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)

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

Influence of blood pulsation on diagnostic volume in pulse oximetry and photoplethysmography measurements

Recent advances in the development of ultra-compact semiconductor lasers and technology of printed flexible hybrid electronics have opened broad perspectives for the design of new pulse oximetry and photoplethysmography devices. Conceptual design of optical diagnostic devices requires careful selection of various technical parameters, including spectral range; polarization and intensity of incident light; actual size, geometry, and sensitivity of the detector; and mutual position of the source and detector on the surface of skin. In the current study utilizing a unified Monte Carlo computational tool, we explore the variations in diagnostic volume due to arterial blood pulsation for typical transmitted and back-scattered probing configurations in a human finger. The results of computational studies show that the variations in diagnostic volumes due to arterial pulse wave are notably (up to 45%) different in visible and near-infrared spectral ranges in both transmitted and back-scattered probing geometries. While these variations are acceptable for relative measurements in pulse oximetry and/or photoplethysmography, for absolute measurements, an alignment normalization of diagnostic volume is required and can be done by a computational approach utilized in the framework of the current study

Characterisation of a 'blanch-blush' mechano-response in palmer skin

Palmar finger skin reacts to extension under mechanical load – blanching over proximal (intercrease skin, ICS) and middle phalanges, while blushing in crease skin (CS), which we have called the Blanch-Blush Reaction (BBR). The idea that the BBR is a result of surface capillary blood flow changes that relate to predictable deformation of aligned collagen matrices under applied uniaxial loads was tested. Nondestructive techniques, digital image analysis (DIA), laser Doppler scanning, and elastic scatter spectroscopy (ESS) were used to measure color and blood flow changes in healthy fingers when at rest and extended. Skin strain increased directly with applied load and DIA identified blanching (loss of redness) in the ICS, reflected by a decrease in hemoglobin (by ESS). Laser Doppler flowmetry identified an increase in blood flow in the CS zone on extension, with a minor increase in blood flow in the ICS zone, apparently due to diversion of flow to deeper vessels, when monitored by this technique. These changes correlated with the BBR, owing to altered capillary flow in the ICS and CS. The histology of orientation of collagen fibers and vessels in the two zones was consistent with this mechanism. This study demonstrates the interdependence between matrix orientation, applied load, and flow. It represents an elegant demonstration of collagenous tissue function through an everyday tissue reaction, which has not been described previously