A Parallel Scheme for Three-Dimensional Reconstruction in Large-Field Electron Tomography
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.
KeywordsElectron tomography Three-dimensional reconstruction Iterative methods Nonlinear projection model TxBR
Unable to display preview. Download preview PDF.
- 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
- 9.Censor, Y.: Parallel optimization: theory, algorithms and applications. Oxford University Press (1997)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