MCML-Monte Carlo modeling of light transport in multi-layered tissues
01 Jan 1995-
TL;DR: A Monte Carlo model of steady-state light transport in multi-layered tissues (MCML) has been coded in ANSI Standard C; therefore, the program can be used on various computers and has been in the public domain since 1992.
Abstract: A Monte Carlo model of steady-state light transport in multi-layered tissues (MCML) has been coded in ANSI Standard C; therefore, the program can be used on various computers. Dynamic data allocation is used for MCML, hence the number of tissue layers and grid elements of the grid system can be varied by users at run time. The coordinates of the simulated data for each grid element in the radial and angular directions are optimized. Some of the MCML computational results have been verified with those of other theories or other investigators. The program, including the source code, has been in the public domain since 1992.
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TL;DR: An overview of NIR spectroscopy for measuring quality attributes of horticultural produce is given in this article, where the problem of calibration transfer from one spectrophotometer to another is introduced as well as techniques for calibration transfer.
1,780 citations
TL;DR: The practical implementation of various signal processing techniques for removing physiological, instrumental, and motion-artifact noise from optical data are described within the context of the MATLAB-based graphical user interface program, HomER, which is developed and distributed to facilitate the processing of optical functional brain data.
Abstract: Near-infrared spectroscopy (NIRS) is a noninvasive neuroimaging tool for studying evoked hemodynamic changes within the brain. By this technique, changes in the optical absorption of light are recorded over time and are used to estimate the functionally evoked changes in cerebral oxyhemoglobin and deoxyhemoglobin concentrations that result from local cerebral vascular and oxygen metabolic effects during brain activity. Over the past three decades this technology has continued to grow, and today NIRS studies have found many niche applications in the fields of psychology, physiology, and cerebral pathology. The growing popularity of this technique is in part associated with a lower cost and increased portability of NIRS equipment when compared with other imaging modalities, such as functional magnetic resonance imaging and positron emission tomography. With this increasing number of applications, new techniques for the processing, analysis, and interpretation of NIRS data are continually being developed. We review some of the time-series and functional analysis techniques that are currently used in NIRS studies, we describe the practical implementation of various signal processing techniques for removing physiological, instrumental, and motion-artifact noise from optical data, and we discuss the unique aspects of NIRS analysis in comparison with other brain imaging modalities. These methods are described within the context of the MATLAB-based graphical user interface program, HomER, which we have developed and distributed to facilitate the processing of optical functional brain data.
1,174 citations
TL;DR: Light-driven proton pumps represent a high-performance and extremely versatile class of ‘optogenetic’ voltage and ion modulator, which will broadly enable new neuroscientific, biological, neurological and psychiatric investigations.
Abstract: The ability to silence the activity of genetically specified neurons in a temporally precise fashion would provide the opportunity to investigate the causal role of specific cell classes in neural computations, behaviours and pathologies. Here we show that members of the class of light-driven outward proton pumps can mediate powerful, safe, multiple-colour silencing of neural activity. The gene archaerhodopsin-3 (Arch) from Halorubrum sodomense enables near-100% silencing of neurons in the awake brain when virally expressed in the mouse cortex and illuminated with yellow light. Arch mediates currents of several hundred picoamps at low light powers, and supports neural silencing currents approaching 900 pA at light powers easily achievable in vivo. Furthermore, Arch spontaneously recovers from light-dependent inactivation, unlike light-driven chloride pumps that enter long-lasting inactive states in response to light. These properties of Arch are appropriate to mediate the optical silencing of significant brain volumes over behaviourally relevant timescales. Arch function in neurons is well tolerated because pH excursions created by Arch illumination are minimized by self-limiting mechanisms to levels comparable to those mediated by channelrhodopsins or natural spike firing. To highlight how proton pump ecological and genomic diversity may support new innovation, we show that the blue-green light-drivable proton pump from the fungus Leptosphaeria maculans (Mac) can, when expressed in neurons, enable neural silencing by blue light, thus enabling alongside other developed reagents the potential for independent silencing of two neural populations by blue versus red light. Light-driven proton pumps thus represent a high-performance and extremely versatile class of 'optogenetic' voltage and ion modulator, which will broadly enable new neuroscientific, biological, neurological and psychiatric investigations.
