publication . Article . 2019

ValoMC: a Monte Carlo software and MATLAB toolbox for simulating light transport in biological tissue

Leino, A. A.; Pulkkinen, A.; Tarvainen, T.;
Open Access English
  • Published: 15 Mar 2019
  • Publisher: The Optical Society
Abstract
A Monte Carlo method for photon transport has gained wide popularity in biomedical optics for studying light behaviour in tissue. Nowadays, typical computation times range from a few minutes to hours. Although various implementations of the Monte Carlo algorithm exist, there is only a limited number of free software available. In addition, these packages may require substantial learning efforts. To address these issues, we present a new Monte Carlo software with a user-friendly interface. The simulation geometry is defined using an unstructured (triangular or tetrahedral) mesh. The program solves the photon fluence in the computation domain and the exitance at t...
67 references, page 1 of 5

1. A. Sassaroli and F. Martelli, “Equivalence of four Monte Carlo methods for photon migration in turbid media,” J. Opt. Soc. Am. A 29(10), 2110-2117 (2012).

2. C. Zhu and Q. Liu, “Review of Monte Carlo modeling of light transport in tissues,” J. Biomed. Opt. 18(5), 050902 (2013).

3. S. A. Prahl, M. Keijzer, S. L. Jacques, and A. J. Welch, “A Monte Carlo model of light propagation in tissue,” in “SPIE Proceedings of Dosimetry of Laser Radiation in Medicine and Biology,” G. Müller and D. Sliney, eds. (1989), vol. IS 5, pp. 102-111.

4. M. Hiraoka, M. Firbank, M. Essenpreis, M. Cope, S. Arridge, P. van der Zee, and D. Delpy, “A Monte Carlo investigation of optical pathlength in inhomogeneous tissue and its application to near-infrared spectroscopy,” Phys. Med. Biol. 38(12), 1859-1876 (1993).

5. L. Wang, S. Jacques, and L. Zheng, “MCML - Monte Carlo modeling of photon transport in multi-layered tissues,” Comput. Methods Programs Biomed. 47(2), 131-146 (1995).

6. L. Wang, R. Nordquist, and W. Chen, “Optimal beam size for light delivery to absorption-enhanced tumors buried in biological tissues and effect of multiple-beam delivery: a Monte Carlo study,” Appl. Opt. 36(31), 8286-8291 (1997). [OpenAIRE]

7. V. Periyasamya and M. Pramanik, “Monte Carlo simulation of light transport in turbid medium with embedded object - spherical, cylindrical, ellipsoidal, or cuboidal objects embedded within multilayered tissues,” J. Biomed. Opt. 19(4), 045003 (2014).

8. T. Pfefer, J. K. Barton, E. Chan, M. Ducros, B. Sorg, T. Milner, J. Nelson, and A. Welch, “A three-dimensional modular adaptable grid numerical model for light propagation during laser irradiation of skin tissue,” IEEE J. Sel. Top. Quantum Electron. 2(4), 934-942 (1996). [OpenAIRE]

9. 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(3), 159-170 (2002).

10. J. Heiskala, I. Nissilä, T. Neuvonen, S. Järvenpää, and E. Somersalo, “Modeling anisotropic light propagation in a realistic model of the human head,” Appl. Opt. 44(11), 2049-2057 (2005).

11. Y. Fukui, Y. Ajichi, and E. Okada, “Monte Carlo prediction of near-infrared light propagation in realistic adult and neonatal head models,” Appl. Opt. 42(16), 2881-2887 (2003).

12. Q. Fang and D. Boas, “Monte Carlo simulation of photon migration in 3D turbid media accelerated by graphics processing units,” Opt. Express 17(22), 20178-20190 (2009).

13. S. Patwardhan, A. Dhawan, and P. Relue, “Monte Carlo simulation of light-tissue interaction: Three-dimensional simulation for trans-illumination-based imaging of skin lesions,” IEEE Trans. Biomed. Eng. 52(7), 1227-1236 (2005).

14. Y. Liu, S. Jacques, M. Azimipour, J. Rogers, R. Pashaie, and K. Eliceiri, “OptogenSIM: a 3D Monte Carlo simulation platform for light delivery design in optogenetics,” Biomed. Opt. Express 6(12), 4859-4870 (2015).

15. R. Hochuli, S. Powell, S. Arridge, and B. Cox, “Quantitative photoacoustic tomography using forward and adjoint Monte Carlo models of radiance,” J. Biomed. Opt. 21(12), 126004 (2016).

