The use of the Henyey-Greenstein phase function in Monte Carlo simulations in biomedical optics

In vivooptogenetics using a Utah Optrode Array with enhanced light output and spatial selectivity

Objective.Optogenetics allows the manipulation of neural circuitsin vivowith high spatial and temporal precision. However, combining this precision with control over a significant portion of the brain is technologically challenging (especially in larger animal models).Approach.Here, we have developed, optimised, and testedin vivo, the Utah Optrode Array (UOA), an electrically addressable array of optical needles and interstitial sites illuminated by 181μLEDs and used to optogenetically stimulate the brain. The device is specifically designed for non-human primate studies.Main results.Thinning the combinedμLED and needle backplane of the device from 300μm to 230μm improved the efficiency of light delivery to tissue by 80%, allowing lowerμLED drive currents, which improved power management and thermal performance. The spatial selectivity of each site was also improved by integrating an optical interposer to reduce stray light emission. These improvements were achieved using an innovative fabrication method to create an anodically bonded glass/silicon substrate with through-silicon vias etched, forming an optical interposer. Optical modelling was used to demonstrate that the tip structure of the device had a major influence on the illumination pattern. The thermal performance was evaluated through a combination of modelling and experiment, in order to ensure that cortical tissue temperatures did not rise by more than 1 °C. The device was testedin vivoin the visual cortex of macaque expressing ChR2-tdTomato in cortical neurons.Significance.It was shown that the UOA produced the strongest optogenetic response in the region surrounding the needle tips, and that the extent of the optogenetic response matched the predicted illumination profile based on optical modelling-demonstrating the improved spatial selectivity resulting from the optical interposer approach. Furthermore, different needle illumination sites generated different patterns of low-frequency potential activity.

In vivo optogenetics using a Utah Optrode Array with enhanced light output and spatial selectivity

Optogenetics allows manipulation of neural circuits in vivo with high spatial and temporal precision. However, combining this precision with control over a significant portion of the brain is technologically challenging (especially in larger animal models). Here, we have developed, optimised, and tested in vivo, the Utah Optrode Array (UOA), an electrically addressable array of optical needles and interstitial sites illuminated by 181 µLEDs and used to optogenetically stimulate the brain. The device is specifically designed for non-human primate studies. Thinning the combined µLED and needle backplane of the device from 300 µm to 230 µm improved the efficiency of light delivery to tissue by 80%, allowing lower µLED drive currents, which improved power management and thermal performance. The spatial selectivity of each site was also improved by integrating an optical interposer to reduce stray light emission. These improvements were achieved using an innovative fabrication method to create an anodically bonded glass/silicon substrate with through-silicon vias etched, forming an optical interposer. Optical modelling was used to demonstrate that the tip structure of the device had a major influence on the illumination pattern. The thermal performance was evaluated through a combination of modelling and experiment, in order to ensure that cortical tissue temperatures did not rise by more than 1°C. The device was tested in vivo in the visual cortex of macaque expressing ChR2-tdTomato in cortical neurons. It was shown that the strongest optogenetic response occurred in the region surrounding the needle tips, and that the extent of the optogenetic response matched the predicted illumination profile based on optical modelling - demonstrating the improved spatial selectivity resulting from the optical interposer approach. Furthermore, different needle illumination sites generated different patterns of low-frequency potential (LFP) activity.

MCOCT: an experimentally and numerically validated, open-source Monte Carlo simulator for optical coherence tomography

Here, we present MCOCT, a Monte Carlo simulator for optical coherence tomography (OCT), incorporating a Gaussian illumination scheme and bias to increase backscattered event collection. MCOCT optical fluence was numerically compared and validated to an established simulator (MCX) and showed concordance at the focus while diverging slightly with distance to it. MCOCT OCT signals were experimentally compared and validated to OCT signals acquired in tissue-mimicking phantoms with known optical properties and showed a similar attenuation pattern with increasing depth while diverging beyond 1.5 mm and proximal to layer interfaces. MCOCT may help in the design of OCT systems for a wide range of applications.

