Abstract
The formal concept of a workflow to single-particle analysis of cryo-electron microscopy (cryo-EM) images in the RELION program is described. In this approach, the structure-determination process is considered as a graph, where intermediate results in the form of images or metadata are the vertices, and different functionalities of the program are the edges. The new implementation automatically logs all user actions, facilitates file management and disk cleaning, and allows convenient browsing of the history of a project. Moreover, new functionality to iteratively execute consecutive jobs allows on-the-fly image processing, which will lead to more efficient data acquisition by providing faster feedback on data quality. The possibility of exchanging data-processing procedures among users will contribute to the development of standardized image-processing procedures, and hence increase accessibility for new users in this rapidly expanding field.
Highlights
Recent advances in cryo-electron microscopy (cryo-EM) instrumentation and imageprocessing software have substantially expanded the scope of structure determination by single-particle analysis (Fernandez-Leiro & Scheres, 2016)
With many new users turning to cryo-EM structure determination, efforts in methods development are increasingly focused on improving the accessibility of the technique
This paper describes the implementation of a pipeline approach to cryo-EM structure-determination protocols in the RELION program (Scheres, 2012b)
Summary
Recent advances in cryo-EM instrumentation and imageprocessing software have substantially expanded the scope of structure determination by single-particle analysis (Fernandez-Leiro & Scheres, 2016). With many new users turning to cryo-EM structure determination, efforts in methods development are increasingly focused on improving the accessibility of the technique Examples of this are the development of robots for sample preparation and transfer of the sample into the microscope (Cheng et al, 2007; Vos et al, 2008; Kim et al, 2010; Coudray et al, 2011); the introduction of automated data-acquisition and processing software (Suloway et al, 2005; Stagg et al, 2006; Mastronarde, 2005; Li et al, 2015); the introduction of image-processing software suites with convenient graphical user interfaces (GUIs; Tang et al, 2007; Hohn et al, 2007; Baxter et al, 2007; de la Rosa-Trevın et al, 2013); and the development of integrated software environments and file formats that allow convenient interchanging between the different programs (Lander et al, 2009; de la Rosa-Trevın et al, 2016; Marabini et al, 2016). A three-dimensional mask (in .MRC format) A _model.star file for selecting classes menu on the GUI
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