OSA's Digital Library

Virtual Journal for Biomedical Optics

Virtual Journal for Biomedical Optics

| EXPLORING THE INTERFACE OF LIGHT AND BIOMEDICINE

  • Editors: Andrew Dunn and Anthony Durkin
  • Vol. 6, Iss. 8 — Aug. 26, 2011

Graphics processing unit parallel accelerated solution of the discrete ordinates for photon transport in biological tissues

Kuan Peng, Xinbo Gao, Xiaochao Qu, Nunu Ren, Xueli Chen, Xiaowei He, Xiaorei Wang, Jimin Liang, and Jie Tian  »View Author Affiliations


Applied Optics, Vol. 50, Issue 21, pp. 3808-3823 (2011)
http://dx.doi.org/10.1364/AO.50.003808


View Full Text Article

Enhanced HTML    Acrobat PDF (1675 KB)





Browse Journals / Lookup Meetings

Browse by Journal and Year


   


Lookup Conference Papers

Close Browse Journals / Lookup Meetings

Article Tools

Share
Citations

Abstract

As a widely used numerical solution for the radiation transport equation (RTE), the discrete ordinates can predict the propagation of photons through biological tissues more accurately relative to the diffusion equation. The discrete ordinates reduce the RTE to a serial of differential equations that can be solved by source iteration (SI). However, the tremendous time consumption of SI, which is partly caused by the expensive computation of each SI step, limits its applications. In this paper, we present a graphics processing unit (GPU) parallel accelerated SI method for discrete ordinates. Utilizing the calculation independence on the levels of the discrete ordinate equation and spatial element, the proposed method reduces the time cost of each SI step by parallel calculation. The photon reflection at the boundary was calculated based on the results of the last SI step to ensure the calculation independence on the level of the discrete ordinate equation. An element sweeping strategy was proposed to detect the calculation independence on the level of the spatial element. A GPU parallel frame called the compute unified device architecture was employed to carry out the parallel computation. The simulation experiments, which were carried out with a cylindrical phantom and numerical mouse, indicated that the time cost of each SI step can be reduced up to a factor of 228 by the proposed method with a GTX 260 graphics card.

© 2011 Optical Society of America

OCIS Codes
(170.3010) Medical optics and biotechnology : Image reconstruction techniques
(170.6960) Medical optics and biotechnology : Tomography
(230.6080) Optical devices : Sources

ToC Category:
Medical Optics and Biotechnology

History
Original Manuscript: April 4, 2011
Revised Manuscript: May 5, 2011
Manuscript Accepted: June 2, 2011
Published: July 11, 2011

Virtual Issues
Vol. 6, Iss. 8 Virtual Journal for Biomedical Optics

Citation
Kuan Peng, Xinbo Gao, Xiaochao Qu, Nunu Ren, Xueli Chen, Xiaowei He, Xiaorei Wang, Jimin Liang, and Jie Tian, "Graphics processing unit parallel accelerated solution of the discrete ordinates for photon transport in biological tissues," Appl. Opt. 50, 3808-3823 (2011)
http://www.opticsinfobase.org/vjbo/abstract.cfm?URI=ao-50-21-3808


