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

Journal of Structural Biology, vol. 214, pp. 107872

Abstract

Image processing in cryogenic electron tomography (cryoET) is currently at a similar state as Single Particle Analysis (SPA) in cryogenic electron microscopy (cryoEM) was a few years ago. Its data processing workflows are far from being well defined and the user experience is still not smooth. Moreover, file formats of different software packages and their associated metadata are not standardized, mainly since different packages are developed by different groups, focusing on different steps of the data processing pipeline. The Scipion framework, originally developed for SPA (de la Rosa-Trevín et al., 2016), has a generic python workflow engine that gives it the versatility to be extended to other fields, as demonstrated for model building (Martínez et al., 2020). In this article, we provide an extension of Scipion based on a set of tomography plugins (referred to as ScipionTomo hereafter), with a similar purpose: to allow users to be focused on the data processing and analysis instead of having to deal with multiple software installation issues and the inconvenience of switching from one to another, converting metadata files, managing possible incompatibilities, scripting (writing a simple program in a language that the computer must convert to machine language each time the program is run), etcetera. Additionally, having all the software available in an integrated platform allows comparing the results of different algorithms trying to solve the same problem. In this way, the commonalities and differences between estimated parameters shed light on which results can be more trusted than others. ScipionTomo is developed by a collaborative multidisciplinary team composed of Scipion team engineers, structural biologists, and in some cases, the developers whose software packages have been integrated. It is open to anyone in the field willing to contribute to this project. The result is a framework extension that combines the acquired knowledge of Scipion developers in close collaboration with third-party developers, and the on-demand design of functionalities requested by beta testers applying this solution to actual biological problems.

Authors 30

1. J. Jiménez de la Morena

   Consejo Superior de Investigaciones Científicas · Centro Nacional de Biotecnología · Universidad Autónoma de Madrid

   Affiliation as printed

   National Center of Biotechnology (CNB-CSIC), Madrid, Spain

   CNB-CSIC - Centro Nacional de Biotecnología [Madrid] (Campus de la Universidad Autónoma de Madrid, 28049 Madrid - Espagne)

   Centro Nacional de Biotecnología [Madrid]

2. Pablo Conesa

   Consejo Superior de Investigaciones Científicas · Centro Nacional de Biotecnología · Universidad Autónoma de Madrid

   Affiliation as printed

   National Center of Biotechnology (CNB-CSIC), Madrid, Spain

   CNB-CSIC - Centro Nacional de Biotecnología [Madrid] (Campus de la Universidad Autónoma de Madrid, 28049 Madrid - Espagne)

   Centro Nacional de Biotecnología [Madrid]

3. Yunior C. Fonseca

   Consejo Superior de Investigaciones Científicas · Centro Nacional de Biotecnología · Universidad Autónoma de Madrid

   Affiliation as printed

   National Center of Biotechnology (CNB-CSIC), Madrid, Spain

   CNB-CSIC - Centro Nacional de Biotecnología [Madrid] (Campus de la Universidad Autónoma de Madrid, 28049 Madrid - Espagne)

   Centro Nacional de Biotecnología [Madrid]

4. F.P. de Isidro-Gómez

   Consejo Superior de Investigaciones Científicas · Centro Nacional de Biotecnología · Universidad Autónoma de Madrid

   Affiliation as printed

   National Center of Biotechnology (CNB-CSIC), Madrid, Spain

   CNB-CSIC - Centro Nacional de Biotecnología [Madrid] (Campus de la Universidad Autónoma de Madrid, 28049 Madrid - Espagne)

   Centro Nacional de Biotecnología [Madrid]

5. David Herreros

   Consejo Superior de Investigaciones Científicas · Centro Nacional de Biotecnología · Universidad Autónoma de Madrid

   Affiliation as printed

   National Center of Biotechnology (CNB-CSIC), Madrid, Spain

   CNB-CSIC - Centro Nacional de Biotecnología [Madrid] (Campus de la Universidad Autónoma de Madrid, 28049 Madrid - Espagne)

   Centro Nacional de Biotecnología [Madrid]

6. Estrella Fernández-Giménez

   Consejo Superior de Investigaciones Científicas · Centro Nacional de Biotecnología · Universidad Autónoma de Madrid

   Affiliation as printed

   National Center of Biotechnology (CNB-CSIC), Madrid, Spain

   CNB-CSIC - Centro Nacional de Biotecnología [Madrid] (Campus de la Universidad Autónoma de Madrid, 28049 Madrid - Espagne)

   Centro Nacional de Biotecnología [Madrid]

7. David Střelák

   Consejo Superior de Investigaciones Científicas · Masaryk University · Centro Nacional de Biotecnología · Universidad Autónoma de Madrid

   Affiliation as printed

   National Center of Biotechnology (CNB-CSIC), Madrid, Spain; Masaryk University, Brno, Czech Republic

