Medical Optics
Optoacoustic imaging
Soft Matter Physics
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Last update: 09.01.2019
Polarized light propagation in biological tissue
JaMCp3 software package

In the frame of our ongoing research work on light propagation in tissue, we have developed a general purpose Monte Carlo simulation package largely 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. This software (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++) was initially created with medical applications in mind, but its scope is far from being restricted to radiative transfer in tissues. 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 Jaro Rička (jaroslav.ricka at iap.unibe.ch ) or Günhan Akarçay ( hidayet.akarcay at iap.unibe.ch ).

(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.)

Monte Carlo modeling of polarized light propagation: Stokes vs Jones

This bipartite comparative study (see references (3) and (4) above) aims at inspecting the similarities and differences between the Jones and Stokes-Mueller formalisms when modeling polarized light propagation with numerical simulations of the Monte Carlo type. We investigated theoretically and experimentally light propagation and detection with both pure and partially/totally unpolarized states: we have demonstrated that Jones and Stokes-Mueller are equally apt to model fluctuations / “depolarization effects” and yield identical results.

We present here simulation results (our simulated datasets are made available for download below, for we deem it to constitute a valuable reference for other groups who develop MC programs ) yielded by two independent Monte Carlo programs: (i) the first one being jaMCp3, which uses the Jones formalism and (ii) the second one being a program implemented at the ILM in Ulm ( link ) with the Stokes notation. The simulated polarimetric experiments involve suspensions of polystyrene spheres with varying size. Reflection and refraction at the sample/air interfaces are also considered. For more details on the simulations, please refer to the corresponding papers. If you have any remarks or questions, please contact Jaro Rička (jaroslav.ricka at iap.unibe.ch ) or Günhan Akarçay ( hidayet.akarcay at iap.unibe.ch ).

- The first link ''stokes_jones_ascii_data'' contains all the simulation results from both programs (jaMCp3 and Ulm) for all 9 samples (with AND without Fresnel interfaces) listed in Reference (4). These are ascii data corresponding to the images/2D arrays of the ''Primary data'', ''Output Stokes vectors'', and ''Imaging Perrin-Mueller matrices''. The naming of the files follows the nomenclature employed in the paper. For the ''Primary data'', the files are named as : 'input state' underscore 'output state'. For the ''Output Stokes vectors'', the files are named as : 'input state' underscore 'element of the corresponding Output Stokes vector'. For the ''Imaging Perrin-Mueller matrices'', the files are named according to the matrix element: m 'row' 'column'.
- The second link ''data_sheet'' a .pdf file, where all the simulation results are shown, similarly to the representation codes used in the paper. This is nothing but a visualization of all the data provided in the first link ''stokes_jones_ascii_data''.

>> This is a test link
>> DOWNLOAD LINK (Ascii data + .pdf file)