MCmatlab: an open-source, user-friendly, MATLAB-integrated three-dimensional 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

Research output: Contribution to journalJournal articleResearchpeer-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 threedimensional MC 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 is written in parallelized C and implemented
as MATLAB MEX functions, combining the speed of C with the familiarity and versatility of MATLAB. We compare the RTE solver to Steven Jacques’ mcxyz, which it is inspired by, and present example results generated by 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 languageEnglish
Article number121622
JournalJournal of Biomedical Optics
Volume23
Issue number12
Number of pages7
ISSN1083-3668
DOIs
Publication statusPublished - 2018

Keywords

  • Monte Carlo methods
  • Photothermal effects
  • Three-dimensional modeling
  • Tissue optics
  • Scattering
  • Absorption

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