67 references, page 1 of 5
Abstract
A Monte Carlo method for photon transport has gained wide popularity in biomedical optics for studying light behaviour in tissue. Nowadays, typical computation times range from a few minutes to hours. Although various implementations of the Monte Carlo algorithm exist, there is only a limited number of free software available. In addition, these packages may require substantial learning efforts. To address these issues, we present a new Monte Carlo software with a user-friendly interface. The simulation geometry is defined using an unstructured (triangular or tetrahedral) mesh. The program solves the photon fluence in the computation domain and the exitance at t...
67 references, page 1 of 5

1. A. Sassaroli and F. Martelli, “Equivalence of four Monte Carlo methods for photon migration in turbid media,” J. Opt. Soc. Am. A 29(10), 2110-2117 (2012).

2. C. Zhu and Q. Liu, “Review of Monte Carlo modeling of light transport in tissues,” J. Biomed. Opt. 18(5), 050902 (2013).

3. S. A. Prahl, M. Keijzer, S. L. Jacques, and A. J. Welch, “A Monte Carlo model of light propagation in tissue,” in “SPIE Proceedings of Dosimetry of Laser Radiation in Medicine and Biology,” G. Müller and D. Sliney, eds. (1989), vol. IS 5, pp. 102-111.

4. M. Hiraoka, M. Firbank, M. Essenpreis, M. Cope, S. Arridge, P. van der Zee, and D. Delpy, “A Monte Carlo investigation of optical pathlength in inhomogeneous tissue and its application to near-infrared spectroscopy,” Phys. Med. Biol. 38(12), 1859-1876 (1993).

5. L. Wang, S. Jacques, and L. Zheng, “MCML - Monte Carlo modeling of photon transport in multi-layered tissues,” Comput. Methods Programs Biomed. 47(2), 131-146 (1995).

6. L. Wang, R. Nordquist, and W. Chen, “Optimal beam size for light delivery to absorption-enhanced tumors buried in biological tissues and effect of multiple-beam delivery: a Monte Carlo study,” Appl. Opt. 36(31), 8286-8291 (1997). [OpenAIRE]

7. V. Periyasamya and M. Pramanik, “Monte Carlo simulation of light transport in turbid medium with embedded object - spherical, cylindrical, ellipsoidal, or cuboidal objects embedded within multilayered tissues,” J. Biomed. Opt. 19(4), 045003 (2014).

8. T. Pfefer, J. K. Barton, E. Chan, M. Ducros, B. Sorg, T. Milner, J. Nelson, and A. Welch, “A three-dimensional modular adaptable grid numerical model for light propagation during laser irradiation of skin tissue,” IEEE J. Sel. Top. Quantum Electron. 2(4), 934-942 (1996). [OpenAIRE]

9. 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(3), 159-170 (2002).

10. J. Heiskala, I. Nissilä, T. Neuvonen, S. Järvenpää, and E. Somersalo, “Modeling anisotropic light propagation in a realistic model of the human head,” Appl. Opt. 44(11), 2049-2057 (2005).

11. Y. Fukui, Y. Ajichi, and E. Okada, “Monte Carlo prediction of near-infrared light propagation in realistic adult and neonatal head models,” Appl. Opt. 42(16), 2881-2887 (2003).

12. Q. Fang and D. Boas, “Monte Carlo simulation of photon migration in 3D turbid media accelerated by graphics processing units,” Opt. Express 17(22), 20178-20190 (2009).

13. S. Patwardhan, A. Dhawan, and P. Relue, “Monte Carlo simulation of light-tissue interaction: Three-dimensional simulation for trans-illumination-based imaging of skin lesions,” IEEE Trans. Biomed. Eng. 52(7), 1227-1236 (2005).

14. Y. Liu, S. Jacques, M. Azimipour, J. Rogers, R. Pashaie, and K. Eliceiri, “OptogenSIM: a 3D Monte Carlo simulation platform for light delivery design in optogenetics,” Biomed. Opt. Express 6(12), 4859-4870 (2015).

15. R. Hochuli, S. Powell, S. Arridge, and B. Cox, “Quantitative photoacoustic tomography using forward and adjoint Monte Carlo models of radiance,” J. Biomed. Opt. 21(12), 126004 (2016).

67 references, page 1 of 5
Powered by OpenAIRE Open Research Graph
Any information missing or wrong?Report an Issue