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

TitlecisTEM, User-friendly software for single-particle image processing
Publication TypeJournal Article
Year of Publication2018
AuthorsGrant, T, Rohou A, Grigorieff N
Refereed DesignationRefereed
JournaleLife
Volume7
Issuee35383
Date Published03/2018
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.

DOI10.7554/eLife.35383
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Grant_eLife2018.pdf2.76 MB