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.

中文翻译：

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cisTEM，用于单粒子图像处理的用户友好软件

我们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、监控其进度和显示结果。它实现了完整的处理管道，包括电影处理、图像散焦确定、自动粒子拾取、2D 分类、从随机参数生成 ab-initio 3D 地图、3D 分类以及高分辨率细化和重建。其中一些步骤实现了新开发的算法；其他的则改编自以前发布的算法。该软件经过优化，可以在高端处理典型数据集（2000 张显微照片，200 k – 300 k 粒子），基于 CPU 的工作站在半天或更短的时间内，堪比 GPU 加速处理。还可以使用适用于大多数计算环境的灵活运行配置文件在大型计算机集群上安排作业。cisTEM 可从 cistem.org 下载。