   CNB-CSIC - Centro Nacional de Biotecnología [Madrid] (Campus de la Universidad Autónoma de Madrid, 28049 Madrid - Espagne)

   Centro Nacional de Biotecnología [Madrid]

   Masaryk University [Brno]

8. Emmanuel Moebel

   Centre Inria de l'Université de Rennes

   Affiliation as printed

   Inria Rennes - Bretagne Atlantique, Rennes, France

   SERPICO - Space-timE RePresentation, Imaging and cellular dynamics of molecular COmplexes (Campus de Beaulieu 35042 Rennes cedex - France)

   Space-timE RePresentation, Imaging and cellular dynamics of molecular COmplexes

9. Tim-Oliver Buchholz

   Center for Systems Biology Dresden · Max Planck Institute of Molecular Cell Biology and Genetics

   Affiliation as printed

   Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Germany; Center for Systems Biology Dresden (CSBD), Germany

   Max Planck Institute of Molecular Cell Biology and Genetics

10. Florian Jug

    Max Planck Society · Human Technopole · Max Planck Institute of Molecular Cell Biology and Genetics

    Affiliation as printed

    Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Germany; Fondazione Human Technopole, Milan, Italy

    Max Planck Institute of Molecular Cell Biology and Genetics

11. Antonio Martínez-Sánchez

    Universidad de Oviedo · Instituto de Investigación Sanitaria del Principado de Asturias

    Affiliation as printed

    University of Oviedo, Department of Computer Sciences, Oviedo, Spain; Health Research Institute of Asturias (ISPA), Oviedo, Spain

    Universidad de Oviedo [Oviedo]

12. Mohamad Harastani

    Centre National de la Recherche Scientifique · Sorbonne Université · Institut de minéralogie, de physique des matériaux et de cosmochimie

    Affiliation as printed

    IMPMC-UMR 7590 CNRS, Sorbonne Université, MNHN, Paris, France

    Bioinformatique et BioPhysique [IMPMC]

    IMPMC_BIBIP - Bioinformatique et BioPhysique [IMPMC] (4, place Jussieu - BC 115 - 75252 Paris Cedex 5 - France)

13. Slavica Jonić

    Centre National de la Recherche Scientifique · Sorbonne Université · Institut de minéralogie, de physique des matériaux et de cosmochimie

    Affiliation as printed

    IMPMC-UMR 7590 CNRS, Sorbonne Université, MNHN, Paris, France

    Bioinformatique et BioPhysique [IMPMC]

    IMPMC_BIBIP - Bioinformatique et BioPhysique [IMPMC] (4, place Jussieu - BC 115 - 75252 Paris Cedex 5 - France)

14. José Javier Conesa

    Consejo Superior de Investigaciones Científicas · Centro Nacional de Biotecnología · Universidad Autónoma de Madrid

    Affiliation as printed

    National Center of Biotechnology (CNB-CSIC), Madrid, Spain

    CNB-CSIC - Centro Nacional de Biotecnología [Madrid] (Campus de la Universidad Autónoma de Madrid, 28049 Madrid - Espagne)

    Centro Nacional de Biotecnología [Madrid]

15. Ana Cuervo

    Consejo Superior de Investigaciones Científicas · Centro Nacional de Biotecnología · Universidad Autónoma de Madrid

    Affiliation as printed

    National Center of Biotechnology (CNB-CSIC), Madrid, Spain

    CNB-CSIC - Centro Nacional de Biotecnología [Madrid] (Campus de la Universidad Autónoma de Madrid, 28049 Madrid - Espagne)

    Centro Nacional de Biotecnología [Madrid]

16. Patricia Losana

    Consejo Superior de Investigaciones Científicas · Centro Nacional de Biotecnología · Universidad Autónoma de Madrid

    Affiliation as printed

    National Center of Biotechnology (CNB-CSIC), Madrid, Spain

    CNB-CSIC - Centro Nacional de Biotecnología [Madrid] (Campus de la Universidad Autónoma de Madrid, 28049 Madrid - Espagne)

    Centro Nacional de Biotecnología [Madrid]

17. Irene Sánchez

    Consejo Superior de Investigaciones Científicas · Centro Nacional de Biotecnología · Universidad Autónoma de Madrid

    Affiliation as printed

    National Center of Biotechnology (CNB-CSIC), Madrid, Spain

    CNB-CSIC - Centro Nacional de Biotecnología [Madrid] (Campus de la Universidad Autónoma de Madrid, 28049 Madrid - Espagne)

    Centro Nacional de Biotecnología [Madrid]

18. Mikel Iceta

    Consejo Superior de Investigaciones Científicas · Centro Nacional de Biotecnología · Universidad Autónoma de Madrid

    Affiliation as printed

    National Center of Biotechnology (CNB-CSIC), Madrid, Spain

    CNB-CSIC - Centro Nacional de Biotecnología [Madrid] (Campus de la Universidad Autónoma de Madrid, 28049 Madrid - Espagne)

