1. Structural Biology and Molecular Biophysics

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
https://doi.org/10.7554/eLife.35383
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  1. Timothy Grant
  2. Alexis Rohou
  3. Nikolaus Grigorieff
(2018)
cisTEM, User-friendly software for single-particle image processing
eLife 7:e35383.
https://doi.org/10.7554/eLife.35383
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Abstract

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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The following previously published data sets were used

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Author details

  1. Timothy Grant

    Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
    For correspondence
    tim@tgrant.co.uk
    Competing interests
    No competing interests declared.

  2. Alexis Rohou

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

Funding

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.

Copyright

© 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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  1. Timothy Grant
  2. Alexis Rohou
  3. Nikolaus Grigorieff
(2018)
cisTEM, User-friendly software for single-particle image processing
eLife 7:e35383.
https://doi.org/10.7554/eLife.35383

Share this article

https://doi.org/10.7554/eLife.35383

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Further reading

    1. Structural Biology and Molecular Biophysics

    CTFFIND5 provides improved insight into quality, tilt, and thickness of TEM samples

    Johannes Elferich, Lingli Kong ... Nikolaus Grigorieff
    Research Advance

    Images taken by transmission electron microscopes are usually affected by lens aberrations and image defocus, among other factors. These distortions can be modeled in reciprocal space using the contrast transfer function (CTF). Accurate estimation and correction of the CTF is essential for restoring the high-resolution signal in cryogenic electron microscopy (cryoEM). Previously, we described the implementation of algorithms for this task in the cisTEM software package (Grant et al., 2018). Here we show that taking sample characteristics, such as thickness and tilt, into account can improve CTF estimation. This is particularly important when imaging cellular samples, where measurement of sample thickness and geometry derived from accurate modeling of the Thon ring pattern helps judging the quality of the sample. This improved CTF estimation has been implemented in CTFFIND5, a new version of the cisTEM program CTFFIND. We evaluated the accuracy of these estimates using images of tilted aquaporin crystals and eukaryotic cells thinned by focused ion beam milling. We estimate that with micrographs of sufficient quality CTFFIND5 can measure sample tilt with an accuracy of 3° and sample thickness with an accuracy of 5 nm.