Deducing effective light transport parameters in optically thin systems

We present an extensive Monte Carlo study on light transport in optically thin slabs, addressing both axial and transverse propagation. We completely characterize the so-called ballistic-to-diffusive transition, notably in terms of the spatial variance of the transmitted/reflected profile. We test the validity of the prediction cast by diffusion theory, that the spatial variance should grow independently of absorption and, to a first approximation, of the sample thickness and refractive index contrast. Based on a large set of simulated data, we build a freely available look-up table routine allowing reliable and precise determination of the microscopic transport parameters starting from robust observables which are independent of absolute intensity measurements. We also present the Monte Carlo software package that was developed for the purpose of this study

Incorporating reflection boundary conditions in the Neumann series radiative transport equation: Application to photon propagation and reconstruction in diffuse optical imaging

We propose a formalism to incorporate boundary conditions in a Neumann-series-based radiative transport equation. The formalism accurately models the reflection of photons at the tissue-external medium interface using Fresnel’s equations. The formalism was used to develop a gradient descent-based image reconstruction technique. The proposed methods were implemented for 3D diffuse optical imaging. In computational studies, it was observed that the average root-mean-square error (RMSE) for the output images and the estimated absorption coefficients reduced by 38% and 84%, respectively, when the reflection boundary conditions were incorporated. These results demonstrate the importance of incorporating boundary conditions that model the reflection of photons at the tissue-external medium interface

Propagation of coherent polarized light in turbid highly scattering medium

Within the framework of further development of unified Monte Carlo code for the needs of biomedical optics and biophotonics, we present an approach for modeling of coherent polarized light propagation in highly scattering turbid media, such as biological tissues. The temporal coherence of light, linear and circular polarization, interference, and the helicity flip of circularly polarized light due to reflection at the medium boundary and/ or backscattering events are taken into account. To achieve higher accuracy in the results and to speed up the modeling, the implementation of the code utilizes parallel computing on NVIDIA graphics processing units using Compute Unified Device Architecture. The results of the simulation of coherent linearly and circularly polarized light are presented in comparison with the results of known theoretical studies and the results of alternative modelings

Online object oriented Monte Carlo computational tool for the needs of biomedical optics

Conceptual engineering design and optimization of laser-based imaging techniques and optical diagnostic systems used in the field of biomedical optics requires a clear understanding of the light-tissue interaction and peculiarities of localization of the detected optical radiation within the medium. The description of photon migration within the turbid tissue-like media is based on the concept of radiative transfer that forms a basis of Monte Carlo (MC) modeling. An opportunity of direct simulation of influence of structural variations of biological tissues on the probing light makes MC a primary tool for biomedical optics and optical engineering. Due to the diversity of optical modalities utilizing different properties of light and mechanisms of light-tissue interactions a new MC code is typically required to be developed for the particular diagnostic application. In current paper introducing an object oriented concept of MC modeling and utilizing modern web applications we present the generalized online computational tool suitable for the major applications in biophotonics. The computation is supported by NVIDEA CUDA Graphics Processing Unit providing acceleration of modeling up to 340 times

Propagation of Cylindrical Vector Laser Beams in Turbid Tissue-Like Scattering Media

We explore the propagation of the cylindrical vector beams (CVB) in turbid tissue-like scattering medium in comparison with the conventional Gaussian laser beam. The study of propagation of CVB and Gaussian laser beams in the medium is performed utilizing the unified electric field Monte Carlo model. The implemented Monte Carlo model is a part of a generalized on-line computational tool and utilizes parallel computing, executed on the NVIDIA Graphics Processing Units (GPUs) supporting Compute Unified Device Architecture (CUDA). Using extensive computational studies, we demonstrate that after propagation through the turbid tissue-like scattering medium, the degree of fringe contrast for CVB becomes at least twice higher in comparison to the conventional linearly polarized Gaussian beam. The results of simulations agree with the results of experimental studies. Both experimental and theoretical results suggest that there is a high potential of the application of CVB in the diagnosis of biological tissues

Next-generation acceleration and code optimization for light transport in turbid media using GPUs

