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. 2021 Oct 15;26(20):6224.
doi: 10.3390/molecules26206224.

Advances in Xmipp for Cryo-Electron Microscopy: From Xmipp to Scipion

David Strelak  1   2 , Amaya Jiménez-Moreno  2 , José L Vilas  2 , Erney Ramírez-Aportela  2 , Ruben Sánchez-García  3 , David Maluenda  4 , Javier Vargas  5 , David Herreros  2 , Estrella Fernández-Giménez  2 , Federico P de Isidro-Gómez  2 , Jan Horacek  6 , David Myska  6 , Martin Horacek  6 , Pablo Conesa  2 , Yunior C Fonseca-Reyna  2 , Jorge Jiménez  2 , Marta Martínez  2 , Mohamad Harastani  7 , Slavica Jonić  7 , Jiri Filipovic  6 , Roberto Marabini  2 , José M Carazo  2 , Carlos O S Sorzano  2
Affiliations

Advances in Xmipp for Cryo-Electron Microscopy: From Xmipp to Scipion

David Strelak et al. Molecules. .

Abstract

Xmipp is an open-source software package consisting of multiple programs for processing data originating from electron microscopy and electron tomography, designed and managed by the Biocomputing Unit of the Spanish National Center for Biotechnology, although with contributions from many other developers over the world. During its 25 years of existence, Xmipp underwent multiple changes and updates. While there were many publications related to new programs and functionality added to Xmipp, there is no single publication on the Xmipp as a package since 2013. In this article, we give an overview of the changes and new work since 2013, describe technologies and techniques used during the development, and take a peek at the future of the package.

Keywords: Cryo-EM; Scipion; Xmipp; single-particle analysis.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Typical steps of the Single Particle Analysis processing pipeline [3].
Figure 2
Figure 2
Xmipp related publications by category.
Figure 3
Figure 3
Citations of the Xmipp related publications by category.
Figure 4
Figure 4
Xmipp related publications by year.
Figure 5
Figure 5
Citations of Xmipp related publications by year.
See this image and copyright information in PMC

References

    1. de la Rosa-Trevín J.M., Quintana A., del Caño L., Zaldívar A., Foche I., Gutiérrez J., Gómez-Blanco J., Burguet-Castell J., Cuenca-Alba J., Abrishami V., et al. Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy. J. Struct. Biol. 2016;195:93–99. doi: 10.1016/j.jsb.2016.04.010. - DOI - PubMed
    1. de la Rosa-Trevín J.M., Otón J., Marabini R., Zaldívar A., Vargas J., Carazo J.M., Sorzano C.Ó.S. Xmipp 3.0: An improved software suite for image processing in electron microscopy. J. Struct. Biol. 2013;184:321–328. doi: 10.1016/j.jsb.2013.09.015. - DOI - PubMed
    1. Bendory T., Bartesaghi A., Singer A. Single-Particle Cryo-Electron Microscopy: Mathematical Theory, Computational Challenges, and Opportunities. IEEE Signal Process. Mag. 2019;37:58–76. doi: 10.1109/MSP.2019.2957822. - DOI - PMC - PubMed
    1. Vargas J., Franken E., Sorzano C.Ó.S., Gomez-Blanco J., Schoenmakers R., Koster A., Carazo J.M. Foil-hole and data image quality assessment in 3DEM: Towards high-throughput image acquisition in the electron microscope. J. Struct. Biol. 2016;196:515–524. doi: 10.1016/j.jsb.2016.10.006. - DOI - PubMed
    1. Abrishami V., Vargas J., Li X., Cheng Y., Marabini R., Sorzano C.Ó.S., Carazo J.M. Alignment of direct detection device micrographs using a robust Optical Flow approach. J. Struct. Biol. 2015;189:163–176. doi: 10.1016/j.jsb.2015.02.001. - DOI - PubMed

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