Literature DB >> 18045333

Modular software platform for low-dose electron microscopy and tomography.

Michael P Marsh1, Juan T Chang, Christopher R Booth, Nathan L Liang, Michael F Schmid, Wah Chiu.   

Abstract

Transmission electron microscopy imaging protocols required by structural scientists vary widely and can be laborious without tailor-made applications. We present here the jeol automated microscopy expert system (james) api integrator, a programming library for computer control of transmission electron microscopy operations and equipment. james has been implemented on JEOL microscopes with Gatan CCDs but is designed to be modular so it can be adapted to run on different microscopes and detectors. We have used the james api integrator to develop two applications for low-dose digital imaging: james imaging application and the mr t tomographic imaging application. Both applications have been widely used within our NCRR-supported Center for routine data collection and are now made available for public download.

Mesh：

Year:  2007        PMID： 18045333      PMCID： PMC4384816          DOI： 10.1111/j.1365-2818.2007.01856.x

Source DB:  PubMed          Journal:  J Microsc        ISSN： 0022-2720            Impact factor:   1.758


  27 in total

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Journal:  J Microsc       Date:  2002-02       Impact factor: 1.758

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Authors:  Sukyeong Lee; Mathew E Sowa; Yo-hei Watanabe; Paul B Sigler; Wah Chiu; Masasuke Yoshida; Francis T F Tsai
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Journal:  Microsc Microanal       Date:  2003-12       Impact factor: 4.127

4.  Automated electron microscope tomography using robust prediction of specimen movements.

Authors:  David N Mastronarde
Journal:  J Struct Biol       Date:  2005-10       Impact factor: 2.867

5.  The pore structure of the closed RyR1 channel.

Authors:  Steven J Ludtke; Irina I Serysheva; Susan L Hamilton; Wah Chiu
Journal:  Structure       Date:  2005-08       Impact factor: 5.006

6.  UCSF tomography: an integrated software suite for real-time electron microscopic tomographic data collection, alignment, and reconstruction.

Authors:  Shawn Q Zheng; Bettina Keszthelyi; Eric Branlund; John M Lyle; Michael B Braunfeld; John W Sedat; David A Agard
Journal:  J Struct Biol       Date:  2006-06-23       Impact factor: 2.867

7.  SPARX, a new environment for Cryo-EM image processing.

Authors:  Michael Hohn; Grant Tang; Grant Goodyear; P R Baldwin; Zhong Huang; Pawel A Penczek; Chao Yang; Robert M Glaeser; Paul D Adams; Steven J Ludtke
Journal:  J Struct Biol       Date:  2006-07-16       Impact factor: 2.867

8.  Structure of epsilon15 bacteriophage reveals genome organization and DNA packaging/injection apparatus.

Authors:  Wen Jiang; Juan Chang; Joanita Jakana; Peter Weigele; Jonathan King; Wah Chiu
Journal:  Nature       Date:  2006-02-02       Impact factor: 49.962

9.  Genome sequence, structural proteins, and capsid organization of the cyanophage Syn5: a "horned" bacteriophage of marine synechococcus.

Authors:  Welkin H Pope; Peter R Weigele; Juan Chang; Marisa L Pedulla; Michael E Ford; Jennifer M Houtz; Wen Jiang; Wah Chiu; Graham F Hatfull; Roger W Hendrix; Jonathan King
Journal:  J Mol Biol       Date:  2007-02-22       Impact factor: 5.469

10.  Structure of the bifunctional and Golgi-associated formiminotransferase cyclodeaminase octamer.

Authors:  Yuxin Mao; Nand K Vyas; Meenakshi N Vyas; Dong-Hua Chen; Steven J Ludtke; Wah Chiu; Florante A Quiocho
Journal:  EMBO J       Date:  2004-07-22       Impact factor: 11.598
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  5 in total

Review 1.  Automated data collection in single particle electron microscopy.

Authors:  Yong Zi Tan; Anchi Cheng; Clinton S Potter; Bridget Carragher
Journal:  Microscopy (Oxf)       Date:  2015-12-15       Impact factor: 1.571

2.  An approach to automated acquisition of cryoEM images from lacey carbon grids.

Authors:  William V Nicholson; Howard White; John Trinick
Journal:  J Struct Biol       Date:  2010-09-08       Impact factor: 2.867

3.  A Script-Assisted Microscopy (SAM) package to improve data acquisition rates on FEI Tecnai electron microscopes equipped with Gatan CCD cameras.

Authors:  Jian Shi; Dewight R Williams; Phoebe L Stewart
Journal:  J Struct Biol       Date:  2008-06-04       Impact factor: 2.867

4.  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

5.  Estimating contrast transfer function and associated parameters by constrained non-linear optimization.

Authors:  C Yang; W Jiang; D-H Chen; U Adiga; E G Ng; W Chiu
Journal:  J Microsc       Date:  2009-03       Impact factor: 1.758
  5 in total

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