Quantitative Assessment on Optical Properties as a Basis for Bioluminescence Imaging: An Experimental and Numerical Approach to the Transport of Optical Photons in Phantom Materials

Bioluminescence imaging (BLI) is a widely used technique in preclinical scientific research, particularly in the development of mRNA-based medications and non-invasive tumor diagnostics. It has become an essential tool in current science. However, the current state of bioluminescence imaging is primarily qualitative, making it challenging to obtain quantitative measurements and to draw accurate conclusions. This fact is caused by the unique properties of optical photons and tissue interactions. In this paper, we propose an experimental setup and Geant4-simulations to gain a better understanding of the optical properties and processes involved in bioluminescence imaging. Our goal is to advance the field towards more quantitative measurements. We will discuss the details of our experimental setup, the data we collected, the outcomes of the Geant4-simulations, and additional information on the underlying physical processes.

Efficiency scale for scattering luminescent particles linked to fundamental and measurable spectroscopic properties

Comparing the performance of molecular and nanoscale luminophores and luminescent micro- and nanoparticles and estimating achievable signal amplitudes and limits of detection requires a standardizable intensity scale. This initiated the development of the relative MESF (number of molecules of equivalent soluble fluorochromes) and ERF (equivalent reference fluorophores) scales for flow cytometry and fluorescence microscopy. Both intensity scales rely on fluorescence intensity values assigned to fluorescent calibration beads by an intensity comparison to spectrally closely matching fluorophore solutions of known concentration using a spectrofluorometer. Alternatively, the luminophore or bead brightness (B) can be determined that equals the product of the absorption cross section (σ_a) at the excitation wavelength (σ_a(λ_ex)) and the photoluminescence quantum yield (Φ_pl). Thereby, an absolute scale based on fundamental and measurable spectroscopic properties can be realized which is independent of particle size, material, and luminophore staining or labeling density and considers the sensitivity of the optical properties of luminophores to their environment. Aiming for establishing such a brightness scale for light-scattering dispersions of luminescent particles with sizes exceeding a few ten nanometers, we demonstrate how the brightness of quasi-monodisperse 25 nm, 100 nm, and 1 µm sized polystyrene particles (PSP), loaded with two different dyes in varying concentrations, can be obtained with a single custom-designed integrating sphere setup that enables the absolute determination of Φ_pl and transmittance and diffuse reflectance measurements. The resulting Φ_pl, σ_a(λ_ex), imaginary parts of the refractive index, and calculated B values of these samples are given in dependence of the number of incorporated dye molecule per particle. Finally, a unitless luminescence efficiency (LE) is defined allowing for the direct comparison of luminescence efficiencies of particles with different sizes.

Simulation of light interaction with seedless grapes

BACKGROUND

Spectroscopic techniques are widely used for the non-destructive maturation and quality monitoring of different fruits. To develop new sensor devices for this purpose, knowing the optical properties of the agricultural sample is crucial for enabling the prediction of the interaction of the incident light with the fruit.

RESULTS

In the present study, the optical properties of three different seedless grape varieties (ARRA15, Tawny and Melody/Blagratwo) were determined from 400 to 1000 nm using a UV-visible/near-infrared spectrometer with an integrating sphere and subsequent calculation of the absorption and scattering coefficients and the anisotropy factor using the inverse adding doubling method. The results indicate that the optical properties of different grape varieties have significant differences, especially in the visible wavelength region, whereas these are less distinct in the near-infrared range. Independent of grape variety, the grape berry skin has a higher scattering coefficient and scattering occurs predominantly in the forward direction. Based on the optical properties of the grape berries, a three-dimensional grape berry model is generated within OpticStudio (Zemax, LLC) for the different varieties that can be used in optical illumination simulations. The bulk scattering inside the fruit is modeled by the Henyey-Greenstein distribution. A comparison of the simulated values for the total transmission and the specular reflection determined experimentally shows that realistic optical grape models can be created within OpticStudio.

CONCLUSION

Overall, the procedure for creating optical grape models presented here will be helpful for the development of optical applications used in pre- and post-harvest food quality monitoring. © 2022 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Monte Carlo-based full-wavelength simulator of Fourier-domain optical coherence tomography

