scholarly journals Low cost, high performance processing of single particle cryo-electron microscopy data in the cloud

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Michael A Cianfrocco ◽  
Andres E Leschziner
Keyword(s):  
Electron Microscopy ◽  
Cloud Computing ◽  
High Resolution ◽  
Single Particle ◽  
High Performance ◽  
Low Cost ◽  
Computing Environment ◽  
Cryo Electron Microscopy ◽  
Electron Microscopes ◽  
Microscopy Data

The advent of a new generation of electron microscopes and direct electron detectors has realized the potential of single particle cryo-electron microscopy (cryo-EM) as a technique to generate high-resolution structures. Calculating these structures requires high performance computing clusters, a resource that may be limiting to many likely cryo-EM users. To address this limitation and facilitate the spread of cryo-EM, we developed a publicly available ‘off-the-shelf’ computing environment on Amazon's elastic cloud computing infrastructure. This environment provides users with single particle cryo-EM software packages and the ability to create computing clusters with 16–480+ CPUs. We tested our computing environment using a publicly available 80S yeast ribosome dataset and estimate that laboratories could determine high-resolution cryo-EM structures for $50 to $1500 per structure within a timeframe comparable to local clusters. Our analysis shows that Amazon's cloud computing environment may offer a viable computing environment for cryo-EM.

scholarly journals Low cost, high performance processing of single particle cryo-electron microscopy data in the cloud

2015 ◽  
Author(s):  
Michael A. Cianfrocco ◽  
Andres E. Leschziner
Keyword(s):  
Electron Microscopy ◽  
Single Particle ◽  
High Performance ◽  
Low Cost ◽  
Cost Effective ◽  
Cryo Electron Microscopy ◽  
Software Packages ◽  
Electron Microscopes ◽  
Microscopy Data ◽  
New Generation

The advent of a new generation of electron microscopes and direct electron detectors has realized the potential of single particle cryo-electron microscopy (cryo-EM) as a technique to generate high-resolution structures. However, calculating these structures requires high performance computing clusters, a resource that may be limiting to many likely cryo-EM users. To address this limitation and facilitate the spread of cryo-EM, we developed a publicly available ‘off-the-shelf’ computing environment on Amazon’s elastic cloud computing infrastructure. This environment provides users with single particle cryo-EM software packages and the ability to create computing clusters that can range in size from 16 to 480+ CPUs. Importantly, these computing clusters are also cost-effective, as we illustrate here by determining a near-atomic resolution structure of the 80S yeast ribosome for $28.89 USD in ~10 hours.

How Good Can Single-Particle Cryo-EM Become? What Remains Before It Approaches Its Physical Limits?

2019 ◽  
Vol 48 (1) ◽  
pp. 45-61 ◽  
Author(s):  
Robert M. Glaeser
Keyword(s):  
Electron Microscopy ◽  
High Resolution ◽  
Single Particle ◽  
Energy Use ◽  
Optimal Choice ◽  
Structural Basis ◽  
Detective Quantum Efficiency ◽  
Quantum Metrology ◽  
Cryo Electron Microscopy ◽  
Induced Motion

Impressive though the achievements of single-particle cryo–electron microscopy are today, a substantial gap still remains between what is currently accomplished and what is theoretically possible. As is reviewed here, twofold or more improvements are possible as regards ( a) the detective quantum efficiency of cameras at high resolution, ( b) converting phase modulations to intensity modulations in the image, and ( c) recovering the full amount of high-resolution signal in the presence of beam-induced motion of the specimen. In addition, potential for improvement is reviewed for other topics such as optimal choice of electron energy, use of aberration correctors, and quantum metrology. With the help of such improvements, it does not seem to be too much to imagine that determining the structural basis for every aspect of catalytic control, signaling, and regulation, in any type of cell of interest, could easily be accelerated fivefold or more.

scholarly journals Amino and PEG-amino graphene oxide grids enrich and protect samples for high-resolution single particle cryo-electron microscopy

