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Literature DB >> 26671944

Automated data collection in single particle electron microscopy.

Yong Zi Tan¹, Anchi Cheng², Clinton S Potter¹, Bridget Carragher³.

Abstract

Automated data collection is an integral part of modern workflows in single particle electron microscopy (EM) research. This review surveys the software packages available for automated single particle EM data collection. The degree of automation at each stage of data collection is evaluated, and the capabilities of the software packages are described. Finally, future trends in automation are discussed.

Keywords: automation; data collection; high throughput; single particle electron microscopy; software packages; target acquisition

Mesh：

Year: 2015 PMID： 26671944 PMCID： PMC4749047 DOI： 10.1093/jmicro/dfv369

Source DB: PubMed Journal: Microscopy (Oxf) ISSN： 2050-5698 Impact factor: 1.571

53 in total

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Authors: Joseph A Mindell; Nikolaus Grigorieff
Journal: J Struct Biol Date: 2003-06 Impact factor: 2.867

2. Automated microscopy for electron tomography.

Authors: A J Koster; H Chen; J W Sedat; D A Agard
Journal: Ultramicroscopy Date: 1992-10 Impact factor: 2.689

3. Does contamination buildup limit throughput for automated cryoEM?

Authors: Anchi Cheng; Denis Fellmann; James Pulokas; Clinton S Potter; Bridget Carragher
Journal: J Struct Biol Date: 2006-04-05 Impact factor: 2.867

4. A novel method for improvement of visualization of power spectra for sorting cryo-electron micrographs and their local areas.

Authors: S Jonić; C O S Sorzano; M Cottevieille; E Larquet; N Boisset
Journal: J Struct Biol Date: 2006-08-11 Impact factor: 2.867

5. An improved holey carbon film for cryo-electron microscopy.

Authors: Joel Quispe; John Damiano; Stephen E Mick; David P Nackashi; Denis Fellmann; Teddy G Ajero; Bridget Carragher; Clinton S Potter
Journal: Microsc Microanal Date: 2007-10 Impact factor: 4.127

6. Computer controlled cryo-electron microscopy--TOM² a software package for high-throughput applications.

Authors: Andreas Korinek; Florian Beck; Wolfgang Baumeister; Stephan Nickell; Jürgen M Plitzko
Journal: J Struct Biol Date: 2011-06-17 Impact factor: 2.867

7. AutoDrug: fully automated macromolecular crystallography workflows for fragment-based drug discovery.

Authors: Yingssu Tsai; Scott E McPhillips; Ana González; Timothy M McPhillips; Daniel Zinn; Aina E Cohen; Michael D Feese; David Bushnell; Theresa Tiefenbrunn; C David Stout; Bertram Ludaescher; Britt Hedman; Keith O Hodgson; S Michael Soltis
Journal: Acta Crystallogr D Biol Crystallogr Date: 2013-04-11

8. The influence of frame alignment with dose compensation on the quality of single particle reconstructions.

Authors: John M Spear; Alex J Noble; Qing Xie; Duncan R Sousa; Michael S Chapman; Scott M Stagg
Journal: J Struct Biol Date: 2015-09-25 Impact factor: 2.867

9. JADAS: a customizable automated data acquisition system and its application to ice-embedded single particles.

Authors: Junjie Zhang; Natsuko Nakamura; Yuko Shimizu; Nathan Liang; Xiangan Liu; Joanita Jakana; Michael P Marsh; Christopher R Booth; Takao Shinkawa; Munetaka Nakata; Wah Chiu
Journal: J Struct Biol Date: 2008-09-30 Impact factor: 2.867

Review 10. How cryo-EM is revolutionizing structural biology.

Authors: Xiao-chen Bai; Greg McMullan; Sjors H W Scheres
Journal: Trends Biochem Sci Date: 2014-11-07 Impact factor: 13.807

17 in total

Review 1. Challenges and opportunities in cryo-EM single-particle analysis.

Authors: Dmitry Lyumkis
Journal: J Biol Chem Date: 2019-02-25 Impact factor: 5.157

Review 2. Development of a deep learning-based method to identify "good" regions of a cryo-electron microscopy grid.

Authors: Yuichi Yokoyama; Tohru Terada; Kentaro Shimizu; Kouki Nishikawa; Daisuke Kozai; Atsuhiro Shimada; Akira Mizoguchi; Yoshinori Fujiyoshi; Kazutoshi Tani
Journal: Biophys Rev Date: 2020-03-11

3. High resolution single particle cryo-electron microscopy using beam-image shift.

Authors: Anchi Cheng; Edward T Eng; Lambertus Alink; William J Rice; Kelsey D Jordan; Laura Y Kim; Clinton S Potter; Bridget Carragher
Journal: J Struct Biol Date: 2018-07-25 Impact factor: 2.867

4. MicroED data collection with SerialEM.

Authors: M Jason de la Cruz; Michael W Martynowycz; Johan Hattne; Tamir Gonen
Journal: Ultramicroscopy Date: 2019-03-19 Impact factor: 2.689

Review 5. 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

6. Non-uniformity of projection distributions attenuates resolution in Cryo-EM.

Authors: Philip R Baldwin; Dmitry Lyumkis
Journal: Prog Biophys Mol Biol Date: 2019-09-13 Impact factor: 3.667

7. Cryogenic electron microscopy approaches that combine images and tilt series.

Authors: Thomas Calcraft; Peter B Rosenthal
Journal: Microscopy (Oxf) Date: 2022-02-18 Impact factor: 1.571

8. Cryo-EM reconstruction of the chlororibosome to 3.2 Å resolution within 24 h.

Authors: Björn O Forsberg; Shintaro Aibara; Dari Kimanius; Bijoya Paul; Erik Lindahl; Alexey Amunts
Journal: IUCrJ Date: 2017-09-22 Impact factor: 4.769

9. Cryo-EM analysis of the T3S injectisome reveals the structure of the needle and open secretin.

Authors: J Hu; L J Worrall; C Hong; M Vuckovic; C E Atkinson; N Caveney; Z Yu; N C J Strynadka
Journal: Nat Commun Date: 2018-09-21 Impact factor: 14.919

Review 10. Towards correlative super-resolution fluorescence and electron cryo-microscopy.

Authors: Georg Wolff; Christoph Hagen; Kay Grünewald; Rainer Kaufmann
Journal: Biol Cell Date: 2016-06-22 Impact factor: 4.458