Monte Carlo (MC) simulation has been widely used to study imaging procedures, including Fourier-domain optical coherence tomography (FD-OCT). Despite the broadband nature of FD-OCT, the results obtained at a single wavelength are often used in previous studies. Some wavelength-relied imaging applications, such as spectroscopic OCT (S-OCT), are unlikely to be simulated in this way due to the lack of information from the entire spectrum. Here, we propose a novel simulator for full-wavelength MC simulation of FD-OCT. All wavelengths within the emission spectrum of the light source will be simulated, and the optical properties derived from Mie theory will be applied. We further combine the inverse discrete Fourier transform (IDFT) with a probability distribution-based signal pre-processing to combat the excessive noises in the OCT signal reconstruction, which is caused by the non-uniform distribution of the scattering events at different wavelengths. Proof-of-concept simulations are conducted to show the excellent performance of the proposed simulator on signal reconstruction and optical properties extraction. Compared with the conventional method, the proposed simulator is more accurate and could better preserve the wavelength-dependent features. For example, the mean square error (MSE) computed between the backscattering coefficient extracted by the proposed simulator and the ground truth is 0.11, which is far less than the value (7.67) of the conventional method. We believe this simulator could be an effective tool to study the wavelength dependency in FD-OCT imaging as well as a preferred solution for simulating spectroscopic OCT.

Establishment of transmission model for broad-spectrum artificial light in case 1 water

A new simulation model for light transmission of broad-spectrum artificial light in case 1 water is introduced in this paper. The model simulates spectrum changes of fishing lamps due to absorption and scattering of seawater. According to underwater spectrum changes, this model restores the light field generated by fishing lamps and demonstrates the distribution of visual stimuli to marine organisms. The accuracy of the transmission model is verified by comparing it with experimental data. In addition, by comparing the simulation results of light transmission models of different fishing lamps in seawater of various fishing grounds, we investigate why current light-emitting diode (LED) lights are not as effective as metal halide (MH) lamps for light fishing. Lastly, suggestions for future optimization of LED fishing lamps in terms of light distribution design and spectrum configuration are provided.

Tutorial on the Use of Deep Learning in Diffuse Optical Tomography

Diffuse optical tomography using deep learning is an emerging technology that has found impressive medical diagnostic applications. However, creating an optical imaging system that uses visible and near-infrared (NIR) light is not straightforward due to photon absorption and multi-scattering by tissues. The high distortion levels caused due to these effects make the image reconstruction incredibly challenging. To overcome these challenges, various techniques have been proposed in the past, with varying success. One of the most successful techniques is the application of deep learning algorithms in diffuse optical tomography. This article discusses the current state-of-the-art diffuse optical tomography systems and comprehensively reviews the deep learning algorithms used in image reconstruction. This article attempts to provide researchers with the necessary background and tools to implement deep learning methods to solve diffuse optical tomography.

Modeling optical design parameters for fine stimulation in sciatic nerve of optogenetic mice

Optogenetics presents an alternative method for interfacing with the nervous system over the gold-standard of electrical stimulation. While electrical stimulation requires electrodes to be surgically embedded in tissue for in vivo studies, optical stimulation offers a less-invasive approach that may yield more specific, localized stimulation. The advent of optogenetic laboratory animals-whose motor neurons can be activated when illuminated with blue light-enables research into refining optical stimulation of the mammalian nervous system where subsets of nerve fibers within a nerve may be stimulated without embedding any device directly into the nerve itself. However, optical stimulation has a major drawback in that light is readily scattered and absorbed in tissue thereby limiting the depth with which a single emission source can penetrate. We hypothesize that the use of multiple, focused light emissions deployed around the circumference of a nerve can overcome these light-scattering limitations. To understand the physical parameters necessary to produce pinpointed light stimulation within a single nerve, we employed a simplified Monte Carlo simulation to estimate the size of nerves where this technique may be successful, as well as the necessary optical lens design for emitters to be used during future in vivo studies. By modeling multiple focused beams, we find that only fascicles within a nerve diameter less than 1 mm are fully accessible to focused optical stimulation; a minimum of 4 light sources is required to generate a photon intensity at a point in a nerve over the initial contact along its surface. To elicit the same effect in larger nerves, focusing lenses would require a numerical aperture [Formula: see text]. These simulations inform on the design of instrumentation capable of stimulating disparate motor neurons in mouse sciatic nerve to control hindlimb movement.

