Analytical performance prediction for iterative reconstruction techniques in electron tomography of biological structures

International Journal of High Performance Computing Applications

Volumn 24, Issue 4, 2010, Pages 457-468

  Fritzsche, Paula Cecilia ^a   Fernandez, Jose Jesus ^b,c   Rexachs, Dolores ^a   Garcia, Inmaculada ^b   Luque, Emilio ^a  

^a UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^b UNIVERSITY OF ALMERÍA   (Spain)

^c CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

Author keywords

electron tomography; high performance computing; iterative reconstruction algorithms; parallel computing; performance prediction

Indexed keywords

ELECTRON TOMOGRAPHY; HIGH-PERFORMANCE COMPUTING; ITERATIVE RECONSTRUCTION ALGORITHMS; PARALLEL COMPUTING; PERFORMANCE PREDICTION;

ALGORITHMS; ARTS COMPUTING; COMPUTER HARDWARE; COMPUTERIZED TOMOGRAPHY; CONVERGENCE OF NUMERICAL METHODS; ELECTRIC IMPEDANCE TOMOGRAPHY; FORECASTING; IMAGE RECONSTRUCTION; INDUSTRIAL RESEARCH; ITERATIVE METHODS; MATHEMATICAL MODELS; OPTIMIZATION; PARALLEL ARCHITECTURES; PERMITTIVITY;

THREE DIMENSIONAL;

EID: 78649502559     PISSN: 10943420     EISSN: 17412846     Source Type: Journal    
DOI: 10.1177/1094342010370575     Document Type: Article

References (26)

1. Bilbao-Castro, J.R., Carazo, J.M., Garcia, I. and Fernandez, J.J. (2006). Parallelization of reconstruction algorithms in three-dimensional electron microscopy. Appl. Math. Model. 30: 688-701.
2. Bilbao-Castro, J.R., Marabini, R., Sorzano, C.O.S., Garcia, I., Carazo, J.M. and Fernandez, J.J. (2009). Exploiting desktop supercomputing for three-dimensional electron microscopy reconstructions using ART with blobs. J. Struct. Biol. 165: 19-26.
3. Bruyant, P. (2002). Analytic and iterative reconstruction algorithms in SPECT. Journal on Nuclear Medicine 43: 1343-1358.
4. Castano-Diez, D., Mueller, H. and Frangakis, A.S. (2007). Implementation and performance evaluation of reconstruction algorithms on graphics processors. J. Struct. Biol. 157: 288-295.
5. Censor, Y., Gordon, D. and Gordon, R. (2001 a) BICAV: a block-iterative, parallel algorithm for sparse systems with pixel-related weighting. IEEE Trans. Med. Imag. 20: 1050-1060.
6. Censor, Y., Gordon, D. and Gordon, R. (2001 b). Component averaging: An efficient iterative parallel algorithm for large and sparse unstructured problems. Parallel Computing 27: 777-808.
7. Censor, Y. and Zenios, S.A. (1997). Parallel optimization. Theory, algorithms and applications. Oxford University Press.
8. Deng, J., Yu, H., Ni, J., Wang, L. and Wang, G. (2009). Parallelism of iterative CT reconstruction based on local reconstruction algorithm. J. Supercomputing 48: 1-14.
9. Fernandez, J.J. (2008). High performance computing in structural determination by electron cryomicroscopy. J. Struct. Biol. 164: 1-6.
10. Fernandez, J.J., Carazo, J.M. and García, I. (2004). Three-dimensional reconstruction of cellular structures by electron microscope tomography and parallel computing. J. Parallel Distrib. Comput. 64: 285-300.
11. Fernandez, J.J., Gordon, D. and Gordon, R. (2008). Efficient parallel implementation of iterative reconstruction algorithms for electron tomography. J. Parallel Distrib. Comput. 68: 626-640.
12. Fernandez, J.J., Lawrence, A.F., Roca, J., García, I., Ellisman, M.H. and Carazo, J.M. (2002). High performance electron tomography of complex biological specimens. J. Struct. Biol. 138: 6-20.
13. Fernandez, J.J., Sorzano, C.O.S., Marabini, R. and Carazo, J.M. (2006). Image processing and 3-D reconstruction in electron microscopy. IEEE Signal Process. Mag. 23 (3). 84-94.
14. Frank, J., editor. (2006). Electron Tomography. Methods or Three-Dimensional Visualization or Structures in the Cell. Berlin: Springer.
15. Garcia, I., Roca, J., Sanjurjo, J., Carazo, J.M. and Zapata, E.L. (1996). Implementation and experimental evaluation of the constrained ART algorithm on a multicomputer system. Signal Process. 51: 69-76.
16. Gordon, D. (2006). Parallel ART for image reconstruction in CT using processor arrays. Int. J. Parallel, Emergent Distrib. Syst. 21: 365-380.
17. Gordon, R., Bender, R. and Herman, G.T. (1970). Algebraic reconstruction techniques (ART) for three-dimensional electron microscopy and X-ray photography. J. Theoret. Biol. 29: 471-482.
18. Kak, A.C. and Slaney, M. (2001). Principles or Computerized Tomographic Imaging. Society for Industrial and Applied Mathematics, Philadelphia, PA, USA.
19. Laurent, C., Peyrin, F., Chassery, J.M. and Amiel, M. (1998). Parallel image reconstruction on MIMD computers for three-dimensional cone-beam tomography. Parallel Computing 24: 1461-1479.
20. Leis, A.P., Beck, M., Gruska, M., Best, C., Hegerl, R., Baumeister, W. and Leis, J.W. (2006). Cryo-electron tomography of biological specimens. IEEE Signal Process. Mag. 23 (3). 95-103.
21. Lucic, V., Forster, F. and Baumeister, W. (2005). Structural studies by electron tomography: from cells to molecules. Annu. Rev. Biochem. 74: 833-865.
22. Ni, J., Li, X., He, T. and Wang, G. (2006). Review of parallel computing techniques for computed tomography image reconstruction. Current Medical Imaging Reviews 2: 405-414.
23. Peltier, S.T., Lin, A.W., Lee, D., Mock, S., Lamont, S., Molina, T., Wong, M., Dai, L., Martone, M.E. and Ellisman, M.H. (2003). The telescience portal for tomography applications. J. Paral. Distr. Comp. 63: 539-550.
24. Roerdink, J.B.T.M. and Westenberg, M.A. (1998). Data-parallel tomographic reconstruction: A comparison of filtered backprojection and direct Fourier reconstruction. Parallel Computing 24: 2129-2142.
25. Sali, A., Glaeser, R., Earnest, T. and Baumeister, W. (2003). From words to literature in structural proteomics. Nature 422: 216-225.
26. Zenios, S.A. and Censor, Y. (1991). Parallel computing with block-iterative image reconstruction algorithms. Applied Numerical Mathematics 7: 399-415.