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5. ScipionTomo: Towards cryo-electron tomography software integration, reproducibility, and validation

Author

Jiménez de la Morena, J., primary, Conesa, P., additional, Fonseca, Y.C., additional, de Isidro-Gómez, F.P., additional, Herreros, D., additional, Fernández-Giménez, E., additional, Strelak, D., additional, Moebel, E., additional, Buchholz, T.O., additional, Jug, F., additional, Martinez-Sanchez, A., additional, Harastani, M., additional, Jonic, S., additional, Conesa, J.J., additional, Cuervo, A., additional, Losana, P., additional, Sánchez, I., additional, Iceta, M., additional, del Cano, L., additional, Gragera, M., additional, Melero, R., additional, Sharov, G., additional, Castaño-Díez, D., additional, Koster, A., additional, Piccirillo, J.G., additional, Vilas, J.L., additional, Otón, J., additional, Marabini, R., additional, Sorzano, C.O.S., additional, and Carazo, J.M., additional

Published
2022
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7. Image processing tools for the validation of CryoEM maps

Author

Sorzano, Carlos O. S, Vilas Prieto, José Luis, Ramírez Aportela, Erney, Krieger, J., Hoyo, D. del, Herreros, David, Fernández Giménez, Estrella, Marchán, D., Macías, J. R., Sánchez, I., Caño, L. del, Fonseca Reyna, Y., Conesa, A., García Mena, A., Burguet Castell, Jordi, García Condado, J., Méndez García, J., Martínez, M., Muñoz Barrutia, A., Marabini, R., Vargas Balbuena, Javier, Carazo, J. M., Sorzano, Carlos O. S, Vilas Prieto, José Luis, Ramírez Aportela, Erney, Krieger, J., Hoyo, D. del, Herreros, David, Fernández Giménez, Estrella, Marchán, D., Macías, J. R., Sánchez, I., Caño, L. del, Fonseca Reyna, Y., Conesa, A., García Mena, A., Burguet Castell, Jordi, García Condado, J., Méndez García, J., Martínez, M., Muñoz Barrutia, A., Marabini, R., Vargas Balbuena, Javier, and Carazo, J. M.

Abstract

© The Royal Society of Chemistry 2022. We are thankful to Philip Baldwin, Dmitry Lyumkis, and Gabriel Lander for making their validation methods available (4.h and A.c). Javier Vargas and Jordi Burguet would like to thank the Spanish Ministry of Science and Innovation for financial support through the call 2019 Proyectos de I+D+i - RTI Tipo A (PID2019-108850RA-I00) and Arrate Muñoz Barrutia, PID2019-109820RB-I00, MCIN/AEI/10.13039/501100011033/, cofinanced by European Regional Development Fund (ERDF), "A way of making Europe.". The authors acknowledge the economic support from MICIN of the Instruct Image Processing Center (I2PC) as part of the Spanish participation in Instruct-ERIC, the European Strategic Infrastructure Project (ESFRI) in the area of Structural Biology, Grant PID2019-104757RB-I00 funded by MCIN/AEI/10.13039/501100011033/ and "ERDF A way of making Europe", by the European Union and Grant PRE2020 - 093527 funded by MCIN/AEI/ 10.13039/501100011033 and by "ESF Investing in your future". We also acknowledge support from "Comunidad Autonoma de Madrid" through Grant: S2017/BMD-3817, Instituto de Salud Carlos III (project IMPaCT-Data, exp. IMP/00019), co-funded by the European Union, European Regional Development Fund (ERDF, "A way to make Europe"), and European Union (EU) and Horizon 2020 through grants: EOSC Life (INFRAEOSC-04-2018, Proposal: 824087), HighResCells (ERC - 2018 - SyG, Proposal: 810057), IMpaCT (WIDESPREAD-03-2018 - Proposal: 857203), EOSC - Synergy (EINFRA-EOSC-5, Proposal: 857647), iNEXT-Discovery (Proposal: 871037), EnLaCES (H2020-MSCA-IF-2020, Proposal: 101024130)., The number of maps deposited in public databases (Electron Microscopy Data Bank, EMDB) determined by cryo-electron microscopy has quickly grown in recent years. With this rapid growth, it is critical to guarantee their quality. So far, map validation has primarily focused on the agreement between maps and models. From the image processing perspective, the validation has been mostly restricted to using two half-maps and the measurement of their internal consistency. In this article, we suggest that map validation can be taken much further from the point of view of image processing if 2D classes, particles, angles, coordinates, defoci, and micrographs are also provided. We present a progressive validation scheme that qualifies a result validation status from 0 to 5 and offers three optional qualifiers (A, W, and O) that can be added. The simplest validation state is 0, while the most complete would be 5AWO. This scheme has been implemented in a website https://biocomp.cnb.csic.es/EMValidationService/ to which reconstructed maps and their ESI can be uploaded., Unión Europea. Horizonte 2020, Ministerio de Ciencia e Innovación (MICINN)/FEDER, Ministerio de Ciencia e Innovación (MICINN), Comunidad de Madrid, Depto. de Óptica, Fac. de Ciencias Físicas, TRUE, pub

