Appion: an integrated, database-driven pipeline to facilitate EM image processing.
Appion: an integrated, database-driven pipeline to facilitate EM image processing.
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DOI：
10.1016/j.jsb.2009.01.002
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发表时间：
2009-04
影响因子：
3
通讯作者：
Carragher, Bridget
中科院分区：
文献类型：
--
作者：
Lander, Gabriel C.;Stagg, Scott M.;Voss, Neil R.;Cheng, Anchi;Fellmann, Denis;Pulokas, James;Yoshioka, Craig;Irving, Christopher;Mulder, Anke;Lau, Pick-Wei;Lyumkis, Dmitry;Potter, Clinton S.;Carragher, Bridget
关键词：
冷冻EM和三维图像重建的使用变得越来越普遍。我们对这项技术的愿景是提供一种直接的方式，用户可以通过管道从原始数据进行可靠的3D重建，这既有利于处理步骤的管理，又使每个步骤的结果更加透明。Appion与关系SQL数据库紧密集成，是一个模块化和透明的管道，可扩展现有的软件应用程序和程序。用户通过基于Web的表单管理和控制软件模块，并且所有结果都可以使用直接链接到底层数据库的基于Web的查看器来获得，即使是幼稚的用户也可以快速推断其结果的质量。Appion API的设计原则是，应用程序应与广泛的标本兼容，库和例程是模块化和可扩展的。这里介绍的是一个描述的设计和架构的工作Appion管道原型和它的使用的一些结果。
The use of cryo-EM and three-dimensional image reconstruction is becoming increasingly common. Our vision for this technique is to provide a straightforward manner in which users can proceed from raw data to a reliable 3D reconstruction through a pipeline that both facilitates management of the processing steps and makes the results at each step more transparent. Tightly integrated with a relational SQL database, Appion is a modular and transparent pipeline that extends existing software applications and procedures. The user manages and controls the software modules via web-based forms, and all results are similarly available using web-based viewers directly linked to the underlying database, enabling even naive users to quickly deduce the quality of their results. The Appion API was designed with the principle that applications should be compatible with a broad range of specimens and that libraries and routines are modular and extensible. Presented here is a description of the design and architecture of the working Appion pipeline prototype and some results of its use.
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