A highly optimized Monte Carlo (MC) code package for simulating light transport is developed on the latest graphics processing unit (GPU) built for general-purpose computing from NVIDIA - the Fermi GPU. In biomedical optics, the MC method is the gold standard approach for simulating light transport in biological tissue, both due to its accuracy and its flexibility in modelling realistic, heterogeneous tissue geometry in 3-D. However, the widespread use of MC simulations in inverse problems, such as treatment planning for PDT, is limited by their long computation time. Despite its parallel nature, optimizing MC code on the GPU has been shown to be a challenge, particularly when the sharing of simulation result matrices among many parallel threads demands the frequent use of atomic instructions to access the slow GPU global memory. This paper proposes an optimization scheme that utilizes the fast shared memory to resolve the performance bottleneck caused by atomic access, and discusses numerous other optimization techniques needed to harness the full potential of the GPU. Using these techniques, a widely accepted MC code package in biophotonics, called MCML, was successfully accelerated on a Fermi GPU by approximately 600x compared to a state-of-the-art Intel Core i7 CPU. A skin model consisting of 7 layers was used as the standard simulation geometry. To demonstrate the possibility of GPU cluster computing, the same GPU code was executed on four GPUs, showing a linear improvement in performance with an increasing number of GPUs. The GPU-based MCML code package, named GPU-MCML, is compatible with a wide range of graphics cards and is released as an open-source software in two versions: an optimized version tuned for high performance and a simplified version for beginners (http://code.google.com/p/gpumcml)

Optical spectroscopy of turbid media: time-domain measurements and accelerated Monte Carlo modelling

Optical spectroscopy is a versatile and powerful tool to probe translucent materials. In this work, the focus is on characterization of strongly scattering (turbid) materials by means of time-of-flight spectroscopy (TOFS). Instrumentation and modelling aspects of TOFS were investigated and improved, enabling significantly more accurate spectroscopic measurements. It was shown that the commonly used diffusion theory fails to accurately describe time-domain light propagation in e.g. tissue. A fully scalable Monte Carlo (MC) scheme (WMC) was developed, enabling MC to replace diffusion models in TOFS data evaluation. Consequently, the accuracy and capabilities of TOFS were significantly improved. Graphics processing units (GPUs) were introduced for acceleration of MC simulations in general, resulting in three orders of magnitude speedup. It was shown that proper utilization of the capabilities of modern GPUs allow similar performance, even for more complex problems. TOFS in combination with WMC was used in in vivo interstitial spectroscopy of the human prostate, demonstrating the need for better modelling in many clinical applications. To aid future interstitial in vivo measurements, a single-fibre TOFS system was developed and demonstrated in phantom experiments. Turning to investigations of pharmaceutical samples, a time-of-flight spectrometer, covering the 650-1400 nm spectral range, was developed, enabling TOFS for vibrational spectroscopy of solids. In spatially resolved TOFS measurements, compaction induced anisotropic light diffusion was observed. This is of great importance for the application of model-based optical spectroscopic tech- niques and may, in addition, provide important information about the sample microstructure. Furthermore, TOFS was used together with laser-based gas sensing to probe porous solids. Although a need for better models was revealed, excellent correlation between optical and actual porosity was demonstrated

Investigating ultrasound–light interaction in scattering media

Significance: Ultrasound-assisted optical imaging techniques, such as ultrasound-modulated optical tomography, allow for imaging deep inside scattering media. In these modalities, a fraction of the photons passing through the ultrasound beam is modulated. The efficiency by which the photons are converted is typically referred to as the ultrasound modulation’s “tagging efficiency.” Interestingly, this efficiency has been defined in varied and discrepant fashion throughout the scientific literature. Aim: The aim of this study is the ultrasound tagging efficiency in a manner consistent with its definition and experimentally verify the contributive (or noncontributive) relationship between the mechanisms involved in the ultrasound optical modulation process. Approach: We adopt a general description of the tagging efficiency as the fraction of photons traversing an ultrasound beam that is frequency shifted (inclusion of all frequency-shifted components). We then systematically studied the impact of ultrasound pressure and frequency on the tagging efficiency through a balanced detection measurement system that measured the power of each order of the ultrasound tagged light, as well as the power of the unmodulated light component. Results: Through our experiments, we showed that the tagging efficiency can reach 70% in a scattering phantom with a scattering anisotropy of 0.9 and a scattering coefficient of 4  mm⁻¹ for a 1-MHz ultrasound with a relatively low (and biomedically acceptable) peak pressure of 0.47 MPa. Furthermore, we experimentally confirmed that the two ultrasound-induced light modulation mechanisms, particle displacement and refractive index change, act in opposition to each other. Conclusion: Tagging efficiency was quantified via simulation and experiments. These findings reveal avenues of investigation that may help improve ultrasound-assisted optical imaging techniques