Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.
UNEAC Manzanillo, Cuba.
Acta Crystallogr D Struct Biol. 2020 Apr 1;76(Pt 4):350-356. doi: 10.1107/S2059798320003769. Epub 2020 Mar 31.
Image-processing software has always been an integral part of structure determination by cryogenic electron microscopy (cryo-EM). Recent advances in hardware and software are recognized as one of the key factors in the so-called cryo-EM resolution revolution. Increasing computational power has opened many possibilities to consider more demanding algorithms, which in turn allow more complex biological problems to be tackled. Moreover, data processing has become more accessible to many experimental groups, with computations that used to last for many days at supercomputing facilities now being performed in hours on personal workstations. All of these advances, together with the rapid expansion of the community, continue to pose challenges and new demands on the software-development side. In this article, the development of emcore and emvis, two basic software libraries for image manipulation and data visualization in cryo-EM, is presented. The main goal is to provide basic functionality organized in modular components that other developers can reuse to implement new algorithms or build graphical applications. An additional aim is to showcase the importance of following established practices in software engineering, with the hope that this could be a first step towards a more standardized way of developing and distributing software in the field.
图像处理软件一直是低温电子显微镜（cryo-EM）结构测定的一个组成部分。硬件和软件的最新进展被认为是所谓的 cryo-EM 分辨率革命的关键因素之一。计算能力的提高为考虑更具挑战性的算法开辟了许多可能性，这反过来又允许解决更复杂的生物学问题。此外，数据处理对许多实验组来说变得更加容易，以前在超级计算设施上需要花费数天时间的计算现在可以在个人工作站上数小时内完成。所有这些进展，以及该领域社区的快速扩张，继续给软件开发方面带来挑战和新的需求。本文介绍了用于 cryo-EM 图像处理和数据可视化的两个基本软件库 emcore 和 emvis 的开发。主要目标是提供组织在模块化组件中的基本功能，其他开发人员可以重复使用这些组件来实现新算法或构建图形应用程序。另一个目标是展示在软件工程中遵循既定实践的重要性，希望这能成为在该领域以更标准化的方式开发和分发软件的第一步。
