cisTEM, user-friendly software for single-particle image processing.
cisTEM, user-friendly software for single-particle image processing.
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DOI：
10.7554/elife.35383
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发表时间：
2018-03-07
期刊：
影响因子：
7.7
通讯作者：
Grigorieff N
中科院分区：
文献类型：
--
作者：
Grant T;Rohou A;Grigorieff N
我们已经开发了新的开源软件，称为cisTEM（透射电子显微镜计算成像系统），用于处理高分辨率电子冷冻显微镜和单粒子平均的数据。cisTEM具有图形用户界面，用于提交作业、监控作业进度和显示结果。它实现了一个完整的处理流水线，包括电影处理，图像散焦确定，自动粒子拾取，2D分类，从头算3D地图生成随机参数，3D分类，高分辨率的细化和重建。其中一些步骤实现了新开发的算法;另一些则改编自以前发布的算法。该软件经过优化，能够在基于CPU的高端工作站上处理典型数据集（2000张显微照片，200 k - 300 k粒子），耗时半天或更短，与GPU加速处理相当。作业也可以在大型计算机集群上使用灵活的运行配置文件进行调度，这些配置文件可以适用于大多数计算环境。cisTEM可从cistem.org下载。
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.