    Centro Nacional de Biotecnología [Madrid]

19. Laura del Caño

    Consejo Superior de Investigaciones Científicas · Centro Nacional de Biotecnología · Universidad Autónoma de Madrid

    Affiliation as printed

    National Center of Biotechnology (CNB-CSIC), Madrid, Spain

    CNB-CSIC - Centro Nacional de Biotecnología [Madrid] (Campus de la Universidad Autónoma de Madrid, 28049 Madrid - Espagne)

    Centro Nacional de Biotecnología [Madrid]

20. Marcos Gragera

    Consejo Superior de Investigaciones Científicas · Centro Nacional de Biotecnología · Universidad Autónoma de Madrid

    Affiliation as printed

    National Center of Biotechnology (CNB-CSIC), Madrid, Spain

    CNB-CSIC - Centro Nacional de Biotecnología [Madrid] (Campus de la Universidad Autónoma de Madrid, 28049 Madrid - Espagne)

    Centro Nacional de Biotecnología [Madrid]

21. Roberto Melero

    Consejo Superior de Investigaciones Científicas · Centro Nacional de Biotecnología · Universidad Autónoma de Madrid

    Affiliation as printed

    National Center of Biotechnology (CNB-CSIC), Madrid, Spain

    CNB-CSIC - Centro Nacional de Biotecnología [Madrid] (Campus de la Universidad Autónoma de Madrid, 28049 Madrid - Espagne)

    Centro Nacional de Biotecnología [Madrid]

22. Grigory Sharov

    MRC Laboratory of Molecular Biology · University of Cambridge

    Affiliation as printed

    Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom

    Laboratory of Molecular Biology [Cambridge]

23. Daniel Castaño‐Díez

    University of Basel

    Affiliation as printed

    BioEM Lab, Biozentrum, University of Basel, Basel, Switzerland

    Université de Bâle = University of Basel

24. Abraham J. Koster Aachen

    Leiden University

    Affiliation as printed

    University of Leiden, Ultrastructural and Molecular Imaging, Leiden, the Netherlands

    Universiteit Leiden = Leiden University

25. Jonathan Piccirillo

    Consejo Superior de Investigaciones Científicas · Centro Nacional de Biotecnología · Universidad Autónoma de Madrid

    Affiliation as printed

    National Center of Biotechnology (CNB-CSIC), Madrid, Spain

    CNB-CSIC - Centro Nacional de Biotecnología [Madrid] (Campus de la Universidad Autónoma de Madrid, 28049 Madrid - Espagne)

    Centro Nacional de Biotecnología [Madrid]

26. José Luis Vilas

    Consejo Superior de Investigaciones Científicas · Centro Nacional de Biotecnología · Universidad Autónoma de Madrid

    Affiliation as printed

    National Center of Biotechnology (CNB-CSIC), Madrid, Spain

    CNB-CSIC - Centro Nacional de Biotecnología [Madrid] (Campus de la Universidad Autónoma de Madrid, 28049 Madrid - Espagne)

    Centro Nacional de Biotecnología [Madrid]

27. Joaquı́n Otón

    ALBA Synchrotron (Spain)

    Affiliation as printed

    Alba Synchrotron - CELLS (ICTS), Barcelona, Spain

    ALBA Synchrotron light source [Barcelone]

28. R. Marabini

    Consejo Superior de Investigaciones Científicas · Centro Nacional de Biotecnología · Universidad Autónoma de Madrid

    Affiliation as printed

    National Center of Biotechnology (CNB-CSIC), Madrid, Spain; Superior Polytechnic School. Univ. Autónoma of Madrid. Madrid, Spain

    Centro Nacional de Biotecnología [Madrid]

    Universidad Autónoma de Madrid

29. Carlos Óscar S. Sorzano

    Consejo Superior de Investigaciones Científicas · Centro Nacional de Biotecnología · Universidad Autónoma de Madrid

    Affiliation as printed

    National Center of Biotechnology (CNB-CSIC), Madrid, Spain. Electronic address: coss@cnb.csic.es

    CNB-CSIC - Centro Nacional de Biotecnología [Madrid] (Campus de la Universidad Autónoma de Madrid, 28049 Madrid - Espagne)

    Centro Nacional de Biotecnología [Madrid]

30. J.M. Carazo

    Consejo Superior de Investigaciones Científicas · Centro Nacional de Biotecnología · Universidad Autónoma de Madrid

    Affiliation as printed

    National Center of Biotechnology (CNB-CSIC), Madrid, Spain. Electronic address: carazo@cnb.csic.es

    CNB-CSIC - Centro Nacional de Biotecnología [Madrid] (Campus de la Universidad Autónoma de Madrid, 28049 Madrid - Espagne)

    Centro Nacional de Biotecnología [Madrid]