1,124 citations
TL;DR: The current status of PDT with an emphasis on the contributions of physics, biophysics and technology, and the challenges remaining in the optimization and adoption of this treatment modality are reviewed.
Abstract: Photodynamic therapy (PDT) uses light-activated drugs to treat diseases ranging from cancer to age-related macular degeneration and antibiotic-resistant infections. This paper reviews the current status of PDT with an emphasis on the contributions of physics, biophysics and technology, and the challenges remaining in the optimization and adoption of this treatment modality. A theme of the review is the complexity of PDT dosimetry due to the dynamic nature of the three essential components—light, photosensitizer and oxygen. Considerable progress has been made in understanding the problem and in developing instruments to measure all three, so that optimization of individual PDT treatments is becoming a feasible target. The final section of the review introduces some new frontiers of research including low dose rate (metronomic) PDT, two-photon PDT, activatable PDT molecular beacons and nanoparticle-based PDT.
885 citations
Cites methods from "MCML-Monte Carlo modeling of light ..."
...A free, widely used Monte Carlo code for light propagation in tissue is available (Wang et al 1995)....
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TL;DR: An exhaustive overview of recent advances in underwater optical wireless communication is provided and a hybrid approach to an acousto-optic communication system is presented that complements the existing acoustic system, resulting in high data rates, low latency, and an energy-efficient system.
Abstract: Underwater wireless information transfer is of great interest to the military, industry, and the scientific community, as it plays an important role in tactical surveillance, pollution monitoring, oil control and maintenance, offshore explorations, climate change monitoring, and oceanography research. In order to facilitate all these activities, there is an increase in the number of unmanned vehicles or devices deployed underwater, which require high bandwidth and high capacity for information transfer underwater. Although tremendous progress has been made in the field of acoustic communication underwater, however, it is limited by bandwidth. All this has led to the proliferation of underwater optical wireless communication (UOWC), as it provides higher data rates than the traditional acoustic communication systems with significantly lower power consumption and simpler computational complexities for short-range wireless links. UOWC has many potential applications ranging from deep oceans to coastal waters. However, the biggest challenge for underwater wireless communication originates from the fundamental characteristics of ocean or sea water; addressing these challenges requires a thorough understanding of complex physio-chemical biological systems. In this paper, the main focus is to understand the feasibility and the reliability of high data rate underwater optical links due to various propagation phenomena that impact the performance of the system. This paper provides an exhaustive overview of recent advances in UOWC. Channel characterization, modulation schemes, coding techniques, and various sources of noise which are specific to UOWC are discussed. This paper not only provides exhaustive research in underwater optical communication but also aims to provide the development of new ideas that would help in the growth of future underwater communication. A hybrid approach to an acousto-optic communication system is presented that complements the existing acoustic system, resulting in high data rates, low latency, and an energy-efficient system.
859 citations
Cites methods from "MCML-Monte Carlo modeling of light ..."
...Another popular approach to model UOWC employs numerical methods with Monte Carlo simulation [123], [136], [139], [142], [144], [145] as it is flexible, easy to program and provide accurate solution....
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References
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Book•
01 Jan 1978
TL;DR: This IEEE Classic Reissue presents a unified introduction to the fundamental theories and applications of wave propagation and scattering in random media and is expressly designed for engineers and scientists who have an interest in optical, microwave, or acoustic wave propagate and scattering.
Abstract: A volume in the IEEE/OUP Series on Electromagnetic Wave Theory Donald G. Dudley, Series Editor This IEEE Classic Reissue presents a unified introduction to the fundamental theories and applications of wave propagation and scattering in random media. Now for the first time, the two volumes of Wave Propagation and Scattering in Random Media previously published by Academic Press in 1978 are combined into one comprehensive volume. This book presents a clear picture of how waves interact with the atmosphere, terrain, ocean, turbulence, aerosols, rain, snow, biological tissues, composite material, and other media. The theories presented will enable you to solve a variety of problems relating to clutter, interference, imaging, object detection, and communication theory for various media. This book is expressly designed for engineers and scientists who have an interest in optical, microwave, or acoustic wave propagation and scattering. Topics covered include:
5,877 citations
TL;DR: The known optical properties (absorption, scattering, total attenuation, effective attenuation and/or anisotropy coefficients) of various biological tissues at a variety of wavelengths are reviewed in this article.
