Open Access
Open access
eLife, volume 7

cisTEM, user-friendly software for single-particle image processing

Grant Timothy 1
Rohou Alexis 1
Grigorieff Nikolaus 1
1
 
Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United states
Publication typeJournal Article
Publication date2018-03-07
Journal: eLife
Quartile SCImago
Q1
Quartile WOS
Q1
Impact factor7.7
ISSN2050084X
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.

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Grant T., Rohou A., Grigorieff N. cisTEM, user-friendly software for single-particle image processing // eLife. 2018. Vol. 7.
GOST all authors (up to 50) Copy
Grant T., Rohou A., Grigorieff N. cisTEM, user-friendly software for single-particle image processing // eLife. 2018. Vol. 7.
RIS |
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RIS Copy
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 -
BibTex
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BibTex Copy
@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}
}
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