Image processing for electron microscopy single-particle analysis using XMIPP
Image processing for electron microscopy single-particle analysis using XMIPP
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DOI：
10.1038/nprot.2008.62
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发表时间：
2008-01-01
期刊：
影响因子：
14.8
通讯作者：
Marabini, Roberto
中科院分区：
文献类型：
--
作者：
Scheres, Sjors H. W.;Nunez-Ramirez, Rafael;Marabini, Roberto
我们描述了使用XMIPP软件包的电子显微镜单粒子分析的标准化图像处理协议的集合。这些协议允许执行从数字化显微照片到3D模型的最终细化和评估的整个处理工作流程。特别强调的是通过最大似然改进和自组织地图处理结构异构数据，以及通过随机锥形倾斜重建方法为这些数据集生成初始3D模型。所有提供的协议都被实现为独立的、可执行的python脚本，并为此开发了专用的图形用户界面。因此，它们可以为新手用户提供一种方便的工具，以便在了解这个综合包的详细信息时，以最小的努力快速获得有用的结果。应用实例介绍了六聚解旋酶G40P的阴性染色随机锥形倾斜数据集和玻璃化冰中嵌入的70S大肠杆菌核糖体的结构异质数据集。
We describe a collection of standardized image processing protocols for electron microscopy single-particle analysis using the XMIPP software package. These protocols allow performing the entire processing workflow starting from digitized micrographs up to the final refinement and evaluation of 3D models. A particular emphasis has been placed on the treatment of structurally heterogeneous data through maximum-likelihood refinements and self-organizing maps as well as the generation of initial 3D models for such data sets through random conical tilt reconstruction methods. All protocols presented have been implemented as stand-alone, executable python scripts, for which a dedicated graphical user interface has been developed. Thereby, they may provide novice users with a convenient tool to quickly obtain useful results with minimum efforts in learning about the details of this comprehensive package. Examples of applications are presented for a negative stain random conical tilt data set on the hexameric helicase G40P and for a structurally heterogeneous data set on 70S Escherichia coli ribosomes embedded in vitrified ice.