Literature DB >> 31121317

Reducing cryoEM file storage using lossy image formats.

Edward T Eng1, Mykhailo Kopylov1, Carl J Negro1, Sarkis Dallaykan1, William J Rice1, Kelsey D Jordan1, Kotaro Kelley1, Bridget Carragher2, Clinton S Potter3.   

Abstract

Recent advances in instrumentation and software for cryoEM have increased the applicability and utility of this method. High levels of automation and faster data acquisition rates require hard decisions to be made regarding data retention. Here we investigate the efficacy of data compression applied to aligned summed movie files. Surprisingly, these images can be compressed using a standard lossy method that reduces file storage by 90-95% and yet can still be processed to provide sub-2 Å reconstructed maps. We do not advocate this as an archival method, but it may provide a useful means for retaining images as an historical record, especially at large facilities.
Copyright © 2019 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  Cryo electron microscopy (cryoEM); Data archiving; File format; Image data; Structural biology

Year:  2019        PMID: 31121317      PMCID: PMC6597182          DOI: 10.1016/j.jsb.2019.04.013

Source DB:  PubMed          Journal:  J Struct Biol        ISSN: 1047-8477            Impact factor:   2.867


  23 in total

1.  FindEM--a fast, efficient program for automatic selection of particles from electron micrographs.

Authors:  A M Roseman
Journal:  J Struct Biol       Date:  2004 Jan-Feb       Impact factor: 2.867

2.  Computer visualization of three-dimensional image data using IMOD.

Authors:  J R Kremer; D N Mastronarde; J R McIntosh
Journal:  J Struct Biol       Date:  1996 Jan-Feb       Impact factor: 2.867

3.  Map Challenge assessment: Fair comparison of single particle cryoEM reconstructions.

Authors:  J Bernard Heymann
Journal:  J Struct Biol       Date:  2018-07-17       Impact factor: 2.867

4.  Appion: an integrated, database-driven pipeline to facilitate EM image processing.

Authors:  Gabriel C Lander; Scott M Stagg; Neil R Voss; Anchi Cheng; Denis Fellmann; James Pulokas; Craig Yoshioka; Christopher Irving; Anke Mulder; Pick-Wei Lau; Dmitry Lyumkis; Clinton S Potter; Bridget Carragher
Journal:  J Struct Biol       Date:  2009-04       Impact factor: 2.867

5.  DoG Picker and TiltPicker: software tools to facilitate particle selection in single particle electron microscopy.

Authors:  N R Voss; C K Yoshioka; M Radermacher; C S Potter; B Carragher
Journal:  J Struct Biol       Date:  2009-05       Impact factor: 2.867

Review 6.  Big data in cryoEM: automated collection, processing and accessibility of EM data.

Authors:  Philip R Baldwin; Yong Zi Tan; Edward T Eng; William J Rice; Alex J Noble; Carl J Negro; Michael A Cianfrocco; Clinton S Potter; Bridget Carragher
Journal:  Curr Opin Microbiol       Date:  2017-10-31       Impact factor: 7.934

7.  cisTEM, user-friendly software for single-particle image processing.

Authors:  Timothy Grant; Alexis Rohou; Nikolaus Grigorieff
Journal:  Elife       Date:  2018-03-07       Impact factor: 8.140

8.  Benchmarking cryo-EM Single Particle Analysis Workflow.

Authors:  Laura Y Kim; William J Rice; Edward T Eng; Mykhailo Kopylov; Anchi Cheng; Ashleigh M Raczkowski; Kelsey D Jordan; Daija Bobe; Clinton S Potter; Bridget Carragher
Journal:  Front Mol Biosci       Date:  2018-06-04

Review 9.  Databases and Archiving for CryoEM.

Authors:  A Patwardhan; C L Lawson
Journal:  Methods Enzymol       Date:  2016-06-16       Impact factor: 1.600

Review 10.  Structural biology data archiving - where we are and what lies ahead.

Authors:  Gerard J Kleywegt; Sameer Velankar; Ardan Patwardhan
Journal:  FEBS Lett       Date:  2018-05-25       Impact factor: 4.124

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  1 in total

1.  Electron-event representation data enable efficient cryoEM file storage with full preservation of spatial and temporal resolution.

Authors:  Hui Guo; Erik Franken; Yuchen Deng; Samir Benlekbir; Garbi Singla Lezcano; Bart Janssen; Lingbo Yu; Zev A Ripstein; Yong Zi Tan; John L Rubinstein
Journal:  IUCrJ       Date:  2020-08-07       Impact factor: 4.769

  1 in total

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