Published
2022

9. On bias, variance, overfitting, gold standard and consensus in single-particle analysis by cryo-electron microscopy

Author

Sorzano, C. O. S., primary, Jiménez-Moreno, A., additional, Maluenda, D., additional, Martínez, M., additional, Ramírez-Aportela, E., additional, Krieger, J., additional, Melero, R., additional, Cuervo, A., additional, Conesa, J., additional, Filipovic, J., additional, Conesa, P., additional, del Caño, L., additional, Fonseca, Y. C., additional, Jiménez-de la Morena, J., additional, Losana, P., additional, Sánchez-García, R., additional, Strelak, D., additional, Fernández-Giménez, E., additional, de Isidro-Gómez, F. P., additional, Herreros, D., additional, Vilas, J. L., additional, Marabini, R., additional, and Carazo, J. M., additional

Published
2022
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11. Image processing tools for the validation of CryoEM maps

Author

Sorzano, C. O. S., primary, Vilas, J. L., additional, Ramírez-Aportela, E., additional, Krieger, J., additional, del Hoyo, D., additional, Herreros, D., additional, Fernandez-Giménez, E., additional, Marchán, D., additional, Macías, J. R., additional, Sánchez, I., additional, del Caño, L., additional, Fonseca-Reyna, Y., additional, Conesa, P., additional, García-Mena, A., additional, Burguet, J., additional, García Condado, J., additional, Méndez García, J., additional, Martínez, M., additional, Muñoz-Barrutia, A., additional, Marabini, R., additional, Vargas, J., additional, and Carazo, J. M., additional

Published
2022
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13. Cryo-EM and Single-Particle Analysis with Scipion

Author

Jiménez-Moreno, A., primary, del Caño, L., primary, Martínez, M., primary, Ramírez-Aportela, E., primary, Cuervo, A., primary, Melero, R., primary, Sánchez-García, R., primary, Strelak, D., primary, Fernández-Giménez, E., primary, de Isidro-Gómez, F.P., primary, Herreros, D., primary, Conesa, P., primary, Fonseca, Y., primary, Maluenda, D., primary, Jiménez de la Morena, J., primary, Macías, J.R., primary, Losana, P., primary, Marabini, R., primary, Carazo, J.M., primary, and Sorzano, C.O.S., primary

Published
2021
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14. HAdV-F41 Capsid

Author

Perez Illana, M., primary, Martinez, M., additional, Mangroo, C., additional, Brown, M., additional, Marabini, R., additional, and San Martin, C., additional

Published
2021
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15. Algorithmic robustness to preferred orientations in single particle analysis by CryoEM

Author

Sorzano, C.O.S., primary, Semchonok, D., additional, Lin, S.-C., additional, Lo, Y.-C., additional, Vilas, J.L., additional, Jiménez-Moreno, A., additional, Gragera, M., additional, Vacca, S., additional, Maluenda, D., additional, Martínez, M., additional, Ramírez-Aportela, E., additional, Melero, R., additional, Cuervo, A., additional, Conesa, J.J., additional, Conesa, P., additional, Losana, P., additional, Caño, L. del, additional, de la Morena, J. Jiménez, additional, Fonseca, Y.C., additional, Sánchez-García, R., additional, Strelak, D., additional, Fernández-Giménez, E., additional, de Isidro, F., additional, Herreros, D., additional, Kastritis, P.L., additional, Marabini, R., additional, Bruce, B.D., additional, and Carazo, J.M., additional

Published
2021
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26. Integration of Cryo-EM Model Building Software in Scipion

