| 1. |
- 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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| 2. |
- Abrishami, Vahid, et al.
(författare)
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Localized reconstruction in Scipion expedites the analysis of symmetry mismatches in cryo-EM data
- 2021
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Ingår i: Progress in Biophysics and Molecular Biology. - : Elsevier BV. - 0079-6107 .- 1873-1732. ; 160, s. 43-52
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Forskningsöversikt (refereegranskat)abstract
- Technological advances in transmission electron microscopes and detectors have turned cryogenic electron microscopy (cryo-EM) into an essential tool for structural biology. A commonly used cryo-EM data analysis method, single particle analysis, averages hundreds of thousands of low-dose images of individual macromolecular complexes to determine a density map of the complex. The presence of symmetry in the complex is beneficial since each projection image can be assigned to multiple views of the complex. However, data processing that applies symmetry can average out asymmetric features and consequently data analysis methods are required to resolve asymmetric structural features. Scipion is a cryo-EM image processing framework that integrates functions from different image processing packages as plugins. To extend its functionality for handling symmetry mismatches, we present here a Scipion plugin termed LocalRec implementing the localized reconstruction method. When tested on an adenovirus data set, the plugin enables resolving the symmetry-mismatched trimeric fibre bound to the five-fold vertices of the capsid. Furthermore, it improves the structure determination of the icosahedral capsid by dealing with the defocus gradient across the particle. LocalRec is expected to be widely applicable in a range of cryo-EM investigations of flexible and symmetry mismatched complexes.
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| 3. |
- Bengtsson, Viktor E. G., 1989-, et al.
(författare)
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Scipion-ED : a graphical user interface for batch processing and analysis of 3D ED/MicroED data
- 2022
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Ingår i: Journal of applied crystallography. - : International Union of Crystallography (IUCr). - 0021-8898 .- 1600-5767. ; 55:3, s. 638-646
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Tidskriftsartikel (refereegranskat)abstract
- Three-dimensional electron diffraction (3D ED)/microcrystal electron diffraction (MicroED) techniques are gaining in popularity. However, the data processing often does not fit existing graphical user interface software, instead requiring the use of the terminal or scripting. Scipion-ED, described in this article, provides a graphical user interface and extendable framework for processing of 3D ED/MicroED data. An illustrative project is described, in which multiple 3D ED/MicroED data sets collected on tetragonal lysozyme were processed with DIALS through the Scipion-ED interface. The ability to resolve unmodelled features in the electrostatic potential map was compared between three strategies for merging data sets.
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| 4. |
- 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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| 5. |
- Gomez-Blanco, J., et al.
(författare)
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Using Scipion for stream image processing at Cryo-EM facilities
- 2018
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Ingår i: Journal of Structural Biology. - : ACADEMIC PRESS INC ELSEVIER SCIENCE. - 1047-8477 .- 1095-8657. ; 204:3, s. 457-463
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Tidskriftsartikel (refereegranskat)abstract
- Three dimensional electron microscopy is becoming a very data-intensive field in which vast amounts of experimental images are acquired at high speed. To manage such large-scale projects, we had previously developed a modular workflow system called Scipion (de la Rosa-Trevfn et al., 2016). We present here a major extension of Scipion that allows processing of EM images while the data is being acquired. This approach helps to detect problems at early stages, saves computing time and provides users with a detailed evaluation of the data quality before the acquisition is finished. At present, Scipion has been deployed and is in production mode in seven Cryo-EM facilities throughout the world.
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| 6. |
- Sharov, Grigory, et al.
(författare)
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Using RELION software within the Scipion framework
- 2021
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Ingår i: Acta Crystallographica Section D. - 2059-7983. ; 77, s. 403-410
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Tidskriftsartikel (refereegranskat)abstract
- Scipion is a modular image-processing framework that integrates several software packages under a unified interface while taking care of file formats and conversions. Here, new developments and capabilities of the Scipion plugin for the widely used RELION software package are presented and illustrated with an image-processing pipeline for published data. The user interfaces of Scipion and RELION are compared and the key differences are highlighted, allowing this manuscript to be used as a guide for both new and experienced users of this software. Different on-the-fly image-processing options are also discussed, demonstrating the flexibility of the Scipion framework.
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