Cryo-electron microscopy single particle reconstruction of virus particles using compressed sensing theory

Min Woo Kim, Jiyoung Choi, Liu Yu, Kyung Eun Lee, Sung Sik Han, Jong Chul Ye

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 Citations (Scopus)

Abstract

Sparse object supports are often encountered in many imaging problems. For such sparse objects, recent theory of compressed sensing tells us that accurate reconstruction of objects are possible even from highly limited number of measurements drastically smaller than the Nyquist sampling limit by solving L1 minimization problem. This paper employs the compressed sensing theory for cryo-electron microscopy (cryo-EM) single particle reconstruction of virus particles. Cryo-EM single particle reconstruction is a nice application of the compressed sensing theory because of the following reasons: 1) in some cases, due to the difficulty in sample collection, each experiment can obtain micrographs with limited number of virus samples, providing undersampled projection data, and 2) the nucleic acid of a viron is enclosed within capsid composed of a few proteins; hence the support of capsid in 3-D real space is quite sparse. In order to minimize the L1 cost function derived from compressed sensing, we develop a novel L1 minimization method based on the sliding mode control theory. Experimental results using synthetic and real virus data confirm that the our algorithm provides superior reconstructions of 3-D viral structures compared to the conventional reconstruction algorithms.

Original languageEnglish
Title of host publicationProceedings of SPIE - The International Society for Optical Engineering
Volume6498
DOIs
Publication statusPublished - 2007 Aug 31
EventComputational Imaging V - San Jose, CA, United States
Duration: 2007 Jan 292007 Jan 31

Other

OtherComputational Imaging V
CountryUnited States
CitySan Jose, CA
Period07/1/2907/1/31

Fingerprint

Compressed sensing
viruses
Viruses
Electron microscopy
electron microscopy
Nucleic acids
Sliding mode control
Control theory
optimization
Cost functions
control theory
nucleic acids
sliding
Sampling
Proteins
Imaging techniques
projection
sampling
proteins
costs

Keywords

  • Compressed sensing
  • Cryo-EM single particle reconstruction
  • Iterative shrinkage
  • L minimization
  • Sliding mode

ASJC Scopus subject areas

  • Electrical and Electronic Engineering
  • Condensed Matter Physics

Cite this

Kim, M. W., Choi, J., Yu, L., Lee, K. E., Han, S. S., & Ye, J. C. (2007). Cryo-electron microscopy single particle reconstruction of virus particles using compressed sensing theory. In Proceedings of SPIE - The International Society for Optical Engineering (Vol. 6498). [64981G] https://doi.org/10.1117/12.705008

Cryo-electron microscopy single particle reconstruction of virus particles using compressed sensing theory. / Kim, Min Woo; Choi, Jiyoung; Yu, Liu; Lee, Kyung Eun; Han, Sung Sik; Ye, Jong Chul.

Proceedings of SPIE - The International Society for Optical Engineering. Vol. 6498 2007. 64981G.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Kim, MW, Choi, J, Yu, L, Lee, KE, Han, SS & Ye, JC 2007, Cryo-electron microscopy single particle reconstruction of virus particles using compressed sensing theory. in Proceedings of SPIE - The International Society for Optical Engineering. vol. 6498, 64981G, Computational Imaging V, San Jose, CA, United States, 07/1/29. https://doi.org/10.1117/12.705008
Kim MW, Choi J, Yu L, Lee KE, Han SS, Ye JC. Cryo-electron microscopy single particle reconstruction of virus particles using compressed sensing theory. In Proceedings of SPIE - The International Society for Optical Engineering. Vol. 6498. 2007. 64981G https://doi.org/10.1117/12.705008
Kim, Min Woo ; Choi, Jiyoung ; Yu, Liu ; Lee, Kyung Eun ; Han, Sung Sik ; Ye, Jong Chul. / Cryo-electron microscopy single particle reconstruction of virus particles using compressed sensing theory. Proceedings of SPIE - The International Society for Optical Engineering. Vol. 6498 2007.
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