MCmatlab: An open-source, user-friendly, MATLAB-integrated 3D Monte Carlo light transport solver with heat diffusion and tissue damage

Dominik Marti; Rikke N. Aasbjerg; Peter E. Andersen; Anders Kragh Hansen

doi:10.1117/12.2507754

MCmatlab: An open-source, user-friendly, MATLAB-integrated 3D Monte Carlo light transport solver with heat diffusion and tissue damage

Dominik Marti, Rikke N. Aasbjerg, Peter E. Andersen, Anders Kragh Hansen^*

^*Corresponding author for this work

Technical University of Denmark

Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

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Abstract

While there exist many Monte Carlo (MC) programs for solving the radiative transfer equation (RTE) in biological tissues, we have identified a need for an open-source MC program that is sufficiently user-friendly for use in an education environment, in which detailed knowledge of compiling or UNIX command-line cannot be assumed. Therefore, we introduce MCmatlab, an open-source codebase thus far consisting of (a) a fast 3D Monte Carlo RTE solver and (b) a finite-element heat diffusion and Arrhenius-based thermal tissue damage simulator, both run in MATLAB. The kernel for both of these solvers are written in parallelized C and implemented as MATLAB MEX functions, combining the speed of C with the familiarity and versatility of MATLAB. We present example results generated by the RTE solver and the thermal model. MCmatlab is easy to install and use and can be used by students and experienced researchers alike for simulating tissue light propagation and, optionally, thermal damage.

Original language	English
Title of host publication	Proceedings of SPIE
Number of pages	12
Publisher	SPIE - International Society for Optical Engineering
Publication date	2019
Article number	108760T
DOIs	https://doi.org/10.1117/12.2507754
Publication status	Published - 2019
Event	SPIE Photonics West 2019: Optical Interactions with Tissue and Cells XXX - Moscone Center, San Francisco, United States Duration: 2 Feb 2019 → 7 Feb 2019 Conference number: 10876 http://spie.org/conferences-and-exhibitions/photonics-west/

Conference

Conference	SPIE Photonics West 2019: Optical Interactions with Tissue and Cells XXX
Number	10876
Location	Moscone Center
Country/Territory	United States
City	San Francisco
Period	02/02/2019 → 07/02/2019
Internet address	http://spie.org/conferences-and-exhibitions/photonics-west/

Series	Progress in Biomedical Optics and Imaging - Proceedings of SPIE
ISSN	1605-7422

Keywords

Monte Carlo methods
Photothermal effects
3D modeling
Tissue optics
Scattering
Absorption

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108760TFinal published version, 2.56 MB
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Marti, D., Aasbjerg, R. N., Andersen, P. E., & Hansen, A. K. (2019). MCmatlab: An open-source, user-friendly, MATLAB-integrated 3D Monte Carlo light transport solver with heat diffusion and tissue damage. In Proceedings of SPIE [108760T] SPIE - International Society for Optical Engineering. Progress in Biomedical Optics and Imaging - Proceedings of SPIE https://doi.org/10.1117/12.2507754

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title = "MCmatlab: An open-source, user-friendly, MATLAB-integrated 3D Monte Carlo light transport solver with heat diffusion and tissue damage",

abstract = "While there exist many Monte Carlo (MC) programs for solving the radiative transfer equation (RTE) in biological tissues, we have identified a need for an open-source MC program that is sufficiently user-friendly for use in an education environment, in which detailed knowledge of compiling or UNIX command-line cannot be assumed. Therefore, we introduce MCmatlab, an open-source codebase thus far consisting of (a) a fast 3D Monte Carlo RTE solver and (b) a finite-element heat diffusion and Arrhenius-based thermal tissue damage simulator, both run in MATLAB. The kernel for both of these solvers are written in parallelized C and implemented as MATLAB MEX functions, combining the speed of C with the familiarity and versatility of MATLAB. We present example results generated by the RTE solver and the thermal model. MCmatlab is easy to install and use and can be used by students and experienced researchers alike for simulating tissue light propagation and, optionally, thermal damage.",

