1. Structural Biology and Molecular Biophysics
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cisTEM, User-friendly software for single-particle image processing

  1. Timothy Grant  Is a corresponding author
  2. Alexis Rohou  Is a corresponding author
  3. Nikolaus Grigorieff  Is a corresponding author
  1. Janelia Research Campus, Howard Hughes Medical Institute, United States
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Cite this article as: eLife 2018;7:e35383 doi: 10.7554/eLife.35383


We have developed new open-source software called cisTEM (computational imaging system for transmission electron microscopy) for the processing of data for high-resolution electron cryo-microscopy and single-particle averaging. cisTEM features a graphical user interface that is used to submit jobs, monitor their progress, and display results. It implements a full processing pipeline including movie processing, image defocus determination, automatic particle picking, 2D classification, ab-initio 3D map generation from random parameters, 3D classification, and high-resolution refinement and reconstruction. Some of these steps implement newly-developed algorithms; others were adapted from previously published algorithms. The software is optimized to enable processing of typical datasets (2000 micrographs, 200k - 300k particles) on a high-end, CPU-based workstation in half a day or less, comparable to GPU-accelerated processing. Jobs can also be scheduled on large computer clusters using flexible run profiles that can be adapted for most computing environments. cisTEM is available for download from cistem.org.

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Author details

  1. Timothy Grant

    Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
    For correspondence
    Competing interests
    No competing interests declared.
  2. Alexis Rohou

    Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
    For correspondence
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3343-9621
  3. Nikolaus Grigorieff

    Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
    For correspondence
    Competing interests
    Nikolaus Grigorieff, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1506-909X


Howard Hughes Medical Institute

  • Timothy Grant
  • Alexis Rohou
  • Nikolaus Grigorieff

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Edward H Egelman, University of Virginia, United States

Publication history

  1. Received: January 24, 2018
  2. Accepted: March 2, 2018
  3. Accepted Manuscript published: March 7, 2018 (version 1)
  4. Version of Record published: March 15, 2018 (version 2)


© 2018, Grant et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.


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