| 1. |
- Alerstam, Erik
(författare)
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Anisotropic diffusive transport: Connecting microscopic scattering and macroscopic transport properties
- 2014
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Ingår i: Physical Review E (Statistical, Nonlinear, and Soft Matter Physics). - 1539-3755. ; 89:6
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Tidskriftsartikel (refereegranskat)abstract
- This work concerns the modeling of radiative transfer in anisotropic turbid media using diffusion theory. A theory for the relationship between microscopic scattering properties (i.e., an arbitrary differential scattering cross-section) and the macroscopic diffusion tensor, in the limit of independent scatterers, is presented. The theory is accompanied by a numerical method capable of performing the calculations. In addition, a boundary condition appropriate for modeling systems with anisotropic radiance is derived. It is shown that anisotropic diffusion theory, when based on these developments, indeed can describe radiative transfer in anisotropic turbid media. More specifically, it is reported that solutions to the anisotropic diffusion equation are in excellent agreement with Monte Carlo simulations, both in steady-state and time-domain. This stands in contrast to previous work on the topic, where inadequate boundary conditions and/or incorrect relations between microscopic scattering properties and the diffusion tensor have caused disagreement between simulations and diffusion theory. The present work thus falsify previous claims that anisotropic diffusion theory cannot describe anisotropic radiative transfer, and instead open for accurate quantitative diffusion-based modeling of anisotropic turbid materials.
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| 2. |
- Alerstam, Erik, et al.
(författare)
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Improved accuracy in time-resolved diffuse reflectance spectroscopy.
- 2008
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Ingår i: Optics Express. - 1094-4087. ; 16:14, s. 10440-10454
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Tidskriftsartikel (refereegranskat)abstract
- Significant improvements in the accuracy of time-resolved diffuse reflectance spectroscopy are reached by using a Monte Carlo scheme for evaluation of measured photon time-of-flight distributions. The use of time-resolved diffusion theory of photon migration, being the current standard scheme for data evaluation, is shown defective. In particular, the familiar problem sometimes referred to as absorption-to-scattering coupling or crosstalk, is identified as an error related to the breakdown of the diffusion approximation. These systematic errors are investigated numerically using Monte Carlo simulations, and their influence on data evaluation of experimental recordings are accurately predicted. The proposed Monte Carlo-based data evaluation avoids these errors, and can be used for routine data evaluation. The accuracy and reproducibility of both MC and diffusion modeling are investigated experimentally using the MEDPHOT set of solid tissue-simulating phantoms, and provides convincing arguments that Monte Carlo-based evaluation is crucial in important ranges of optical properties. In contrast to diffusion-based evaluation, the Monte Carlo scheme results in optical properties consistent with phantom design. Since the MEDPHOT phantoms are used for international comparisons and performance assessment, the performed characterization is carefully reported.
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| 3. |
- Alerstam, Erik, et al.
(författare)
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Next-generation acceleration and code optimization for light transport in turbid media using GPUs
- 2010
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Ingår i: Biomedical Optics Express. - 2156-7085. ; 1:2, s. 658-675
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Tidskriftsartikel (refereegranskat)abstract
- 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).
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| 4. |
- Alerstam, Erik, et al.
(författare)
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Observation of anisotropic diffusion of light in compacted granular porous materials
- 2012
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Ingår i: Physical Review E (Statistical, Nonlinear, and Soft Matter Physics). - 1539-3755. ; 85:4
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Tidskriftsartikel (refereegranskat)abstract
- By analyzing spatio-temporal characteristics of short optical pulses diffusively transmitted through compacted granular materials, we reveal that powder compaction can give rise to strongly anisotropic light diffusion. Our disclosure represents a revision of the understanding of optics of powder compacts. Routes to material characterization and investigation of compression-induced structural anisotropy are opened, and the falsification of isotropic models have implications for quantitative spectroscopy of powder compacts (e.g., pharmaceutical tablets).
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| 5. |
- Alerstam, Erik
(författare)
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Optical spectroscopy of turbid media: time-domain measurements and accelerated Monte Carlo modelling
- 2011
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- 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.
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| 6. |
- Alerstam, Erik, et al.
(författare)
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Parallel computing with graphics processing units for high-speed Monte Carlo simulation of photon migration.
- 2008
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Ingår i: Journal of Biomedical Optics. - : SPIE-Intl Soc Optical Eng. - 1083-3668. ; 13:6
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Tidskriftsartikel (refereegranskat)abstract
- General-purpose computing on graphics processing units (GPGPU) is shown to dramatically increase the speed of Monte Carlo simulations of photon migration. In a standard simulation of time-resolved photon migration in a semi-infinite geometry, the proposed methodology executed on a low-cost graphics processing unit (GPU) is a factor 1000 faster than simulation performed on a single standard processor. In addition, we address important technical aspects of GPU-based simulations of photon migration. The technique is expected to become a standard method in Monte Carlo simulations of photon migration.
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| 7. |
- Alerstam, Erik, et al.
(författare)
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Single-fiber diffuse optical time-of-flight spectroscopy
- 2012
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Ingår i: Optics Letters. - 0146-9592. ; 37:14, s. 2877-2879
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Tidskriftsartikel (refereegranskat)abstract
- We demonstrate interstitial diffuse optical time-of-fight spectroscopy based on a single fiber for both light delivery and detection. Detector saturation due to the massive short-time reflection is avoided by ultrafast gating of a single photon avalanche diode. We show that the effects of scattering and absorption are separable and that absorption can be assessed independently of scattering. Measurements on calibrated liquid phantoms and subsequent Monte Carlo-based evaluation illustrate that absorption coefficients can be accurately assessed over a wide range of medically relevant optical properties. Our findings pave the way to simplified and less invasive interstitial in vivo spectroscopy. (C) 2012 Optical Society of America
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| 8. |
- Alerstam, Erik, et al.