Sort:  Author  |  Year  |  Journal  |  Reset  

References

  1. A. P. Gibson, J. C. Hebden, and S. R. Arridge, “Recent advances in diffuse optical imaging,” Phys. Med. Biol. 50, 1–43 (2005). [CrossRef]
  2. R. Weissleder and V. Ntziachristos, “Shedding light onto live molecular targets,” Nat. Med. 9, 123–128 (2003). [CrossRef] [PubMed]
  3. V. Ntziachristos, “Fluorescence molecular imaging,” Annu. Rev. Biomed. Eng. 8, 1–33 (2006). [CrossRef] [PubMed]
  4. V. Ntziachristos, J. Ripoll, LH. Wang, and R. Weissleder, “Looking and listening to light: the evolution of whole body photonic imaging,” Nat. Biotechnol. 23, 313–320 (2005). [CrossRef] [PubMed]
  5. G. Wang, W. Cong, Y. Li, W. Han, D. Kumar, X. Qian, H. Shen, M. Jiang, T. Zhou, J. Cheng, J. Tian, Y. Lv, H. Li, and J. Luo. “Recent development in bioluminescence tomography,” Curr. Med. Imaging Rev. 2, 453–457 (2006). [CrossRef]
  6. K. M. Yoo, F. Liu, and R. R. Alfano, “When does the diffusion approximation fail to describe photon transport in random media?” Phys. Rev. Lett. 64, 2647–2650 (1990). [CrossRef] [PubMed]
  7. S. Patwardhan, S. Bloch, S. Achilefu, and J. Culver, “Time-dependent whole-body fluorescence tomography of probe bio-distributions in mice,” Opt. Express 13, 2564–2577 (2005). [CrossRef] [PubMed]
  8. E. E. Graves, J. Ripoll, R. Weissleder, and V. Ntziachristos, “A submillimeter resolution fluorescence molecular imaging system for small animal imaging,” Med. Phys. 30, 901–911(2003). [CrossRef] [PubMed]
  9. E. D. Aydin, C. R. E. Oliveira, and A. J. H. Goddard, “A comparison between transport and diffusion calculations using a finite element-spherical harmonics radiation transport method,” Med. Phys. 29, 2013–2023 (2002). [CrossRef] [PubMed]
  10. A. D. Klose and E. W. Larsen, “Light transport in biological tissue based on the simplified spherical harmonics equations,” J. Comput. Phys. 220, 441–470 (2006). [CrossRef]
  11. J. C. Rasmussen, A. Joshi, T. Pan, T. Wareing, J. McGhee, and E. M. Sevick-Muraca, “Radiative transport in fluorescence-enhanced frequency-domain photon migration,” Med. Phys. 33, 4685–4700 (2006). [CrossRef]
  12. E. E. Lewis and W. F. Miller, Computational Methods of Neutron Transport (Wiley, 1984).
  13. T. A. Wareing, J. M. McGhee, J. E. Morel, and S. D. Pautz, “Discontinuous finite element SN methods on three-dimensional unstructured grids,” Nucl. Sci. Eng. 138, 256–268 (2001).
  14. A. D. Klose, V. Ntziachristos, and A. H. Hielscher, “The inverse source problem based on the radiative transfer equation in optical molecular imaging,” J. Comput. Phys. 202, 323–345(2005). [CrossRef]
  15. A. D. Klose and A. H. Hielscher, “Fluorescence tomography with simulated data based on the equation of radiative transfer,” Opt. Lett. 28, 1019–1021 (2003). [CrossRef] [PubMed]
  16. K. Ren, G. S. Abdoulaev, G. Bal, and A. H. Hielscher, “Algorithm for solving the equation of radiative transfer in the frequency domain,” Opt. Lett. 29, 578–580 (2004). [CrossRef] [PubMed]
  17. H. Gao and H. K. Zhao, “A fast forward solver of radiative transfer equation,” Transp. Theory Stat. Phys. 38, 149–192(2009). [CrossRef]
  18. M. L. Adams, T. A. Wareing, and W. F. Walters, “Characteristic methods in thick diffusive problems,” Nucl. Sci. Eng. 130, 18–46 (1998).
  19. M. L. Adams and E. W. Larsen, “Fast iterative methods for discrete-ordinates particle transport calculations,” Prog. Nucl. Energy 40, 3–159 (2002). [CrossRef]
  20. G. Longoni, A. Haghighat, C. Yi, and G. E. Sjoden, “Benchmarking of PENTRAN-SSN parallel transport code and fast preconditioning algorithm using the VENUS-2 MOX-fueled benchmark problem,” J. ASTM Int. 3, 321–330 (2006). [CrossRef]