Author

Martínez, M., primary, Jiménez-Moreno, A., additional, Maluenda, D., additional, Ramírez-Aportela, E., additional, Melero, R., additional, Cuervo, A., additional, Conesa, P., additional, del Caño, L., additional, Fonseca, Y. C., additional, Sánchez-García, R., additional, Strelak, D., additional, Conesa, J. J., additional, Fernández-Giménez, E., additional, de Isidro, F., additional, Sorzano, C. O. S., additional, Carazo, J. M., additional, and Marabini, R., additional

Published
2020
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27. Measurement of local resolution in electron tomography

Author

Vilas, J.L., primary, Oton, J., additional, Messaoudi, C., additional, Melero, R., additional, Conesa, P., additional, Ramirez-Aportela, E., additional, Mota, J., additional, Martinez, M., additional, Jimenez, A., additional, Marabini, R., additional, Carazo, J.M., additional, Vargas, J., additional, and Sorzano, C.O.S., additional

Published
2020
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33. Flexible workflows for on-the-fly electron-microscopy single-particle image processing using Scipion

Author

Maluenda, D., primary, Majtner, T., additional, Horvath, P., additional, Vilas, J. L., additional, Jiménez-Moreno, A., additional, Mota, J., additional, Ramírez-Aportela, E., additional, Sánchez-García, R., additional, Conesa, P., additional, del Caño, L., additional, Rancel, Y., additional, Fonseca, Y., additional, Martínez, M., additional, Sharov, G., additional, García, C.A., additional, Strelak, D., additional, Melero, R., additional, Marabini, R., additional, Carazo, J. M., additional, and Sorzano, C. O. S., additional

Published
2019
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34. Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy

Author

Sorzano, C. O. S., primary, Jiménez, A., additional, Mota, J., additional, Vilas, J. L., additional, Maluenda, D., additional, Martínez, M., additional, Ramírez-Aportela, E., additional, Majtner, T., additional, Segura, J., additional, Sánchez-García, R., additional, Rancel, Y., additional, del Caño, L., additional, Conesa, P., additional, Melero, R., additional, Jonic, S., additional, Vargas, J., additional, Cazals, F., additional, Freyberg, Z., additional, Krieger, J., additional, Bahar, I., additional, Marabini, R., additional, and Carazo, J. M., additional

Published
2019
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35. Using Scipion for stream image processing at Cryo-EM facilities

Author

Gómez-Blanco, J., primary, de la Rosa-Trevín, J.M., additional, Marabini, R., additional, del Cano, L., additional, Jiménez, A., additional, Martínez, M., additional, Melero, R., additional, Majtner, T., additional, Maluenda, D., additional, Mota, J., additional, Rancel, Y., additional, Ramírez-Aportela, E, additional, Vilas, J.L., additional, Carroni, M., additional, Fleischmann, S., additional, Lindahl, E., additional, Ashton, A.W., additional, Basham, M., additional, Clare, D.K., additional, Savage, K., additional, Siebert, C.A., additional, Sharov, G.G., additional, Sorzano, C.O.S., additional, Conesa, P., additional, and Carazo, J.M., additional

Published
2018
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37. Using Scipion for stream image processing at Cryo-EM facilities

Author

Gomez-Blanco, J., de la Rosa-Trevin, J. M., Marabini, R., del Cano, L., Jimenez, A., Martinez, M., Melero, R., Majtner, T., Maluenda, D., Mota, J., Rancel, Y., Ramirez-Aportela, E., Vilas, J. L., Carroni, M., Fleischmann, S., Lindahl, Erik, Ashton, A. W., Basham, M., Clare, D. K., Savage, K., Siebert, C. A., Sharov, G. G., Sorzano, C. O. S., Conesa, P., Carazo, J. M., Gomez-Blanco, J., de la Rosa-Trevin, J. M., Marabini, R., del Cano, L., Jimenez, A., Martinez, M., Melero, R., Majtner, T., Maluenda, D., Mota, J., Rancel, Y., Ramirez-Aportela, E., Vilas, J. L., Carroni, M., Fleischmann, S., Lindahl, Erik, Ashton, A. W., Basham, M., Clare, D. K., Savage, K., Siebert, C. A., Sharov, G. G., Sorzano, C. O. S., Conesa, P., and Carazo, J. M.

