Dynamo Catalogue: Geometrical tools and data management for particle picking in subtomogram averaging of cryo-electron tomograms

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• 作者：Daniel Castañ ; o-Dí ; ez^a ; ^b ; ^{daniel.castano@unibas.ch} ; Mikhail Kudryashev^b ; ^c ; ^d ; Henning Stahlberg^b
• 关键词：2D ; two dimensions/dimensional ; 3D ; three dimensions/dimensional ; EM ; electron microscope ; cryo-EM ; cryo-electron microscopy ; cryo-ET ; cryo-electron tomography ; EMDB ; electron microscopy data bank (www.emdatabank.org) ; FSC ; Fourier shell correlation ; SNR ; signal-to-noise ratio ; STA ; subtomogram averaging
• 刊名：Journal of Structural Biology
• 出版年：2017
• 出版时间：February 2017
• 年：2017
• 卷：197
• 期：2
• 页码：135-144
• 全文大小：3458 K
• 卷排序：197

文摘

Cryo electron tomography allows macromolecular complexes within vitrified, intact, thin cells or sections thereof to be visualized, and structural analysis to be performed in situ by averaging over multiple copies of the same molecules. Image processing for subtomogram averaging is specific and cumbersome, due to the large amount of data and its three dimensional nature and anisotropic resolution. Here, we streamline data processing for subtomogram averaging by introducing an archiving system, Dynamo Catalogue. This system manages tomographic data from multiple tomograms and allows visual feedback during all processing steps, including particle picking, extraction, alignment and classification. The file structure of a processing project file structure includes logfiles of performed operations, and can be backed up and shared between users. Command line commands, database queries and a set of GUIs give the user versatile control over the process. Here, we introduce a set of geometric tools that streamline particle picking from simple (filaments, spheres, tubes, vesicles) and complex geometries (arbitrary 2D surfaces, rare instances on proteins with geometric restrictions, and 2D and 3D crystals). Advanced functionality, such as manual alignment and subboxing, is useful when initial templates are generated for alignment and for project customization. Dynamo Catalogue is part of the open source package Dynamo and includes tools to ensure format compatibility with the subtomogram averaging functionalities of other packages, such as Jsubtomo, PyTom, PEET, EMAN2, XMIPP and Relion.