Analysis of Milk from Different Sources Based on Light Propagation and Random Laser Properties

Milk is a valuable contributor to a healthy diet as it contains nutritional components such as fats, proteins, carbohydrates, calcium, phosphorous and vitamins. This research aimed to differentiate milk from animal, plant and human sources based on light propagation and random-laser properties. Experimental, statistical and theoretical analyses were used. Light propagation in different types of milk such as almond milk, oat milk, soy milk, fresh milk, goat milk and human breast milk was measured using the spectrometry method. Near-IR and visible light transmission through the diluted milk samples were compared. Soy milk and fresh milk have the highest absorbance and fluorescence of light, respectively, due to a high content of fat, protein and carbohydrates. Principal component analysis was used to determine the accuracy of the experimental results. The research method is comprehensive as it covers light propagation from 350 nm to 1650 nm of wavelength range and non-intrusive as it does not affect the sample. Meanwhile, analysis of milk was also conducted based on random-laser properties such as multiple emission peaks and lasing threshold. Higher fat content in milk produces a lower random lasing threshold. Thus, we found that milk from animals, plants and humans can be analyzed using light absorption, fluorescence and random lasers. The research method might be useful for future study of milk contaminants that change the properties of milk.

Study of a laser echo in an inhomogeneous dust environment with a continuous field Monte Carlo radiative transfer model

A continuous field Monte Carlo radiative transfer model with an improved semianalytic approach is developed to study laser propagation in an inhomogeneous dust environment. In the proposed model, the photon step size can vary with the mass concentration of the dust environment. Additionally, the scattering properties of the dust particles are calculated with the T-matrix method and the T-matrix scattering phase function is applied to the Monte Carlo simulation with a rejection method. Using this model, the influences of the particle sizes and shapes on the backscattering properties are studied. Finally, the laser echoes simulated by our proposed model are compared with those of traditional Monte Carlo method and experimental results. Different mass concentration distributions indeed influence the simulated laser echo. The simulated results (of our proposed model) agree well with the measured data, demonstrating the effectiveness and accuracy of our approach for inhomogeneous media.

Beyond diffuse correlations: deciphering random flow in time-of-flight resolved light dynamics

Diffusing wave spectroscopy (DWS) and diffuse correlation spectroscopy (DCS) can assess blood flow index (BFI) of biological tissue with multiply scattered light. Though the main biological function of red blood cells (RBCs) is advection, in DWS/DCS, RBCs are assumed to undergo Brownian motion. To explain this discrepancy, we critically examine the cumulant approximation, a major assumption in DWS/DCS. We present a precise criterion for validity of the cumulant approximation, and in realistic tissue models, identify conditions that invalidate it. We show that, in physiologically relevant scenarios, the first cumulant term for random flow and second cumulant term for Brownian motion alone can cancel each other. In such circumstances, assuming pure Brownian motion of RBCs and the first cumulant approximation, a routine practice in DWS/DCS of BFI, can yield good agreement with data, but only because errors due to two incorrect assumptions cancel out. We conclude that correctly assessing random flow from scattered light dynamics requires going beyond the cumulant approximation and propose a more accurate model to do so.

A Tunable Freeform-Segmented Reflector in a Microfluidic System for Conventional and Surface-Enhanced Raman Spectroscopy

We present a freeform-segmented reflector-based microfluidic system for conventional Raman and Surface-Enhanced Raman Scattering (SERS) analysis. The segmented reflector is directly designed by a numerical approach. The polymer-based Raman system strongly suppresses the undesirable background because it enables confocal detection of Raman scattering through the combination of a freeform reflector and a microfluidic chip. We perform systematic simulations using non-sequential ray tracing with the Henyey-Greenstein model to assess the Raman scattering behavior of the substance under test. We fabricate the freeform reflector and the microfluidic chip by means of ultra-precision diamond turning and laser cutting respectively. We demonstrate the confocal behavior by measuring the Raman spectrum of ethanol. Besides, we calibrate the setup by performing Raman measurements on urea and potassium nitrate solutions with different concentrations. The detection limit of our microfluidic system is approximately 20 mM according to the experiment. Finally, we implement a SERS microfluidic chip and discriminate 100 µM urea and potassium nitrate solutions.

