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

Castaño-Díez, D., Kudryashev, M., & Stahlberg, H. (2017). Dynamo Catalogue: Geometrical tools and data management for particle picking in subtomogram averaging of cryo-electron tomograms. Journal of Structural Biology, 197(2), 135-144. doi:10.1016/j.jsb.2016.06.005.

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 Creators:
Castaño-Díez, Daniel1, 2, Author
Kudryashev, Misha2, 3, 4, Author                 
Stahlberg, Henning2, Author
Affiliations:
1BioEM Lab at C-CINA, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland, ou_persistent22              
2Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland, ou_persistent22              
3Sofja Kovalevskaja Group, Max Planck Institute of Biophysics, Max Planck Society, ou_2253651              
4Buchman Institute for Molecular Life Sciences, Goethe University of Frankfurt, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany, ou_persistent22              

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Free keywords: Cryo electron tomography; Subtomogram averaging; Data management
 Abstract: 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

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Language(s): eng - English
 Dates: 2016-02-272016-06-072016-06-082017-02
 Publication Status: Issued
 Pages: 10
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1016/j.jsb.2016.06.005
 Degree: -

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Title: Journal of Structural Biology
  Abbreviation : J. Struct. Biol.
Source Genre: Journal
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Publ. Info: Orlando, Fla. : Academic Press
Pages: - Volume / Issue: 197 (2) Sequence Number: - Start / End Page: 135 - 144 Identifier: ISSN: 1047-8477
CoNE: https://pure.mpg.de/cone/journals/resource/954922650160