We have developed a general purpose Monte Carlo simulation package based on the concepts outlined by Rička et al. in “Optical-Thermal Response of Laser-Irradiated Tissue” (Springer, 2011) and initially intended to model light propagation in soft condensed matter such as biological tissues, but whose scope is far from being restricted to radiative transfer in tissues. The software is playfully named jaMCp3: just another Monte Carlo program for polarized photon propagation and composed of a user interface in IDL/GDL and a stand-alone photon path generation routine implemented in C++. Besides the Mie scattering model, the program includes a novel scattering model (the “polarized version of the generalized Henyey-Greenstein” scattering law) containing a structure factor parameter. The latter is particularly well-suited to describe light propagation in soft condensed matter such as biological tissue. Moreover, the simulations are conducted in a voxel space, where custom and complex geometrical structures can easily be generated. These also allow for the treatment of Fresnel reflection/refraction processes.
JaMCp3 has previously been subject to preliminary writings in its embryonic stages: “Simulating light propagation: towards realistic tissue models” (SPIE proceeding, 2011) and “Polarized Light Propagation in Biological Tissue: Towards Realistic Modeling” (Doctoral thesis, 2011). Yet, over the past years, jaMCp3 underwent rigorous testing stages (see references below). Certainly, the validation of such a MC program is a prime challenge, as quantitative comparisons, either with experiments or other simulation programs, are difficult to perform, and furthermore, the modeling of complex geometrical structures is bound to induce various numerical singularities, which might not be apparent at first glance. We are currently preparing a manuscript that details our program's main features and gives examples of its diverse possible outputs (3D fluence, 3D absorbed dose, polarimetric images...). The package, together with its user's manual, will soon be made available here for download, however, it is already possible to use it by contacting Günhan Akarçay ( hidayet.akarcay at iap.unibe.ch ).
References:
(1) Akarçay et al., “Determining the optical properties of a gelatin‑TiO2 phantom at 780 nm,” Biomed. Opt. Exp. 3 (2012).
(2) Hiltpold, “Bestimmung optischer Gewebeparameter,” Bachelor thesis (2012).
(3) Akarçay et al., “Monte Carlo modeling of polarized light propagation: Stokes vs Jones–Part I,” Appl. Opt. (2014).
(4) Akarçay et al., “Monte Carlo modeling of polarized light propagation: Stokes vs Jones–Part II,” Appl. Opt. (2014).
ERRATUM in (4): We noticed a small error in the last column (input state |O>) of the ''Primary data'' shown in Figure 1. The images corresponding to < L+ | and < L- | analyzers should be exchanged with the images obtained with < C- | and < C+ | analyzers, respectively. This was just a small bug in the representation of the data and does not affect the other figures/results. (See entirety of figures in the .pdf file linked at the bottom of this page.)