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author = "Dominik Marti and Aasbjerg, {Rikke N.} and Andersen, {Peter E.} and Hansen, {Anders Kragh}",

year = "2019",

doi = "10.1117/12.2507754",

language = "English",

series = "Progress in Biomedical Optics and Imaging - Proceedings of SPIE",

publisher = "SPIE - International Society for Optical Engineering",

booktitle = "Proceedings of SPIE",

note = "SPIE Photonics West 2019: Optical Interactions with Tissue and Cells XXX ; Conference date: 02-02-2019 Through 07-02-2019",

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Marti, D, Aasbjerg, RN, Andersen, PE & Hansen, AK 2019, MCmatlab: An open-source, user-friendly, MATLAB-integrated 3D Monte Carlo light transport solver with heat diffusion and tissue damage. in Proceedings of SPIE., 108760T, SPIE - International Society for Optical Engineering, Progress in Biomedical Optics and Imaging - Proceedings of SPIE, SPIE Photonics West 2019: Optical Interactions with Tissue and Cells XXX, San Francisco, California, United States, 02/02/2019. https://doi.org/10.1117/12.2507754

MCmatlab: An open-source, user-friendly, MATLAB-integrated 3D Monte Carlo light transport solver with heat diffusion and tissue damage. / Marti, Dominik; Aasbjerg, Rikke N.; Andersen, Peter E. et al.

Proceedings of SPIE. SPIE - International Society for Optical Engineering, 2019. 108760T (Progress in Biomedical Optics and Imaging - Proceedings of SPIE).

Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

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T1 - MCmatlab: An open-source, user-friendly, MATLAB-integrated 3D Monte Carlo light transport solver with heat diffusion and tissue damage

AU - Marti, Dominik

AU - Aasbjerg, Rikke N.

AU - Andersen, Peter E.

AU - Hansen, Anders Kragh

N1 - Conference code: 10876

PY - 2019

Y1 - 2019

N2 - While there exist many Monte Carlo (MC) programs for solving the radiative transfer equation (RTE) in biological tissues, we have identified a need for an open-source MC program that is sufficiently user-friendly for use in an education environment, in which detailed knowledge of compiling or UNIX command-line cannot be assumed. Therefore, we introduce MCmatlab, an open-source codebase thus far consisting of (a) a fast 3D Monte Carlo RTE solver and (b) a finite-element heat diffusion and Arrhenius-based thermal tissue damage simulator, both run in MATLAB. The kernel for both of these solvers are written in parallelized C and implemented as MATLAB MEX functions, combining the speed of C with the familiarity and versatility of MATLAB. We present example results generated by the RTE solver and the thermal model. MCmatlab is easy to install and use and can be used by students and experienced researchers alike for simulating tissue light propagation and, optionally, thermal damage.

AB - While there exist many Monte Carlo (MC) programs for solving the radiative transfer equation (RTE) in biological tissues, we have identified a need for an open-source MC program that is sufficiently user-friendly for use in an education environment, in which detailed knowledge of compiling or UNIX command-line cannot be assumed. Therefore, we introduce MCmatlab, an open-source codebase thus far consisting of (a) a fast 3D Monte Carlo RTE solver and (b) a finite-element heat diffusion and Arrhenius-based thermal tissue damage simulator, both run in MATLAB. The kernel for both of these solvers are written in parallelized C and implemented as MATLAB MEX functions, combining the speed of C with the familiarity and versatility of MATLAB. We present example results generated by the RTE solver and the thermal model. MCmatlab is easy to install and use and can be used by students and experienced researchers alike for simulating tissue light propagation and, optionally, thermal damage.

KW - Monte Carlo methods

KW - Photothermal effects

KW - 3D modeling

KW - Tissue optics

KW - Scattering

KW - Absorption

U2 - 10.1117/12.2507754

DO - 10.1117/12.2507754

M3 - Article in proceedings

T3 - Progress in Biomedical Optics and Imaging - Proceedings of SPIE

BT - Proceedings of SPIE

PB - SPIE - International Society for Optical Engineering

T2 - SPIE Photonics West 2019: Optical Interactions with Tissue and Cells XXX

Y2 - 2 February 2019 through 7 February 2019

ER -

MCmatlab: An open-source, user-friendly, MATLAB-integrated 3D Monte Carlo light transport solver with heat diffusion and tissue damage

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Keywords

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