Measuring light scattering and absorption in corals with Inverse Spectroscopic Optical Coherence Tomography (ISOCT): a new tool for non-invasive monitoring

The success of reef-building corals for >200 million years has been dependent on the mutualistic interaction between the coral host and its photosynthetic endosymbiont dinoflagellates (family Symbiodiniaceae) that supply the coral host with nutrients and energy for growth and calcification. While multiple light scattering in coral tissue and skeleton significantly enhance the light microenvironment for Symbiodiniaceae, the mechanisms of light propagation in tissue and skeleton remain largely unknown due to a lack of technologies to measure the intrinsic optical properties of both compartments in live corals. Here we introduce ISOCT (inverse spectroscopic optical coherence tomography), a non-invasive approach to measure optical properties and three-dimensional morphology of living corals at micron- and nano-length scales, respectively, which are involved in the control of light propagation. ISOCT enables measurements of optical properties in the visible range and thus allows for characterization of the density of light harvesting pigments in coral. We used ISOCT to characterize the optical scattering coefficient (μ_s) of the coral skeleton and chlorophyll a concentration of live coral tissue. ISOCT further characterized the overall micro- and nano-morphology of live tissue by measuring differences in the sub-micron spatial mass density distribution (D) that vary throughout the tissue and skeleton and give rise to light scattering, and this enabled estimates of the spatial directionality of light scattering, i.e., the anisotropy coefficient, g. Thus, ISOCT enables imaging of coral nanoscale structures and allows for quantifying light scattering and pigment absorption in live corals. ISOCT could thus be developed into an important tool for rapid, non-invasive monitoring of coral health, growth and photophysiology with unprecedented spatial resolution.

Recent methodology advances in fluorescence molecular tomography

Molecular imaging (MI) is a novel imaging discipline that has been continuously developed in recent years. It combines biochemistry, multimodal imaging, biomathematics, bioinformatics, cell & molecular physiology, biophysics, and pharmacology, and it provides a new technology platform for the early diagnosis and quantitative analysis of diseases, treatment monitoring and evaluation, and the development of comprehensive physiology. Fluorescence Molecular Tomography (FMT) is a type of optical imaging modality in MI that captures the three-dimensional distribution of fluorescence within a biological tissue generated by a specific molecule of fluorescent material within a biological tissue. Compared with other optical molecular imaging methods, FMT has the characteristics of high sensitivity, low cost, and safety and reliability. It has become the research frontier and research hotspot of optical molecular imaging technology. This paper took an overview of the recent methodology advances in FMT, mainly focused on the photon propagation model of FMT based on the radiative transfer equation (RTE), and the reconstruction problem solution consist of forward problem and inverse problem. We introduce the detailed technologies utilized in reconstruction of FMT. Finally, the challenges in FMT were discussed. This survey aims at summarizing current research hotspots in methodology of FMT, from which future research may benefit.

Using electron microscopy to calculate optical properties of biological samples

The microscopic structural origins of optical properties in biological media are still not fully understood. Better understanding these origins can serve to improve the utility of existing techniques and facilitate the discovery of other novel techniques. We propose a novel analysis technique using electron microscopy (EM) to calculate optical properties of specific biological structures. This method is demonstrated with images of human epithelial colon cell nuclei. The spectrum of anisotropy factor g, the phase function and the shape factor D of the nuclei are calculated. The results show strong agreement with an independent study. This method provides a new way to extract the true phase function of biological samples and provides an independent validation for optical property measurement techniques.

Estimation of anisotropy coefficient of swine pancreas, liver and muscle at 1064 nm based on goniometric technique

Optical properties of tissues are required for theoretical modeling of Laser Ablation in tumor therapy. The light scattering characteristic of tissues is described by the anisotropy coefficient, g. The relationship between the angular distribution of scattered light and g is given by the Henyey-Greenstein (HG) phase function. This work describes the estimation of anisotropy coefficients of ex vivo swine pancreas, liver and muscle at 1064 nm. The intensities of scattered light at fixed angles were measured under repeatability conditions. Experimental data were fitted with a two-term HG, estimating the anisotropy coefficients for the forward (e.g., 0.956 for pancreas, 0.964 for liver and 0.968 for muscle) and the backward (e.g., -0.481 for pancreas, -0.414 for liver and -0.372 for muscle) scattering. Experimental set up employed to estimate the anisotropy coefficient of biological tissues. The image on the left depicts the holder used to house tissue, laser fiber and photodetector; on the left an example of scattered light beam is shown, as well as the effect due to Snell's law.

Intravital fluorescence imaging of mouse brain using implantable semiconductor devices and epi-illumination of biological tissue

The application of the fluorescence imaging method to living animals, together with the use of genetically engineered animals and synthesized photo-responsive compounds, is a powerful method for investigating brain functions. Here, we report a fluorescence imaging method for the brain surface and deep brain tissue that uses compact and mass-producible semiconductor imaging devices based on complementary metal-oxide semiconductor (CMOS) technology. An image sensor chip was designed to be inserted into brain tissue, and its size was 1500 × 450 μm. Sample illumination is also a key issue for intravital fluorescence imaging. Hence, for the uniform illumination of the imaging area, we propose a new method involving the epi-illumination of living biological tissues, and we performed investigations using optical simulations and experimental evaluation.

