MiniRead: A simple and inexpensive do-it-yourself device for multiple analyses of micro-organism growth kinetics

Fitness in micro-organisms can be proxied by growth parameters on different media and/or temperatures. This is achieved by measuring optical density at 600 nm using a spectrophotometer, which measures the effect of absorbance and side scattering due to turbidity of cells suspensions. However, when growth kinetics must be monitored in many 96-well plates at the same time, buying several 96-channel spectrophotometers is often beyond budgets. The MiniRead device presented here is a simple and inexpensive do-it-yourself 96-well temperature-controlled turbidimeter designed to measure the interception of white light via absorption or side scattering through liquid culture medium. Turbidity is automatically recorded in each well at regular time intervals for up to several days or weeks. Output tabulated text files are recorded into a micro-SD memory card to be easily transferred to a computer. We propose also an R package which allows (1) to compute the nonlinear calibration curves required to convert raw readings into cell concentration values, and (2) to analyze growth kinetics output files to automatically estimate proxies of growth parameters such as lag time, maximum growth rate, or cell concentration at the plateau.

Complex coacervation of pea albumin-pectin and ovalbumin-pectin assessed by isothermal titration calorimeter and turbidimetry

BACKGROUND

This study investigates the complexation of a pea albumin-rich fraction and ovalbumin with pectin of different degrees of esterification (DE) and blockiness (DB) as a function of pH and biopolymer mixing ratio by turbidimetric titration and isothermal titration calorimetry (ITC).

RESULTS

Turbidimetric analysis found maximum complexation occurred at a mixing ratio of 4:1 for pea albumin with high methoxy pectin, 8:1 for pea albumin with low methoxy pectin, and 8:1 for ovalbumin with low methoxy pectin. In the case of ovalbumin with high methoxy pectin, interactions were very weak. The pectin with high levels of esterification and blockiness displayed greater interactions with the pea albumin in both turbidimetry and ITC. However, low methoxy pectin imparted better interactions with ovalbumin and displayed higher optical density values than high methoxy pectin.

CONCLUSIONS

The current study indicated that the different thermodynamic parameters of PA-pectin complexes can be tuned by controlling the structural characteristics (DB, DE, and d-galacturonic acid) of the pectin. © 2020 Society of Chemical Industry.

Use of High-Resolution Pressure Nephelometry To Measure Gas Vesicle Collapse as a Means of Determining Growth and Turgor Changes in Planktonic Cyanobacteria

Previous work has demonstrated that the physical properties of intracellular bacterial gas vesicles (GVs) can be analyzed in vivo using pressure nephelometry. In analyzing the buoyant state of GV-containing cyanobacteria, hydrostatic pressure within a sample cell is increased in a stepwise manner, where the concomitant collapse of GVs due to pressure and the resultant decrease in suspended cells are detected by changes in nephelometric scattering. As the relative pressure at which GVs collapse is a function of turgor pressure and cellular osmotic gradients, pressure nephelometry is a powerful tool for assaying changes in metabolism that affect turgor, such as photosynthetic and osmoregulatory processes. We have developed an updated and automated pressure nephelometer that utilizes visible-infrared (Vis-IR) spectra to accurately quantify GV critical collapse pressure, critical collapse pressure distribution, and cell turgor pressure. Here, using the updated pressure nephelometer and axenic cultures of Microcystis aeruginosa PCC7806, we demonstrate that GV critical collapse pressure is stable during mid-exponential growth phase, introduce pressure-sensitive turbidity as a robust metric for the abundance of gas-vacuolate cyanobacteria, and demonstrate that pressure-sensitive turbidity is a more accurate proxy for abundance and growth than photopigment fluorescence. As cyanobacterium-dominated harmful algal bloom (cyanoHAB) formation is dependent on the constituent cells possessing gas vesicles, characterization of environmental cyanobacteria populations via pressure nephelometry is identified as an underutilized monitoring method. Applications of this instrument focus on physiological and ecological studies of cyanobacteria, for example, cyanoHAB dynamics and the drivers associated with cyanotoxin production in aquatic ecosystems.IMPORTANCE The increased prevalence of bloom-forming cyanobacteria and associated risk of exposure to cyanobacterial toxins through drinking water utilities and recreational waterways are growing public health concerns. Cost-effective, early-detection methodologies specific to cyanobacteria are crucial for mitigating these risks, with a gas vesicle-specific signal offering a number of benefits over photopigment fluorescence, including improved detection limits and discrimination against non-gas-vacuolate phototrophs. Here, we present a multiplexed instrument capable of quantifying the relative abundance of cyanobacteria based on the signal generated from the presence of intracellular gas vesicles specific to bloom-forming cyanobacteria. Additionally, as cell turgor can be measured in vivo via pressure nephelometry, the measurement furnishes information about the internal osmotic pressure of gas-vacuolate cyanobacteria, which relates to the metabolic state of the cell. Together these advances may improve routine waterway monitoring and the mitigation of human health threats due to cyanobacterial blooms.

