| 1. |
- de la Rosa-Trevín, José Miguel, et al.
(författare)
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Development of basic building blocks for cryo-EM : the emcore and emvis software libraries
- 2020
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Ingår i: Acta Crystallographica Section D. - : INT UNION CRYSTALLOGRAPHY. - 2059-7983. ; 76, s. 350-356
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 2. |
- Luis Vilas, Jose, et al.
(författare)
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MonoRes : Automatic and Accurate Estimation of Local Resolution for Electron Microscopy Maps
- 2018
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Ingår i: Structure. - : Elsevier BV. - 0969-2126 .- 1878-4186. ; 26:2, s. 337-344
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Tidskriftsartikel (refereegranskat)abstract
- Since the beginning of electron microscopy, resolution has been a critical parameter. In this article, we propose a fully automatic, accurate method for determining the local resolution of a 3D map (MonoRes). The foundation of this algorithm is an extension of the concept of analytic signal, termed monogenic signal. The map is filtered at different frequencies and the amplitude of the monogenic signal is calculated, after which a criterion is applied to determine the resolution at each voxel. MonoRes is fully automatic without compulsory user parameters, with great accuracy in all tests, and is computationally more rapid than existing methods in the field. In addition, MonoRes offers the option of local filtering of the original map based on the calculated local resolution.
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