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-Trevfn 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., QC 20190118

Published
2018
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38. Perfectionistic traits and importance given to parenthood are associated with infertility-related quality of life in a sample of infertile women with and without endometriosis

Author

Zarbo, C, Brugnera, A, Compare, A, Candeloro, I, Secomandi, R, Betto, E, Fusi, F, Marabini, R, Malandrino, C, Carnelli, M, Trezzi, G, Bondi, E, Rabboni, M, Frigerio, L, Zarbo, Cristina, Brugnera, Agostino, Compare, Angelo, Candeloro, Ilario, Secomandi, Rita, Betto, Enrico, Fusi, Francesco, Marabini, Roberta, Malandrino, Chiara, Carnelli, Marco, Trezzi, Gaetano, Bondi, Emi, Rabboni, Massimo, Frigerio, Luigi, Zarbo, C, Brugnera, A, Compare, A, Candeloro, I, Secomandi, R, Betto, E, Fusi, F, Marabini, R, Malandrino, C, Carnelli, M, Trezzi, G, Bondi, E, Rabboni, M, Frigerio, L, Zarbo, Cristina, Brugnera, Agostino, Compare, Angelo, Candeloro, Ilario, Secomandi, Rita, Betto, Enrico, Fusi, Francesco, Marabini, Roberta, Malandrino, Chiara, Carnelli, Marco, Trezzi, Gaetano, Bondi, Emi, Rabboni, Massimo, and Frigerio, Luigi

Abstract

Objective: To assess quality of life and psychological differences between infertile women with endometriosis and without endometriosis. To investigate predictive role of perfectionism, mindful awareness and beliefs about parenthood to quality of life in a sample of women with fertility problems. Methods: 43 infertile women (22 with endometriosis; 21 without endometriosis) who recurred to Assisted Reproductive Treatments (ARTs) in the last 12 months took part to this cross-sectional study. Sociodemographic and clinical data were collected by means of a structured ad hoc questionnaire. Fertility Quality of Life, Fertility Problem Inventory – Need of parenthood subscale, Obsessive Beliefs Questionnaire – Perfectionism subscale, and Cognitive and Affective Mindfulness Scale – Revised were used to assess target outcomes. Results: Any difference in quality of life and psychological condition was found between infertile women with and without endometriosis. Importance given to parenthood (beta = −.60, p <.001) and perfectionism (beta = −.30, p <.05) predicted quality of life related to fertility issues, independently of group. Conclusions: Infertility might elicit self-discrepancy between real-self (i.e. being infertile) and ideal-self (being fertile), which in turn has a negative impact on quality of life. Conclusions about the role of psychologist in ART's team are discussed.

Published
2018

39. A Survey of the Use of Iterative Reconstruction Algorithms in Electron Microscopy

Author

Sorzano, C. O. S., Vargas, J., Otón, J., de la Rosa-Trevín, J. M., Vilas, J. L., Kazemi, M., Melero, R., del Caño, L., Cuenca, J., Conesa, P., Gómez-Blanco, J., Marabini, R., and Carazo, J. M.

Subjects
Article Subject
Abstract

One of the key steps in Electron Microscopy is the tomographic reconstruction of a three-dimensional (3D) map of the specimen being studied from a set of two-dimensional (2D) projections acquired at the microscope. This tomographic reconstruction may be performed with different reconstruction algorithms that can be grouped into several large families: direct Fourier inversion methods, back-projection methods, Radon methods, or iterative algorithms. In this review, we focus on the latter family of algorithms, explaining the mathematical rationale behind the different algorithms in this family as they have been introduced in the field of Electron Microscopy. We cover their use in Single Particle Analysis (SPA) as well as in Electron Tomography (ET).

Published
2017
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40. XTEND: Extending the depth of field in cryo soft X-ray tomography

Author

Otón J., Pereiro E., Conesa J.J., Chichón F.J., Luque D., Rodríguez J.M., Pérez-Berná A.J., Sorzano C.O.S., Klukowska J., Herman G.T., Vargas J., Marabini R., Carrascosa J.L., Carazo J.M. and This work was partially supported by MINECO grants BFU2014-54181 to JLC

