MCmatlab: an open-source, user-friendly, MATLAB-integrated three-dimensional Monte Carlo light transport solver with heat diffusion and tissue damage
Open accessAbstract
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 three-dimensional 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.
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Prior Monte Carlo light propagation studies have not attempted to capture the PPG waveform in its entirety and have focused on an idealized skin model.
“In order to derive a better understanding of devices based on PPG, several groups have conducted light propagation models using Monte Carlo (MC) simulations29–31. Yet to our knowledge, these studies have not attempted to capture the PPG waveform in its entirety and have focused on an idealized skin model.”
From Synthetic photoplethysmography (PPG) of the radial artery through parallelized Monte Carlo and its correlation to body mass index (BMI) (2021) · cites this paper as [29]
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- Marti et al.: MCmatlab: an open-source, user-friendly, MATLAB-integrated three-dimensional Monte Carlo light transport solver. . . Downloaded From: https://www.spiedigitallibrary.org/journals/Journal-of-Biomedical-Optics on 21 Aug 2023 Terms of Use: https://www.spiedigitallibrary.org/terms-of-use Dominik Marti received his MSc and PhD degrees in two-photon fluorescence technologies from the University of Bern, Switzerland. He then joined DTU Fotonik, Denmark, as a researcher in the field of biomedical imaging with a focus on multiphoton microscopy, OCT/OCM, and multimodal imaging, and the translation thereof to clinics.
- Anders K. Hansen received his PhD from Aarhus University, Denmark, in 2013 in the field of laser cooling of atomic and molecular ions and has since worked at the Technical University of Denmark on development and applications of laser systems, especially diode lasers and especially within biophotonics. He also works on numerical methods for optics simulations and phase retrieval. Journal of Biomedical Optics 121622-6 December 2018 • Vol. 23
- Marti et al.: MCmatlab: an open-source, user-friendly, MATLAB-integrated three-dimensional Monte Carlo light transport solver. . . Downloaded From: https://www.spiedigitallibrary.org/journals/Journal-of-Biomedical-Optics on 21 Aug 2023 Terms of Use: https://www.spiedigitallibrary.org/terms-of-use
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Ajmal, Boonya-Ananta, T., Rodriguez, A. J., Du Le, V. N., & Ramella-Roman, J. C. (2021) · Biomedical Optics Express · doi:10.1364/boe.439893 · Cited by 79 · see citing works
Boonya-ananta, T., Rodriguez, A. J., Ajmal, A., Du Le, V. N., Hansen, A. K., Hutcheson, J. D., & Ramella-Roman, J. C. (2021) · Scientific Reports · doi:10.1038/s41598-021-82124-4 · Cited by 70 · see citing works
Self-citation
- Authors
- Marti, D., Aasbjerg, R. N. N., Andersen, P. E. E., & Hansen, A. K. K.
- Affiliations
- Technical University of Denmark (DK)
- Venue
- Journal of Biomedical Optics
- Publisher
- SPIE-Intl Soc Optical Eng
- Published
- 2018-12-15
- Volume
- 23
- Issue
- 12
- Pages
- 1-6
- ISSN
- 1083-3668 (ISSN-L)
- 1560-2281
- OpenAlex
- W2905313281
- Cited by
- 145
- References
- 17
- Citations by year
- 2026: 13 · 2025: 28 · 2024: 28 · 2023: 22 · 2022: 23 · 2021: 18 · 2020: 11 · 2019: 2
- FWCI
- 5.30
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Journal of Biomedical Optics (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU) (submittedVersion, other-oa)
- Funders
- European Commission (667933)
- European Union’s Horizon 2020 (667933)
- European Union’s Horizon 2020 research and innovation programme project MIB (667933)
- Topics
- Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Optical Imaging and Spectroscopy Techniques
- Health Sciences › Medicine › Pulmonary and Respiratory Medicine › Photodynamic Therapy Research Studies
- Physical Sciences › Engineering › Computational Mechanics › Radiative Heat Transfer Studies
- Keywords
- Monte Carlo light transport, radiative transfer equation, thermal diffusion, burns, Arrhenius model, open source software
- MeSH terms
- Blood Vessels, Hot Temperature, Humans, Light, Models, Biological, Monte Carlo Method, Scattering, Radiation, Skin, Software, Finite Element Analysis, Imaging, Three-Dimensional, Optics and Photonics
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