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Development of basic building blocks for cryo-EM: the emcore and emvis software libraries
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab). KTH Royal Institute of Technology, Sweden.
Number of Authors: 42020 (English)In: Acta Crystallographica Section D: Structural Biology , E-ISSN 2059-7983, Vol. 76, p. 350-356Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2020. Vol. 76, p. 350-356
Keywords [en]
cryo-EM, image processing, data visualization, software development
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:su:diva-181342DOI: 10.1107/S2059798320003769ISI: 000524555300006PubMedID: 32254059OAI: oai:DiVA.org:su-181342DiVA, id: diva2:1430999
Available from: 2020-05-18 Created: 2020-05-18 Last updated: 2022-03-23Bibliographically approved

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de la Rosa-Trevín, José MiguelOtón, JoaquínLindahl, Erik

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