Noninvasive optical inhibition with a red-shifted microbial rhodopsin

Optogenetic inhibition of the electrical activity of neurons enables the causal assessment of their contributions to brain functions. Red light penetrates deeper into tissue than other visible wavelengths. We present a red-shifted cruxhalorhodopsin, Jaws, derived from Haloarcula (Halobacterium) salinarum (strain Shark) and engineered to result in red light-induced photocurrents three times those of earlier silencers. Jaws exhibits robust inhibition of sensory-evoked neural activity in the cortex and results in strong light responses when used in retinas of retinitis pigmentosa model mice. We also demonstrate that Jaws can noninvasively mediate transcranial optical inhibition of neurons deep in the brains of awake mice. The noninvasive optogenetic inhibition opened up by Jaws enables a variety of important neuroscience experiments and offers a powerful general-use chloride pump for basic and applied neuroscience.

Assessment of speed distribution of red blood cells in the microvascular network in healthy volunteers and type 1 diabetes using laser Doppler spectra decomposition

We applied a recently reported method of decomposition of laser Doppler power density spectra for in vivo monitoring of speed distributions of red blood cells (RBCs) in the microvascular network. The spectrum decomposition technique allows us to derive the distribution of RBC speed (in absolute units (mm s(-1))) versus RBC concentration (in arbitrary units). We carried out postocclusive reactive hyperaemia (PORH) test in 15 healthy volunteers and 21 diabetic patients in which the duration of type 1 diabetes was longer than 10 years. Measurements were carried out simultaneously with the use of a typical laser Doppler commercial instrument and speed resolved laser Doppler instrument utilizing the new technique based on decomposition of the laser Doppler spectra. We show that for the classical laser Doppler instrument, none of the PORH parameters revealed a statistical significance of difference between the groups analyzed. In contrast, the RBC speed distributions obtained from laser Doppler spectra during rest in the control group and type 1 diabetes are statistically significant. This result suggests that speed distribution measurements in the rest state (without any kind of stimulation test) allows for the assessment of microcirculation disorders. Measurements carried out in healthy subjects show that the first moment of speed distributions (mean speed of the distributions) is 2.32 ± 0.54 mm s(-1) and 2.57 ± 0.41 mm s(-1) for optodes located on the toe and finger of the hand, respectively. Respective values in type 1 diabetes were higher: 3.00 ± 0.36 mm s(-1) and 3.10 ± 0.48 mm s(-1).

Influence of the phase function in generalized diffuse reflectance models: review of current formalisms and novel observations

Diffuse reflectance spectroscopy, which has been demonstrated as a noninvasive diagnostic technique, relies on quantitative models for extracting optical property values from turbid media, such as biological tissues. We review and compare reflectance models that have been published, and we test similar models over a much wider range of measurement parameters than previously published, with specific focus on the effects of the scattering phase function and the source-detector distance. It has previously been shown that the dependence of a forward reflectance model on the scattering phase function can be described more accurately using a variable, γ, which is a more predictive variable for reflectance than the traditional anisotropy factor, g. We show that variations in the reflectance model due to the phase function are strongly dependent on the source-detector separation, and we identify a dimensionless scattering distance at which reflectance is insensitive to the phase function. Further, we evaluate how variations in the phase function and source-detector separation affect the accuracy of inverse property extraction. By simultaneously fitting two or more reflectance spectra, measured at different source-detector separations, we also demonstrate that an estimate of γ can be extracted, in addition to the reduced scattering and absorption coefficients.

Monte Carlo simulation of light scattering in the atmosphere and effect of atmospheric aerosols on the point spread function

We present a Monte Carlo simulation for the scattering of light in the case of an isotropic light source. The scattering phase functions are studied particularly in detail to understand how they can affect the multiple light scattering in the atmosphere. We show that, although aerosols are usually in lower density than molecules in the atmosphere, they can have a non-negligible effect on the atmospheric point spread function. This effect is especially expected for ground-based detectors when large aerosols are present in the atmosphere.