(författare)
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White Monte Carlo for time-resolved photon migration.
- 2008
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Ingår i: Journal of Biomedical Optics. - : SPIE-Intl Soc Optical Eng. - 1083-3668. ; 13:4
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Tidskriftsartikel (refereegranskat)abstract
- A novel scheme for fully scalable White Monte Carlo (WMC) has been developed and is used as a forward solver in the evaluation of experimental time-resolved spectroscopy. Previously reported scaling problems are avoided by storing detection events individually, turning spatial and temporal binning into post-simulation activities. The approach is suitable for modeling of both interstitial and noninvasive settings (i.e., infinite and semi-infinite geometries). Motivated by an interest in in vivo optical properties of human prostate tissue, we utilize WMC to explore the low albedo regime of time-domain photon migration--a regime where the diffusion approximation of radiative transport theory breaks down, leading to the risk of overestimating both reduced scattering (mu(s)') and absorption (mu(a)). Experimental work supports our findings and establishes the advantages of Monte Carlo-based evaluation.
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| 9. |
- Nilsson, Markus, et al.
(författare)
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Evaluating the accuracy and precision of a two-compartment Kärger model using Monte Carlo simulations.
- 2010
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Ingår i: Journal of Magnetic Resonance. - : Elsevier BV. - 1096-0856 .- 1090-7807. ; 206:1, s. 59-67
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Tidskriftsartikel (refereegranskat)abstract
- Specific parameters of the neuronal tissue microstructure, such as axonal diameters, membrane permeability and intracellular water fractions are assessable using diffusion MRI. These parameters are commonly estimated using analytical models, which may introduce bias in the estimated parameters due to the approximations made when deriving the models. As an alternative to using analytical models, a database of signal curves generated by fast Monte Carlo simulations can be employed. Simulated diffusion MRI measurements were generated and evaluated using the two-compartment Kärger model as well as the simulation model based on a database containing signal curves from approximately 60000 simulations performed with different combinations of microstructural parameters. A protocol based on a pulsed gradient spin echo sequence with diffusion times of 30 and 60ms and with gradient amplitudes obtainable with a clinical MRI scanner was employed for the investigations. When using the analytical model, a major negative bias (up to approximately 25%) in the estimated intracellular volume fraction was observed for short exchange times, while almost no bias was seen for the simulation model. In general, the simulation model improved the accuracy of the estimated parameters as compared to the analytical model, except for the exchange time parameter.
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| 10. |
- Svensson, Tomas, et al.
(författare)
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Near-infrared photon time-of-flight spectroscopy of turbid materials up to 1400 nm
- 2009
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Ingår i: Review of Scientific Instruments. - : AIP Publishing. - 1089-7623 .- 0034-6748. ; 80:6
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Tidskriftsartikel (refereegranskat)abstract
- Photon time-of-flight spectroscopy (PTOFS) is a powerful tool for analysis of turbid materials. We have constructed a time-of-flight spectrometer based on a supercontinuum fiber laser, acousto-optical tunable filtering, and an InP/InGaAsP microchannel plate photomultiplier tube. The system is capable of performing PTOFS up to 1400 nm, and thus covers an important region for vibrational spectroscopy of solid samples. The development significantly increases the applicability of PTOFS for analysis of chemical content and physical properties of turbid media. The great value of the proposed approach is illustrated by revealing the distinct absorption features of turbid epoxy resin. Promising future applications of the approach are discussed, including quantitative assessment of pharmaceuticals, powder analysis, and calibration-free near-infrared spectroscopy.
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| 11. |
- Svensson, Tomas, et al.
(författare)
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Optical porosimetry and investigations of the porosity experienced by light interacting with porous media.
- 2010
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Ingår i: Optics Letters. - 1539-4794. ; 35:11, s. 1740-1742
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Tidskriftsartikel (refereegranskat)abstract
- We investigate how light samples disordered porous materials such as ceramics and pharmaceutical materials. By combining photon time-of-flight spectroscopy and sensitive laser-based gas sensing, we obtain information on the extent to which light interacts with solid and pore volumes, respectively. Comparison with mercury intrusion porosimetry shows that light predominantly interacts with the solid. Analysis based on a two-state model does not fully explain observations, revealing a need for refined modeling. Nonetheless, excellent correlation between actual porosity and the porosity experienced by photons demonstrates the potential of nondestructive optical porosimetry based on gas absorption.
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| 12. |
- Svensson, Tomas, et al.
(författare)
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Towards accurate in vivo spectroscopy of the human prostate
- 2008
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Ingår i: Journal of Biophotonics. - : Wiley. - 1864-063X .- 1864-0648. ; 1:3, s. 200-203
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Tidskriftsartikel (refereegranskat)abstract
- The recent interest in photodynamic therapy of human prostate cancer is accompanied by a need for techniques for in vivo monitoring of optical and physiological characteristics. We propose time-of-flight (TOF) spectroscopy in combination with Monte Carlo evaluation as a reliable optical technique for quantitative assessment of absorption, scattering, hemoglobin content and tissue oxygenation in the human prostate. For the first time, we demonstrate Monte Carlo-based evaluation of in vivo TOF photon migration data. We show that this approach is crucial in order to avoid the large errors associated with the use of time-resolved diffusion theory of light propagation in prostate-like tissues. This progress also allows us to present the first in vivo scattering spectroscopy of human prostate tissue. Furthermore, TOF spectroscopy. in contrast to the more common steady-state approach, is insensitive to bleedings, and has been found highly reliable (100% success rate). (C) 2008 by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
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