Skip to main content
SpringerLink
Log in

A Parallel Scheme for Three-Dimensional Reconstruction in Large-Field Electron Tomography

  • Conference paper
Bioinformatics Research and Applications (ISBRA 2014)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 8492))

Included in the following conference series:

Abstract

Large-field high-resolution electron tomography enables visualizing detailed mechanisms under global structure. As field enlarges, the processing time increases and the distortions in reconstruction become more critical. Adopting a nonlinear projection model instead of a linear one can compensate for curvilinear trajectories, nonlinear electron optics and sample warping. But the processing time for the reconstruction with nonlinear projection model is rather considerable. In this work, we propose a new parallel strategy for block iterative reconstruction algorithms. We also adopt a page-based data transfer in this strategy so as to dramatically reduce the processing time for data transfer and communication. We have tested this parallel strategy and it can yield speedups of approximate 40 times according to our experimental results.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Phan, S., Lawrence, A., Molina, T., Lanman, J., Berlanga, M., Terada, M., Kulungowski, A., Obayashi, J., Ellisman, M.: Txbr montage reconstruction for large field electron tomography. Journal of Structural Biology 180, 154–164 (2012)

    Article  Google Scholar 

  2. Wan, X., Phan, S., Lawrence, A., Zhang, F., Han, R., Liu, Z., Ellisman, M.: Iterative methods in large field electron microscope tomography. SIAM Journal on Scientific Computing 35(5), S402–S419 (2013)

    Google Scholar 

  3. Lawrence, A., Phan, S., Singh, R.: Parallel processing and large-field electron microscope tomography. In: World Congress on Computer Science and Information Engineering, pp. 339–343 (2009)

    Google Scholar 

  4. Agulleiro, J.I., Fernández, J.J.: Evaluation of a multicore-optimized implementation for tomographic reconstruction. PloS One 7(11), e48261 (2012)

    Google Scholar 

  5. Gilbert, P.: Iterative methods for the three-dimensional reconstruction of an object from projections. Journal of Theoretical Biology 36(1), 105–117 (1972)

    Article  Google Scholar 

  6. Censor, Y., Gordon, D., Gordon, R.: Bicav: A block-iterative parallel algorithm for sparse systems with pixel-related weighting. IEEE Transactions on Medical Imaging 20(10), 1050–1060 (2001)

    Article  Google Scholar 

  7. Wan, X., Zhang, F., Chu, Q., Zhang, K., Sun, F., Yuan, B., Liu, Z.: Three-dimensional reconstruction using an adaptive simultaneous algebraic reconstruction technique in electron tomography. Journal of Structural Biology 175(3), 277–287 (2011)

    Article  Google Scholar 

  8. Lawrence, A., Bouwer, J.C., Perkins, G., Ellisman, M.H.: Transform-based backprojection for volume reconstruction of large format electron microscope tilt series. Journal of Structural Biology 154(2), 144–167 (2006)

    Article  Google Scholar 

  9. Censor, Y.: Parallel optimization: theory, algorithms and applications. Oxford University Press (1997)

    Google Scholar 

  10. Aharoni, R., Censor, Y.: Block-iterative projection methods for parallel computation of solutions to convex feasibility problems. Linear Algebra and Its Applications 120, 165–175 (1989)

    Article  MATH  MathSciNet  Google Scholar 

  11. Bilbao-Castro, J.R., Carazo, J.M., Fernandez, J.J., García, I.: Parallelization and comparison of 3d iterative reconstruction algorithms. In: Proceedings of the 12th Euromicro Conference on Parallel, Distributed and Network Based Processing, pp. 96–102. IEEE (2004)

    Google Scholar 

  12. Herman, G.T., Meyer, L.B.: Algebraic reconstruction techniques can be made computationally efficient. IEEE Transactions on Medical Imaging 12(3), 600–609 (1993)

    Article  Google Scholar 

  13. Wan, X., Zhang, F., Chu, Q., Liu, Z.: High-performance blob-based iterative reconstruction of electron tomography on multi-GPUs. In: Chen, J., Wang, J., Zelikovsky, A. (eds.) ISBRA 2011. LNCS, vol. 6674, pp. 61–72. Springer, Heidelberg (2011)

    Chapter  Google Scholar 

  14. Fernandez, J.: High performance computing in structural determination by electron cryomicroscopy. Journal of Structural Biology 164(1), 1–6 (2008)

    Article  Google Scholar 

  15. Castaño Díez, D., Mueller, H., Frangakis, A.S.: Implementation and performance evaluation of reconstruction algorithms on graphics processors. Journal of Structural Biology 157(1), 288–295 (2007)

    Article  Google Scholar 

  16. Van der Sluis, A., Van der Vorst, H.: Sirt-and cg-type methods for the iterative solution of sparse linear least-squares problems. Linear Algebra and its Applications 130, 257–303 (1990)

    Article  MATH  MathSciNet  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Key Lab. of Intelligent Information Processing, and Advanced Computing Research Lab., Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China

    Jingrong Zhang, Xiaohua Wan, Fa Zhang, Fei Ren & Zhiyong Liu

  2. University of Chinese Academy of Sciences, Beijing, China

    Jingrong Zhang

  3. Yanshan University, China

    Xuan Wang

Authors
  1. Jingrong Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Xiaohua Wan
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Fa Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Fei Ren
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Xuan Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Zhiyong Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Johns Hopkins University, Computer Science Department, Baltimore, MD 21218, USA and National Science Foundation, 1115, CCF, USA

    Mitra Basu

  2. Department of Computer Science, Georgia State University, 30303, Atlanta, GA, USA

    Yi Pan

  3. School of Information Science and Engineering, Central South University, 410083, Changsha, China

    Jianxin Wang

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer International Publishing Switzerland

About this paper

Cite this paper

Zhang, J., Wan, X., Zhang, F., Ren, F., Wang, X., Liu, Z. (2014). A Parallel Scheme for Three-Dimensional Reconstruction in Large-Field Electron Tomography. In: Basu, M., Pan, Y., Wang, J. (eds) Bioinformatics Research and Applications. ISBRA 2014. Lecture Notes in Computer Science(), vol 8492. Springer, Cham. https://doi.org/10.1007/978-3-319-08171-7_10

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-08171-7_10

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-08170-0

  • Online ISBN: 978-3-319-08171-7

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation