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Scipion

  • Description

    an image processing framework to obtain 3D models of macromolecular complexes using 3D EM that allows you to execute workflows combining different software tools, while taking care of formats and conversions.

  • Usage Notes

    SCIPION uses software that depends on CUDA 8.0 for GPU acceleration
    SCIPION can use a local directory at /programs/local/scipion/1.0.1/data/tests for test datasets that are too large to include with the software.
    SCIPION can download these automatically, but you (or your local sysadmin) will need to create a directory for them.
    Please email bugs@sbgrid.org if you have questions or problems.

  • Installation

    Use the following command to install this title with the CLI client: $ sbgrid install scipion Copy to clipboard

  • 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

    Please cite the following url when citing Scipion: http://scipion.i2pc.es/

  • Webinars

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

    Host: Shaun Rawson
    Recorded on April 21, 2020

    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

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