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Accelerating 3B single-molecule super-resolution microscopy with cloud computing

Nature Methods volume 10, pages 96–97 (2013)Cite this article

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Aside from its flexible and cost-effective super-computing power, the greatest advantages of Amazon EC2 are its accessibility and ease of use. Normally, porting a computational code to a new system involves the configuration of a system-dependent software environment. The convoluted configuration process—not to mention the increased complexity for cluster computing—often discourages scientists without programming backgrounds. Use of Amazon EC2 significantly lowers this entry barrier. By packaging the executable program together with its running environment in a single image file known as the Amazon machine image (AMI), we can distribute 3B analysis to the public through the Amazon Marketplace. Hundreds of processes can run on instances, with each instance configured as an exact copy of the AMI. A user can launch massively parallel 3B processes on the Cloud from a local computer in just a few minutes (Fig. 1b and Supplementary Video 1).

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Figure 1: 3B analysis using Amazon EC2.

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Acknowledgements

We thank E. Rotsen for helping us install the 3B analysis software. This research is supported by the Waitt Foundation.

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Authors and Affiliations

  1. Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, California, USA

    Ying S Hu & Hu Cang

  2. Department of Biomedical Engineering, Oregon Health and Science University, Portland, Oregon, USA

    Xiaolin Nan

  3. Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon, USA

    Xiaolin Nan

  4. Oregon Center for Spatial Systems Biomedicine, School of Medicine, Oregon Health and Science University, Portland, Oregon, USA

    Xiaolin Nan

  5. The Eunice Kennedy Shriver National Institute of Child Health and Human Development, US National Institutes of Health, Bethesda, Maryland, USA

    Prabuddha Sengupta & Jennifer Lippincott-Schwartz

Authors
  1. Ying S Hu
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  2. Xiaolin Nan
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  3. Prabuddha Sengupta
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  4. Jennifer Lippincott-Schwartz
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  5. Hu Cang
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Corresponding author

Correspondence to Hu Cang.

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Supplementary information

Demonstration of Amazon EC2 for 3B analysis

This brief video demonstrates the procedures of setting up an Amazon EC2 account, launching 3B calculation instances using the AMI and bash scripts we supply, visualizing reconstruction results and terminating EC2 instances using a Macintosh computer. (MOV 16669 kb)

Supplementary Software

The Cloud3Bscripts.zip file contains the bash and MATLAB scripts that we prepared to run the 3B analysis on the Amazon EC2 cloud. (ZIP 706 kb)

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Hu, Y., Nan, X., Sengupta, P. et al. Accelerating 3B single-molecule super-resolution microscopy with cloud computing. Nat Methods 10, 96–97 (2013). https://doi.org/10.1038/nmeth.2335

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