Estimation of scattering phase function utilizing laser Doppler power density spectra

A new method for the estimation of the light scattering phase function of particles is presented. The method allows us to measure the light scattering phase function of particles of any shape in the full angular range (0°-180°) and is based on the analysis of laser Doppler (LD) power density spectra. The theoretical background of the method and results of its validation using data from Monte Carlo simulations will be presented. For the estimation of the scattering phase function, a phantom measurement setup is proposed containing a LD measurement system and a simple model in which a liquid sample flows through a glass tube fixed in an optically turbid material. The scattering phase function estimation error was thoroughly investigated in relation to the light scattering anisotropy factor g. The error of g estimation is lower than 10% for anisotropy factors larger than 0.5 and decreases with increase of the anisotropy factor (e.g. for g = 0.98, the error of estimation is 0.01%). The analysis of influence of the noise in the measured LD spectrum showed that the g estimation error is lower than 1% for signal to noise ratio higher than 50 dB.

Ramsauer approach for light scattering on nonabsorbing spherical particles and application to the Henyey-Greenstein phase function

We present a new method to study light scattering on nonabsorbing spherical particles. This method is based on the Ramsauer approach, a model known in atomic and nuclear physics. Its main advantage is its intuitive understanding of the underlying physics phenomena. We show that although the approximations are numerous, the Ramsauer analytical solutions describe fairly well the scattering phase function and the total cross section. Then this model is applied to the Henyey-Greenstein parameterization of the scattering phase function to give a relation between its asymmetry parameter and the mean particle size.

Optogenetics in the nonhuman primate

The nonhuman primate brain, the model system closest to the human brain, plays a critical role in our understanding of neural computation, cognition, and behavior. The continued quest to crack the neural codes in the monkey brain would be greatly enhanced with new tools and technologies that can rapidly and reversibly control the activities of desired cells at precise times during specific behavioral states. Recent advances in adapting optogenetic technologies to monkeys have enabled precise control of specific cells or brain regions at the millisecond timescale, allowing for the investigation of the causal role of these neural circuits in this model system. Validation of optogenetic technologies in monkeys also represents a critical preclinical step on the translational path of new generation cell-type-specific neural modulation therapies. Here, I discuss the current state of the application of optogenetics in the nonhuman primate model system, highlighting the available genetic, optical and electrical technologies, and their limitations and potentials.

Simulation of near-infrared light absorption considering individual head and prefrontal cortex anatomy: implications for optical neuroimaging

Functional near-infrared spectroscopy (fNIRS) is an established optical neuroimaging method for measuring functional hemodynamic responses to infer neural activation. However, the impact of individual anatomy on the sensitivity of fNIRS measuring hemodynamics within cortical gray matter is still unknown. By means of Monte Carlo simulations and structural MRI of 23 healthy subjects (mean age: 25.0±2.8 years), we characterized the individual distribution of tissue-specific NIR-light absorption underneath 24 prefrontal fNIRS channels. We, thereby, investigated the impact of scalp-cortex distance (SCD), frontal sinus volume as well as sulcal morphology on gray matter volumes (V(gray)) traversed by NIR-light, i.e. anatomy-dependent fNIRS sensitivity. The NIR-light absorption between optodes was distributed describing a rotational ellipsoid with a mean penetration depth of (23.6±0.7) mm considering the deepest 5% of light. Of the detected photon packages scalp and bone absorbed (96.4±9.7)% and V(gray) absorbed (3.1±1.8)% of the energy. The mean V(gray) volume (1.1±0.4) cm3 was negatively correlated (r=-.76) with the SCD and frontal sinus volume (r=-.57) and was reduced by 41.5% in subjects with relatively large compared to small frontal sinus. Head circumference was significantly positively correlated with the mean SCD (r=.46) and the traversed frontal sinus volume (r=.43). Sulcal morphology had no significant impact on V(gray). Our findings suggest to consider individual SCD and frontal sinus volume as anatomical factors impacting fNIRS sensitivity. Head circumference may represent a practical measure to partly control for these sources of error variance.