Accuracy of data buoys for measurement of cyanobacteria, chlorophyll, and turbidity in a large lake (Lake Erie, North America): implications for estimation of cyanobacterial bloom parameters from water quality sonde measurements

Microcystin (MCY)-producing harmful cyanobacterial blooms (cHABs) are an annual occurrence in Lake Erie, and buoys equipped with water quality sondes have been deployed to help researchers and resource managers track cHABs. The objective of this study was to determine how well water quality sondes attached to buoys measure total algae and cyanobacterial biomass and water turbidity. Water samples were collected next to two data buoys in western Lake Erie (near Gibraltar Island and in the Sandusky subbasin) throughout summers 2015, 2016, and 2017 to determine correlations between buoy sonde data and water sample data. MCY and nutrient concentrations were also measured. Significant (P < 0.001) linear relationships (R² > 0.75) occurred between cyanobacteria buoy and water sample data at the Gibraltar buoy, but not at the Sandusky buoy; however, the coefficients at the Gibraltar buoy differed significantly across years. There was a significant correlation between buoy and water sample total chlorophyll data at both buoys, but the coefficient varied considerably between buoys and among years. Total MCY concentrations at the Gibraltar buoy followed similar temporal patterns as buoy and water sample cyanobacterial biomass data, and the ratio of MCY to cyanobacteria-chlorophyll decreased with decreased ambient nitrate concentrations. These results suggest that buoy data are difficult to compare across time and space. Additionally, the inclusion of nitrate concentration data can lead to more robust predictions on the relative toxicity of blooms. Overall, deployed buoys with sondes that are routinely cleaned and calibrated can track relative cyanobacteria abundance and be used as an early warning system for potentially toxic blooms.

Performance assessment of a portable nephelometer for outdoor particle mass measurement

The availability of portable nephelometers has improved assessment of exposure to atmospheric particles at a high resolution regarding space and time. However, nephelometer performance has seldom been evaluated for outdoor measurements, especially in Chinese cities. During 37 days of measurements at four outdoor sites in Shanghai, we assessed a popular nephelometer called SidePak (TSI Inc., USA) for PM_1.0, PM_2.5 and PM₁₀ mass measurements and compared them to US federal reference methods (FRMs) based on different measurement principles. The nephelometer showed high measurement precision and stability and was strongly correlated with FRMs, making it superior to the portable light scattering monitors reported in the past and thus indicating the maturity of this principle. The nephelometer measurements overestimated all those of FRMs by a factor of two, which is higher than in evaluations in other international cities. This overestimation showed a descending order for PM_1.0 (2.9-fold), PM_2.5 (2.2-fold) and PM₁₀ (1.9-fold) relative to the FRMs of tapered element oscillating microbalance or beta attenuation combined with nephelometry, based on whole samples. Sites that are far from direct pollution sources showed very good agreement between the nephelometer and FRMs for PM_2.5 mass measurements, while, by comparison, the roadside site showed a lower SidePak/FRM PM_2.5 ratio, which is likely due to higher abundance of elemental carbon in roadside particles. Relative humidity (RH) was shown to be a key factor that distorted the measurement of the nephelometer. An empirical formula incorporating an RH adjustment developed to correct the nephelometer could produce a reasonable result, even across the various sites. This study demonstrates the great potential of the nephelometer for outdoor particle mass measurements, but for accurate and comparable data, a site-specific calibration is strongly recommended before using.

Analysis of Red Blood Cell Aggregation in Cardio-Pulmonary Bypass (CPB) Surgery

Not much is known about red cell aggregation during cardio-pulmonary bypass surgery (CPB). Blood samples from 19 patients undergoing CPB were anticoagulated with EDTA. Hematocrit was adjusted to 40%. A red blood cell aggregometer (LORCA) measured changes in light reflection from each blood sample after cessation of the rotation, and calculated an aggregation index (AI). Reflection measurements were stored. Because LORCA software failed for 87 of 171 samples, we developed new software, and applied it to the stored reflection measurements. This software failed only in 7 out of 171 cases and showed that all LORCA failures occurred for AI < 40%. The new calculations revealed that the aggregation index significantly decreased from 46.6 ± 10.1 (mean ± standard deviation) baseline to 22.8 ± 8.3 at the end of CPB and recovered to 37.1 ± 13.5 at day 1. It is concluded that the new software can be used to study decreased red cell aggregation during CPB.

