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Scipion

  • Description

    Scipion is an open-source cryo-EM workflow platform that supports complete SPA and Tomography pipelines, from raw movies or tilt-series movies to final post-processed maps. It combines Xmipp algorithms with leading cryo-EM software. It can complement or provide an alternative to full-pipeline packages such as RELION and cryoSPARC, while taking care of formats and conversions in a completely transparent way for the user.

  • Usage

    To list all executables provided by Scipion, run: $ sbgrid-list scipion Copy to clipboard

  • Usage Notes

    Check https://docs.sbgrid.org/apps/running_scipion_tutorials/ for plugin availability, detailed information about Scipion in SBGrid, and Scipion configuration.

    Scipion uses software that requires Nvidia GPU acceleration. Please be sure that the appropriate hardware and driver are available.

  • Installation

    Use the following command to install this title with the CLI client: $ sbgrid-cli install scipion Copy to clipboard Available operating systems: Linux 64

  • Primary Citation*

    J. M. de l. Rosa-Trevín, A. Quintana, L. d. Cano, A. Zaldívar, I. Foche, J. Gutiérrez, J. Gómez-Blanco, J. Burguet-Castell, J. Cuenca-Alba, V. Abrishami, J. Vargas, J. Otón, G. Sharov, J. L. Vilas, J. Navas, P. Conesa, M. Kazemi, R. Marabini, C. O. S. Sorzano, and J. M. Carazo. 2016. Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy. Journal of Structural Biology. 195(1): 93-99.


    • *Full citation information available through

  • Citation Note

    Scipion is freely available and its source code is 100% open. In exchange, please cite, not only Scipion, but ALL of the software that helped you to produce your article: http://scipion.i2pc.es/report_protocols/packages

  • Webinars

    Image processing made simple with ScipionTomo.

    SBGrid webinars are hosted with partial support from the NIH R25 Continuing Education for Structural Biology Mentors #GM151273, in collaboration with Co-PI Jamaine Davis of Belmont University.

    Topic:
    Image processing made simple with ScipionTomo.

    Jose Luis Vilas, Ph.D.
    Investigator, National Biotechnology Center, CSIC

    Host: Estrella Fernandez-Gimenez

    Recorded on April 14, 2026

    For more information on ScipionTomo:
    https://sbgrid.org/software/titles/scipion

    ScipionTomo

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

    Presenter: Pablo Conesa Team Leader, Spanish National Research Council

    Host: Jason Key
    Recorded on October 10, 2023

    For more information on Scipion:

    https://sbgrid.org/software/titles/scipion
    https://github.com/pconesa

    Scipion 3.0

    Topic: Scipion 3.0
    Presenter: Jose Miguel de la Rosa Trevin, Ph.D., Research Engineer, Science for Life Laboratory, Stockholm University

    Host: Jason Key
    Recorded on October 20, 2020

    Scipion

    Topic: Quo Vaids Scipion
    Presenter: Pablo Conesa, Senior Software Developer, National Center for Biotechnology

    Host: Shaun Rawson
    Recorded on April 21, 2020

    Scipion

    Topic: Using Scipion for Stream Image Processing at Cryo-EM Facilities
    Presenter: José Miguel de la Rosa Trevin, PhD, Scientific Software Engineer, SciLifeLab, Stockholm University, Sweden

    Host: Jason Key
    Recorded on June 12, 2018

  • Keywords

    Electron Microscopy, Tomography

  • Default Versions

    Linux 64:  3.11.6 (43.5 GB)

  • Other Versions

      Linux 64:

      3.7.1 (19.3 GB)

  • Developers

    Jose-Maria Carazo, Jose Miguel de la Rosa Trevin, Carlos Oscar Sorzano

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