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Biomedical Optics Express

Biomedical Optics Express

  • Editor: Joseph A. Izatt
  • Vol. 4, Iss. 11 — Nov. 1, 2013
  • pp: 2667–2672

Accelerated rescaling of single Monte Carlo simulation runs with the Graphics Processing Unit (GPU)

Owen Yang and Bernard Choi  »View Author Affiliations

Biomedical Optics Express, Vol. 4, Issue 11, pp. 2667-2672 (2013)

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Abstract: To interpret fiber-based and camera-based measurements of remitted light from biological tissues, researchers typically use analytical models, such as the diffusion approximation to light transport theory, or stochastic models, such as Monte Carlo modeling. To achieve rapid (ideally real-time) measurement of tissue optical properties, especially in clinical situations, there is a critical need to accelerate Monte Carlo simulation runs. In this manuscript, we report on our approach using the Graphics Processing Unit (GPU) to accelerate rescaling of single Monte Carlo runs to calculate rapidly diffuse reflectance values for different sets of tissue optical properties. We selected MATLAB to enable non-specialists in C and CUDA-based programming to use the generated open-source code. We developed a software package with four abstraction layers. To calculate a set of diffuse reflectance values from a simulated tissue with homogeneous optical properties, our rescaling GPU-based approach achieves a reduction in computation time of several orders of magnitude as compared to other GPU-based approaches. Specifically, our GPU-based approach generated a diffuse reflectance value in 0.08ms. The transfer time from CPU to GPU memory currently is a limiting factor with GPU-based calculations. However, for calculation of multiple diffuse reflectance values, our GPU-based approach still can lead to processing that is ~3400 times faster than other GPU-based approaches.

© 2013 Optical Society of America

OCIS Codes
(110.7050) Imaging systems : Turbid media
(170.3660) Medical optics and biotechnology : Light propagation in tissues
(170.5280) Medical optics and biotechnology : Photon migration
(200.4960) Optics in computing : Parallel processing

ToC Category:
Optics of Tissue and Turbid Media

Original Manuscript: June 28, 2013
Revised Manuscript: October 14, 2013
Manuscript Accepted: October 18, 2013
Published: October 29, 2013

Virtual Issues
Advances in Optics for Biotechnology, Medicine and Surgery (2013) Biomedical Optics Express

Owen Yang and Bernard Choi, "Accelerated rescaling of single Monte Carlo simulation runs with the Graphics Processing Unit (GPU)," Biomed. Opt. Express 4, 2667-2672 (2013)

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