - P. Horvath
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - J. L. Vilas
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - A. Jiménez-Moreno
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - J. Mota
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | | | - R. Sánchez-García
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - P. Conesa
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - L. del Caño
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - Y. Rancel
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - Y. Fonseca
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - M. Martínez
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - G. Sharov
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, England
| | | | - D. Strelak
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - R. Melero
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - R. Marabini
- Universidad Autónoma de Madrid, Madrid, Spain
| | - J. M. Carazo
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - C. O. S. Sorzano
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
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2
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Sorzano COS, Jiménez A, Mota J, Vilas JL, Maluenda D, Martínez M, Ramírez-Aportela E, Majtner T, Segura J, Sánchez-García R, Rancel Y, del Caño L, Conesa P, Melero R, Jonic S, Vargas J, Cazals F, Freyberg Z, Krieger J, Bahar I, Marabini R, Carazo JM. Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy. Acta Crystallogr F Struct Biol Commun 2019; 75:19-32. [PMID: 30605122 PMCID: PMC6317454 DOI: 10.1107/s2053230x18015108] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 10/26/2018] [Indexed: 11/10/2022] Open
Abstract
Single-particle analysis by electron microscopy is a well established technique for analyzing the three-dimensional structures of biological macromolecules. Besides its ability to produce high-resolution structures, it also provides insights into the dynamic behavior of the structures by elucidating their conformational variability. Here, the different image-processing methods currently available to study continuous conformational changes are reviewed.
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Affiliation(s)
| | - A. Jiménez
- National Center of Biotechnology (CSIC), Spain
| | - J. Mota
- National Center of Biotechnology (CSIC), Spain
| | - J. L. Vilas
- National Center of Biotechnology (CSIC), Spain
| | - D. Maluenda
- National Center of Biotechnology (CSIC), Spain
| | - M. Martínez
- National Center of Biotechnology (CSIC), Spain
| | | | - T. Majtner
- National Center of Biotechnology (CSIC), Spain
| | - J. Segura
- National Center of Biotechnology (CSIC), Spain
| | | | - Y. Rancel
- National Center of Biotechnology (CSIC), Spain
| | - L. del Caño
- National Center of Biotechnology (CSIC), Spain
| | - P. Conesa
- National Center of Biotechnology (CSIC), Spain
| | - R. Melero
- National Center of Biotechnology (CSIC), Spain
| | - S. Jonic
- Sorbonne Université, UMR CNRS 7590, Muséum National d’Histoire Naturelle, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | | | - F. Cazals
- Inria Sophia Antipolis – Méditerranée, France
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3
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Gómez-Blanco J, de la Rosa-Trevín JM, Marabini R, Del Cano L, Jiménez A, Martínez M, Melero R, Majtner T, Maluenda D, Mota J, Rancel Y, Ramírez-Aportela E, Vilas JL, Carroni M, Fleischmann S, Lindahl E, Ashton AW, Basham M, Clare DK, Savage K, Siebert CA, Sharov GG, Sorzano COS, Conesa P, Carazo JM. Using Scipion for stream image processing at Cryo-EM facilities. J Struct Biol 2018; 204:457-463. [PMID: 30296492 PMCID: PMC6303188 DOI: 10.1016/j.jsb.2018.10.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 10/01/2018] [Accepted: 10/03/2018] [Indexed: 12/11/2022]
Abstract
Three dimensional electron microscopy is becoming a very data-intensive field in which vast amounts of experimental images are acquired at high speed. To manage such large-scale projects, we had previously developed a modular workflow system called Scipion (de la Rosa-Trevín et al., 2016). We present here a major extension of Scipion that allows processing of EM images while the data is being acquired. This approach helps to detect problems at early stages, saves computing time and provides users with a detailed evaluation of the data quality before the acquisition is finished. At present, Scipion has been deployed and is in production mode in seven Cryo-EM facilities throughout the world.
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Affiliation(s)
- J Gómez-Blanco
- Department of Anatomy and Cell Biology, McGill University, Montreal, Canada
| | - J M de la Rosa-Trevín
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - R Marabini
- Escuela Politécnica Superior, Universidad Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain.
| | - L Del Cano
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - A Jiménez
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - M Martínez
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - R Melero
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - T Majtner
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - D Maluenda
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - J Mota
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - Y Rancel
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - E Ramírez-Aportela
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - J L Vilas
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - M Carroni
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - S Fleischmann
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - E Lindahl
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden; Swedish e-Science Research Center, KTH Royal Institute of Technology, Stockholm, Sweden
| | - A W Ashton
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - M Basham
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - D K Clare
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - K Savage
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - C A Siebert
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - G G Sharov
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 OQH, United Kingdom
| | - C O S Sorzano
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - P Conesa
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - J M Carazo
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
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4
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Sorzano COS, Fernández-Giménez E, Peredo-Robinson V, Vargas J, Majtner T, Caffarena G, Otón J, Vilas JL, de la Rosa-Trevín JM, Melero R, Gómez-Blanco J, Cuenca J, Del Cano L, Conesa P, Marabini R, Carazo JM. Blind estimation of DED camera gain in Electron Microscopy. J Struct Biol 2018; 203:90-93. [PMID: 29551714 DOI: 10.1016/j.jsb.2018.03.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 03/13/2018] [Accepted: 03/14/2018] [Indexed: 12/17/2022]
Abstract
The introduction of Direct Electron Detector (DED) videos in the Electron Microscope field has boosted Single Particle Analysis to a point in which it is currently considered to be a key technique in Structural Biology. In this article we introduce an approach to estimate the DED camera gain at each pixel from the movies themselves. This gain is needed to have the set of recorded frames into a coherent gray level range, homogeneous over the whole image. The algorithm does not need any other input than the DED movie itself, being capable of providing an estimate of the camera gain image, helping to identify dead pixels and cases of incorrectly calibrated cameras. We propose the algorithm to be used either to validate the experimentally acquired gain image (for instance, to follow its possible change over time) or to verify that there is no residual gain image after experimentally correcting for the camera gain. We show results for a number of DED camera models currently in use (DE, Falcon II, Falcon 3, and K2).
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Affiliation(s)
- C O S Sorzano
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain; Univ. San Pablo - CEU, Campus Urb. Montepríncipe, 28668 Boadilla del Monte, Madrid, Spain.
| | - E Fernández-Giménez
- Univ. San Pablo - CEU, Campus Urb. Montepríncipe, 28668 Boadilla del Monte, Madrid, Spain
| | - V Peredo-Robinson
- Univ. San Pablo - CEU, Campus Urb. Montepríncipe, 28668 Boadilla del Monte, Madrid, Spain
| | - J Vargas
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - T Majtner
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - G Caffarena
- Univ. San Pablo - CEU, Campus Urb. Montepríncipe, 28668 Boadilla del Monte, Madrid, Spain
| | - J Otón
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - J L Vilas
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | | | - R Melero
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - J Gómez-Blanco
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - J Cuenca
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - L Del Cano
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - P Conesa
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - R Marabini
- Univ. Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain
| | - J M Carazo
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
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