  21. V. Kucukboyaci, A. Haghighat, and G. E. Sjoden, “Performance of PENTRAN 3-D parallel particle transport code on the IBM SP2 and PCTRAN cluster,” Lect. Notes Comput. Sci. 2131, 36–43 (2001). [CrossRef]
  22. G. Ghita, G. Sjoden, and J. Baciak, “A Methodology for experimental and 3-D computational radiation transport assessments of Pu-Be neutron sources,” Nucl. Technol. 159, 319–331(2007).
  23. NVIDIA, http://www.nvidia. com.
  24. V. Lebedev, “Values of the nodes and weights of ninth to seventeenth order Gauss–Markov quadrature formulae invariant under the octahedron group with inversion,” USSR Comput. Math. Math. Phys. 15, 44–51 (1975). [CrossRef]
  25. V. Lebedev, “Quadratures on a sphere,” USSR Comput. Math. Math. Phys. 16, 10–24 (1976). [CrossRef]
  26. A. Kienle, F. K. Forster, and R. Hibst, “Influence of the phase function on determination of the optical properties of biological tissue by spatially resolved reflectance,” Opt. Lett. 26, 1571–1573 (2001). [CrossRef]
  27. J. D. Jackson, Classical Electrodynamics (Wiley, 1999).
  28. L. Wang, S. L. Jacques, and L. Zheng, “MCML-Monte Carlo modeling of photon transport in multi-layered tissues,” Comput. Methods Programs Biomed. 47, 131–146 (1995). [CrossRef] [PubMed]
  29. D. Boas, J. Culver, J. Stott, and A. Dunn, “Three dimensional Monte Carlo code for photon migration through complex heterogeneous media including the adult human head,” Opt. Express 10, 159–169 (2002). [PubMed]
  30. N. N. Ren, J. M. Liang, X. C. Qu, J. F. Li, B. J. Lu, and J. Tian, “GPU-based Monte Carlo simulation for light propagation in complex heterogeneous tissues,” Opt. Express 18, 6811–6823(2010). [CrossRef] [PubMed]
  31. B. Dogdas, D. Stout, A. Chatziioannou, and R. M. Leahy, “Digimouse: a 3D whole body mouse atlas from CT and cryosection data,” Phys. Med. Biol. 52, 577–587 (2007). [CrossRef] [PubMed]
  32. G. Alexandrakis, F. R. Rannou, and A. F. Chatziioannou, “Tomographic bioluminescence imaging by use of a combined optical-PET (OPET) system: a computer simulation feasibility study,” Phys. Med. Biol. 50, 4225–4241 (2005). [CrossRef] [PubMed]
  33. A. Nicholls and B. Honig, “A rapid finite difference algorithm utilizing successive over-relaxation to solve the Poisson-Boltzmann equation,” J. Comput. Chem. 12, 435–445 (1991). [CrossRef]
  34. J. V. Dave and J. Gazdag, “A modified Fourier transform method for multiple scattering calculations in a plane parallel Mie atmosphere,” Appl. Opt. 9, 1457–1466 (1970). [CrossRef] [PubMed]
  35. S. Ito and T. Oguchi, “Approximate solutions of the vector radiative transfer equation for linearly polarized light in discrete random media,” J. Opt. Soc. Am. A 6, 1852–1858(1989). [CrossRef]
  36. V. P. Budak and A. V. Kozelskii, “Accuracy and applicability domain of the small angle approximation,” Atmos. Oceanic Opt. 18, 32–37 (2005).
  37. Y. A. Ilyushin and V. P. Budak, “Narrow-beam propagation in a two-dimensional scattering medium,” J. Opt. Soc. Am. A 28, 76–81 (2011). [CrossRef]
  38. S. A. Rukolaine and V. S. Yuferev, “Discrete ordinates quadrature schemes based on the angular interpolation of radiation intensity,” J. Quant. Spectrosc. Radiat. Transfer 69, 257–275(2001). [CrossRef]

Cited By

Alert me when this paper is cited

OSA is able to provide readers links to articles that cite this paper by participating in CrossRef's Cited-By Linking service. CrossRef includes content from more than 3000 publishers and societies. In addition to listing OSA journal articles that cite this paper, citing articles from other participating publishers will also be listed.


« Previous Article  |  Next Article »

OSA is a member of CrossRef.

CrossCheck Deposited