Abstract: The known optical properties (absorption, scattering, total attenuation, effective attenuation, and/or anisotropy coefficients) of various biological tissues at a variety of wavelengths are reviewed. The theoretical foundations for most experimental approaches are outlined. Relations between Kubelka-Munk parameters and transport coefficients are listed. The optical properties of aorta, liver, and muscle at 633 nm are discussed in detail. An extensive bibliography is provided. >
2,858 citations
"MCML-Monte Carlo modeling of light ..." refers background in this paper
...10 (1983) 824-830. [Z] S.& Prahl, M. Keijzer, St. Jacques and A.J. Welch, A Monte Carlo model of light propagation in tissue, Proc. SPIE IS 5 (1989) 102-111....
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01 Jan 1940
TL;DR: In this paper, it was shown that the observed intensity of the diffuse light may be explained as scattered radiation if the phase function governing the scattering of starlight by the interstellar matter is strongly forward-throwing.
Abstract: Observations have been obtained to verify the existence of diffuse interstellar radiation. A Fabry photometer, attached to the 40-inch refractor at the Yerkes Observatory, was used to measure the the brightness of regions over a wide range of galactic latitude. The intensities in the photographic region of the spectrum were calibrated by means of the Polar Sequence stars. The mean of four such runs across the Milky Way, on circles of constant latitude $\ell = 40^{\rm{o}}$, shows a maximum brightness of 80 stars of the tenth magnitude per square degree for the diffuse extra-terrestrial radiation. The mean of three runs near $\ell = 140^{\rm{o}}$ shows a maximum of 35 in the same units. It is shown that the observed intensity of the diffuse light may be explained as scattered radiation if the phase function governing the scattering of starlight by the interstellar matter is strongly forward-throwing. The concentration of the diffuse light toward the galactic circle is also in agreement with this property of the phase function. The observations also indicate that the scattering efficiency, or albedo, of the particles is greater than 0.3.
2,498 citations
01 Jan 1995
TL;DR: Welch et al. as discussed by the authors proposed a Monte Carlo Modeling of Light Transport in Tissue S.C. van Gemert, A.J. van Leeuwen, et al., and C.C., Svaasand.
Abstract: Overview of Optical and Thermal Laser-Tissue Interaction and Nomenclature A.J. Welch, M.J.C. van Gemert. Tissue Optics: Overview of Tissue Optics A.J. Welch, et al. Onedimensional Transport Theory M.J.C. van Gemert, et al. Monte Carlo Modeling of Light Transport in Tissue S. Jacques, L. Wang. Adding-Doubling S. Prahl. Diffusion Theory of Light Transport W. Star. The Diffusion Approximation in Three Dimensions S. Prahl. Thermal Interactions: Overview of Bioheat Transfer C.S. Orr, R.C. Eberhart. Solution of Heat Conduction Equation J. Roider, R. Birngruber. Approximate Solutions for Heat Conduction: Time Constants M.J.C. van Gemert, A.J. Welch. Tissue Thermal Properties and Perfusion J. Valvano. Temperature Measurements J. Valvano, J. Pearce. Pulsed Photo Thermal Radiation A. Vitkin. Medical Applications: Introduction to Medical Applications A.J. Welch, M.J.C. van Gemert. Optics of Fibers and Fiber Probes R.M. Verdaasdonk, C. Borst. Fluorescence R. Richards-Kortum. Pulse Ablation of Soft Tissue T.G. van Leeuwen, et al. Laser-induced Hyperthermia L. Svaasand. Laser Treatment of Port Wine Stains M.J.C. van Gemert, et al. 7 additional articles. Index.
1,478 citations
TL;DR: This paper provides all the details necessary for implementation of a Monte Carlo program andVariance reduction schemes that improve the effiency of the Monte Carlo method are discussed.
Abstract: The Monte Carlo method is rapidly becoming the model of choice for simulating light transport in tissue. This paper provides all the details necessary for implementation of a Monte Carlo program. Variance reduction schemes that improve the eciency of the Monte Carlo method are discussed. Analytic expressions facilitating convolution calculations for finite flat and Gaussian beams are included. Useful validation benchmarks are presented.
691 citations