Published
2017

42. Blind estimation of DED camera gain in Electron Microscopy

Author

Sorzano, C.O.S., primary, Fernández-Giménez, E., additional, Peredo-Robinson, V., additional, Vargas, J., additional, Majtner, T., additional, Caffarena, G., additional, Otón, J., additional, Vilas, J.L., additional, de la Rosa-Trevín, J.M., additional, Melero, R., additional, Gómez-Blanco, J., additional, Cuenca, J., additional, del Cano, L., additional, Conesa, P., additional, Marabini, R., additional, and Carazo, J.M., additional

Published
2018
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43. A survey of the use of iterative reconstruction algorithms in electron microscopy

Author

Sorzano, COS, Vargas, J, Otón, J, de la Rosa-Trevín, JM, Vilas, JL, Kazemi, M, Melero, R, Del Ca no, L, Cuenca, J, Conesa, P, Gomez-Blanco, J, Marabini, R, Carazo, JM, Sorzano, COS, Vargas, J, Otón, J, de la Rosa-Trevín, JM, Vilas, JL, Kazemi, M, Melero, R, Del Ca no, L, Cuenca, J, Conesa, P, Gomez-Blanco, J, Marabini, R, and Carazo, JM

Abstract

One of the key steps in Electron Microscopy is the tomographic reconstruction of a three-dimensional (3D) map of the specimen being studied from a set of two-dimensional (2D) projections acquired at the microscope. This tomographic reconstruction may be performed with different reconstruction algorithms that can be grouped into several large families: direct Fourier inversion methods, back-projection methods, Radon methods, or iterative algorithms. In this review, we focus on the latter family of algorithms, explaining the mathematical rationale behind the different algorithms in this family as they have been introduced in the field of Electron Microscopy. We cover their use in Single Particle Analysis (SPA) as well as in Electron Tomography (ET).

Published
2017

44. XTEND: Extending the depth of field in cryo soft X-ray tomography

Author

Otón J., Pereiro E., Conesa J.J., Chichón F.J., Luque D., Rodríguez J.M., Pérez-Berná A.J., Sorzano C.O.S., Klukowska J., Herman G.T., Vargas J., Marabini R., Carrascosa J.L., Carazo J.M., Otón J., Pereiro E., Conesa J.J., Chichón F.J., Luque D., Rodríguez J.M., Pérez-Berná A.J., Sorzano C.O.S., Klukowska J., Herman G.T., Vargas J., Marabini R., Carrascosa J.L., and Carazo J.M.

Published
2017

48. Soft X-ray tomography imaging for biological samples

Author

Otón J., Sorzano C.O.S., Chichón F.J., Carrascosa J.L., Carazo J.M., Marabini R. and 'Acknowledgements The authors would like to acknowledge the financial support from the Spanish Ministry of Economy and Competitiveness (MEC) through grants AIC-A-2011-0638 and BIO2010-16566',' the Comunidad de Madrid through grant CAM(S2010/BMD-2305)',' and the European Community’s Seventh Framework Programme (FP7/2007–2013) under BioStruct-X (CAP-INFRAS/1376) and NSF grant DMS-1114901. C.O.S. Sorzano is a recipient of a Ramón y Cajal fellowship financed by the European Social Fund and MEC. Joaquín Otón is supported by a Juan de la Cierva fellowship from MEC with reference JCI-2010-07594.'

Published
2014

49. Local analysis of strains and rotations for macromolecular electron microscopy maps

Author

Sorzano, C.O.S., primary, Martín-Ramos, A., additional, Prieto, F., additional, Melero, R., additional, Martín-Benito, J., additional, Jonic, S., additional, Navas-Calvente, J., additional, Vargas, J., additional, Otón, J., additional, Abrishami, V., additional, de la Rosa-Trevín, J.M., additional, Gómez-Blanco, J., additional, Vilas, J.L., additional, Marabini, R., additional, and Carazo, J.M., additional

Published
2016
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50. Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy

Author

de la Rosa-Trevín, J.M., primary, Quintana, A., additional, del Cano, L., additional, Zaldívar, A., additional, Foche, I., additional, Gutiérrez, J., additional, Gómez-Blanco, J., additional, Burguet-Castell, J., additional, Cuenca-Alba, J., additional, Abrishami, V., additional, Vargas, J., additional, Otón, J., additional, Sharov, G., additional, Vilas, J.L., additional, Navas, J., additional, Conesa, P., additional, Kazemi, M., additional, Marabini, R., additional, Sorzano, C.O.S., additional, and Carazo, J.M., additional

Published
2016
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