Open Access
eLife, volume 7
cisTEM, user-friendly software for single-particle image processing
1
Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United states
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Publication type: Journal Article
Publication date: 2018-03-07
PubMed ID:
29513216
General Biochemistry, Genetics and Molecular Biology
General Medicine
General Immunology and Microbiology
General Neuroscience
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, 200 k – 300 k 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.
Citations by journals
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EMBO Journal
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Biochemical Journal
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4 publications, 0.53%
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Citations by publishers
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Springer Nature
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Springer Nature
179 publications, 23.68%
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Elsevier
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Elsevier
130 publications, 17.2%
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American Association for the Advancement of Science (AAAS)
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39 publications, 5.16%
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eLife Sciences Publications
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33 publications, 4.37%
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American Chemical Society (ACS)
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17 publications, 2.25%
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Oxford University Press
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Proceedings of the National Academy of Sciences (PNAS)
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Multidisciplinary Digital Publishing Institute (MDPI)
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American Society for Microbiology
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12 publications, 1.59%
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Frontiers Media S.A.
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Wiley
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Wiley
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7 publications, 0.93%
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Public Library of Science (PLoS)
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Public Library of Science (PLoS)
6 publications, 0.79%
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EMBO press
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EMBO press
6 publications, 0.79%
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Portland Press
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Portland Press
5 publications, 0.66%
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IOP Publishing
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IOP Publishing
3 publications, 0.4%
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Annual Reviews
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3 publications, 0.4%
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The American Association of Immunologists
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Royal Society of Chemistry (RSC)
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Royal Society of Chemistry (RSC)
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Taylor & Francis
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Taylor & Francis
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IEEE
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IEEE
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Cold Spring Harbor Laboratory
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F1000 Research
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Mary Ann Liebert
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Mary Ann Liebert
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- We do not take into account publications that without a DOI.
- Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
- Statistics recalculated weekly.
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Grant T., Rohou A., Grigorieff N. cisTEM, user-friendly software for single-particle image processing // eLife. 2018. Vol. 7.
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Grant T., Rohou A., Grigorieff N. cisTEM, user-friendly software for single-particle image processing // eLife. 2018. Vol. 7.
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TY - JOUR
DO - 10.7554/eLife.35383
UR - https://doi.org/10.7554%2FeLife.35383
TI - cisTEM, user-friendly software for single-particle image processing
T2 - eLife
AU - Grant, Timothy
AU - Rohou, Alexis
AU - Grigorieff, Nikolaus
PY - 2018
DA - 2018/03/07 00:00:00
PB - eLife Sciences Publications
VL - 7
PMID - 29513216
SN - 2050-084X
ER -
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@article{2018_Grant
author = {Timothy Grant and Alexis Rohou and Nikolaus Grigorieff},
title = {cisTEM, user-friendly software for single-particle image processing},
journal = {eLife},
year = {2018},
volume = {7},
publisher = {eLife Sciences Publications},
month = {mar},
url = {https://doi.org/10.7554%2FeLife.35383},
doi = {10.7554/eLife.35383}
}