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

    Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-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 languageEnglish
    Title of host publicationProceedings of SPIE
    Number of pages12
    PublisherSPIE - International Society for Optical Engineering
    Publication date2019
    Article number108760T
    DOIs
    Publication statusPublished - 2019
    EventSPIE Photonics West 2019: Optical Interactions with Tissue and Cells XXX - Moscone Center, San Francisco, United States
    Duration: 2 Feb 20197 Feb 2019
    Conference number: 10876
    http://spie.org/conferences-and-exhibitions/photonics-west/

    Conference

    ConferenceSPIE Photonics West 2019: Optical Interactions with Tissue and Cells XXX
    Number10876
    LocationMoscone Center
    Country/TerritoryUnited States
    CitySan Francisco
    Period02/02/201907/02/2019
    Internet address
    SeriesProgress in Biomedical Optics and Imaging - Proceedings of SPIE
    ISSN1605-7422

    Keywords

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

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