2020 ◽  
Vol 209 (2) ◽  
pp. 107437 ◽  
Author(s):  
Feng Wang ◽  
Zanlin Yu ◽  
Miguel Betegon ◽  
Melody G. Campbell ◽  
Tural Aksel ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Graphene Oxide ◽  
High Resolution ◽  
Single Particle ◽  
Cryo Electron Microscopy ◽  
Resolution Single

High resolution Scanning Electron Microscopy

1989 ◽  
Vol 47 ◽  
pp. 6-7
Author(s):  
David C. Joy
Keyword(s):  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
High Resolution ◽  
High Performance ◽  
Secondary Electron ◽  
Wide Energy Range ◽  
Wide Energy ◽  
Electron Microscopes ◽  
Electron Imaging ◽  
Scanning Electron

High resolution scanning electron microscopy is still a relatively new and unfamiliar concept because in the early days of the SEM it was expected, that secondary electron imaging would be limited to a resolution of between 5 and 10nm at best. Now, however, because of improvements in instrumentation and technique based on advances in the understanding of electron beam interactions with solids current SEMs can demonstrate spatial resolutions below 1nm, rivaling those obtained by transmission instruments.High performance scanning electron microscopes always incorporate two advanced items of instrumentation. Firstly they use field emission guns (FEGs). The high brightness, low energy spread, and small source size of the FEG makes it possible to produce an electron probe of sub-nanometer size which contains sufficient current for secondary electron imaging (i.e 10-12 amps or more) and which can maintain this performance over a wide energy range (3 to 30keV). Secondly, the new high performance instruments place the specimen within a high excitation, immersion, probe forming lens.

scholarly journals Towards on-the-fly Cryo-Electron Microscopy Data Processing by High Performance Data Analysis

2018 ◽  
Vol 955 ◽  
pp. 012005 ◽  
Author(s):  
Evgeny Pichkur ◽  
Timur Baimukhametov ◽  
Anton Teslyuk ◽  
Anton Orekhov ◽  
Roman Kamyshinsky ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Data Analysis ◽  
Data Processing ◽  
High Performance ◽  
Performance Data ◽  
Cryo Electron Microscopy ◽  
Electron Microscopy Data ◽  
Microscopy Data

scholarly journals High-Resolution Insights into Nascent-Chain Conformation by Single-Particle Cryo-Electron Microscopy

2021 ◽  
Vol 120 (3) ◽  
pp. 296a
Author(s):  
Meranda Masse ◽  
Christopher Morgan ◽  
Wanting Wei ◽  
Edward W. Yu ◽  
Silvia Cavagnero
Keyword(s):  
Electron Microscopy ◽  
High Resolution ◽  
Single Particle ◽  
Chain Conformation ◽  
Cryo Electron Microscopy ◽  
Nascent Chain

scholarly journals Live Analysis and Reconstruction of Single-Particle Cryo-Electron Microscopy Data with CryoFLARE

2020 ◽  
Vol 60 (5) ◽  
pp. 2561-2569 ◽  
Author(s):  
Andreas D. Schenk ◽  
Simone Cavadini ◽  
Nicolas H. Thomä ◽  
Christel Genoud
Keyword(s):  
Electron Microscopy ◽  
Single Particle ◽  
Cryo Electron Microscopy ◽  
Electron Microscopy Data ◽  
Microscopy Data

scholarly journals Amino and PEG-Amino Graphene Oxide Grids Enrich and Protect Samples for High-resolution Single Particle Cryo-electron Microscopy

2019 ◽  
Author(s):  
Feng Wang ◽  
Zanlin Yu ◽  
Miguel Betegon ◽  
Melody Campbell ◽  
Tural Aksel ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Graphene Oxide ◽  
High Resolution ◽  
Single Particle ◽  
Particle Distribution ◽  
Water Interface ◽  
Amino Groups ◽  
Cryo Electron Microscopy ◽  
Air Water Interface ◽  
Resolution Single

AbstractCryo-EM samples prepared using the traditional methods often suffer from too few particles, poor particle distribution, or strongly biased orientation, or damage from the air-water interface. Here we report that functionalization of graphene oxide (GO) coated grids with amino groups concentrates samples on the grid with improved distribution and orientation. By introducing a PEG spacer, particles are kept away from both the GO surface and the air-water interface, protecting them from potential denaturation.

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