Choroidal laser Doppler flowmeter with enhanced sensitivity based on a scattering plate

A portable choroidal laser Doppler flowmeter (LDF) with enhanced sensitivity based on a scattering plate is developed. The portable LDF is weighted 2 kg operated at center wavelength of 780 nm, leading to a better penetration into the eye fundus in contrast to the previous LDF operated at center wavelength of 670 nm. Enhancement of number of detected photons that undergo Doppler scattering and improved measured speed of choroidal blood flow are achieved with the use of a scattering plate positioned in front of the eye. The mechanism of detection and sensitivity enhancement is theoretically analyzed. Evaluation of system performance is done by in vivo measurements on ten volunteers. The results demonstrate that an increased percentage of backscattering light at high Doppler shift frequency is collected due to utilization of the scattering plate. However, this kind of light detection influences spatial resolution of the system and decreases the total signal measured. The proposed method for detection and sensitivity enhancement might be useful in a case where the perception of very slight alternation of blood flow is pursued and the spatial resolution is not as critical as that in a choroidal vascular bed.

Calculation of photon path changes due to scatter in Monte Carlo simulations

Computation using Monte Carlo simulations is widely used for modelling the light-tissue interaction. Despite this, many of the methods used for building such simulations are poorly described in the literature. In particular, a scheme for translating the scatter angles produced from a phase function into updated photon direction vectors is not explicitly reported. To address this, a method for calculating the change in photon direction following a scattering event is described, thus illuminating one of the fundamental 'building blocks' for researchers developing their own Monte Carlo models. The equations derived in this paper may be readily incorporated into applicable Monte Carlo program code.

Laser-Doppler spectrum decomposition applied for the estimation of speed distribution of particles moving in a multiple scattering medium

Recently, a method for the estimation of speed distribution of particles moving in an optically turbid medium has been proposed. The method allows potentially absolute measurement of speed of the particles and can be applied in laser-Doppler perfusion measurements. However, the decomposition technique was limited to short source-detector separations for which the assumption that one photon is Doppler scattered not more than once is fulfilled. In the present paper we show a generalized decomposition technique in which photons can be scattered more than once. We show the theoretical background for decomposition in such a case. We apply a decomposition method for the analysis of laser-Doppler spectra obtained by Monte Carlo simulations. This analysis allows showing noise limits in which the technique can be effectively applied in analysis of measured spectra. We propose an approximated scattering model based on the assumption that for one photon consecutive Doppler scattering events occur on particles moving with the same speed, and we show that this approximation does not influence significantly the uncertainty of the resulting speed distribution. The proposed decomposition procedure is validated in measurements on a physical flow model. The decomposition procedure is also validated by analysis of spectra measured on a physical phantom using laser-Doppler flow meter (Oxford Optronix, UK). A diluted solution of milk was pumped through a tube fixed in an optically turbid material with speed varying from 0 mm s(-1) to 4 mm s(-1). We observed a linear relation between actual speed of milk solution and speed estimated from results of spectra decomposition.

Prosthetic systems for therapeutic optical activation and silencing of genetically-targeted neurons

Many neural disorders are associated with aberrant activity in specific cell types or neural projection pathways embedded within the densely-wired, heterogeneous matter of the brain. An ideal therapy would permit correction of activity just in specific target neurons, while leaving other neurons unaltered. Recently our lab revealed that the naturally-occurring light-activated proteins channelrhodopsin-2 (ChR2) and halorhodopsin (Halo/NpHR) can, when genetically expressed in neurons, enable them to be safely, precisely, and reversibly activated and silenced by pulses of blue and yellow light, respectively. We here describe the ability to make specific neurons in the brain light-sensitive, using a viral approach. We also reveal the design and construction of a scalable, fully-implantable optical prosthetic capable of delivering light of appropriate intensity and wavelength to targeted neurons at arbitrary 3-D locations within the brain, enabling activation and silencing of specific neuron types at multiple locations. Finally, we demonstrate control of neural activity in the cortex of the non-human primate, a key step in the translation of such technology for human clinical use. Systems for optical targeting of specific neural circuit elements may enable a new generation of high-precision therapies for brain disorders.

Comment on ‘The use of the Henyey–Greenstein phase function in Monte Carlo simulations in biomedical optics’

In this letter the authors highlight the presence of an error appearing in the discussion of the note 'The use of the Henyey-Greenstein phase function in Monte Carlo simulations in biomedical optics' previously published by them (Binzoni et al 2006 Phys. Med. Biol. 51 N313). In the light of this error, the discussion and conclusions in the original paper are revised in this letter and the role of the use of the phase functions in MC simulations, interpreted in probabilistic terms, is better clarified. The exact definition for the probability density function for the deflection angle, in the case of the Henyey-Greenstein model, is also given.