Factors related to Secchi depths and their stability over time as determined from a probability sample of US lakes

A probabilistic sample of lakes in the 48 coterminous US lakes was made by the United States Environmental Protection Agency in the 2007 National Lakes Assessment. Because of the statistical design, the results of our analyses of Secchi depths (SD) apply to a population of 45,265 lakes. We found statistically significant differences in mean Secchi depths between natural (1.57 m) and man-made lakes (1.18 m). The most important variable correlated with SD was turbidity, an optical measure related to suspended particles in the water column. For most lakes, chlorophyll a was highly correlated with both turbidity and SD, but several lakes had more turbidity and lower SD than expected based on chlorophyll a alone, indicating that non-algal suspended solids were an important factor. On an ecoregion basis, the non-algal suspended solids in the lake waters were related to the average levels of suspended solids in streams located in that ecoregion, and the non-algal suspended solids were more important in man-made than natural lakes. Phosphorus and nitrogen were directly correlated with chlorophyll a and turbidity and inversely correlated with SD. Based on diatom-inferred Secchi depths for the tops and bottoms of sediment cores from lakes in Ecoregions VIII and VII (excluding lakes in Minnesota) representing 40% of the natural lakes in the US, there has been no decrease in water transparency in that population of lakes in the past 70 or more years when the US population increased by 134%. We do not have information to determine if the other 60% of lakes have or have not changed.

Interferometric Near-Infrared Spectroscopy (iNIRS) for determination of optical and dynamical properties of turbid media

We introduce and implement interferometric near-infrared spectroscopy (iNIRS), which simultaneously extracts optical and dynamical properties of turbid media through analysis of a spectral interference fringe pattern. The spectral interference fringe pattern is measured using a Mach-Zehnder interferometer with a frequency-swept narrow linewidth laser. Fourier analysis of the detected signal is used to determine time-of-flight (TOF)-resolved intensity, which is then analyzed over time to yield TOF-resolved intensity autocorrelations. This approach enables quantification of optical properties, which is not possible in conventional, continuous-wave near-infrared spectroscopy (NIRS). Furthermore, iNIRS quantifies scatterer motion based on TOF-resolved autocorrelations, which is a feature inaccessible by well-established diffuse correlation spectroscopy (DCS) techniques. We prove this by determining TOF-resolved intensity and temporal autocorrelations for light transmitted through diffusive fluid phantoms with optical thicknesses of up to 55 reduced mean free paths (approximately 120 scattering events). The TOF-resolved intensity is used to determine optical properties with time-resolved diffusion theory, while the TOF-resolved intensity autocorrelations are used to determine dynamics with diffusing wave spectroscopy. iNIRS advances the capabilities of diffuse optical methods and is suitable for in vivo tissue characterization. Moreover, iNIRS combines NIRS and DCS capabilities into a single modality.

Comparison between optical-resolution photoacoustic microscopy and confocal laser scanning microscopy for turbid sample imaging

Optical-resolution photoacoustic microscopy (ORPAM) in theory provides lateral resolution equivalent to the optical diffraction limit. Scattering media, such as biological turbid media, attenuates the optical signal and also alters the diffraction-limited spot size of the focused beam. The ORPAM signal is generated only from a small voxel in scattering media with dimensions equivalent to the laser spot size after passing through scattering layers and is detected by an acoustic transducer, which is not affected by optical scattering. Thus, both ORPAM and confocal laser scanning microscopy (CLSM) reject scattered light. A multimodal optical microscopy platform that includes ORPAM and CLSM was constructed, and the lateral resolution of both modes was measured using patterned thin metal film with and without a scattering barrier. The effect of scattering media on the lateral resolution was studied using different scattering coefficients and was compared to computational results based on Monte Carlo simulations. It was found that degradation of lateral resolution due to optical scattering was not significant for either ORPAM or CLSM. The depth discrimination capability of ORPAM and CLSM was measured using microfiber embedded in a light scattering phantom material. ORPAM images demonstrated higher contrast compared to CLSM images partly due to reduced acoustic signal scattering.

Binocular open-view system to perform estimations of aberrations and scattering in the human eye

We present a system that integrates a double-pass (DP) instrument and a Hartmann-Shack (HS) wavefront sensor to provide information not only on aberrations, but also on the scattering that occurs in the human eye. A binocular open-view design permits evaluations to be made under normal viewing conditions. Furthermore, the system is able to compensate for both the spherical and astigmatic refractive errors that occur during measurements by using devices with configurable optical power. The DP and HS techniques provide comparable data after estimating wavefront slopes with respect to the intersections of an ideal grid and compensating for residual errors caused by the optical defects of the measuring system. Once comparable data is obtained, it is possible to use this combined manner of assessment to provide information on scattering. Measurements in an artificial eye suggest that the characteristics of the ocular fundus may induce deviations of DP with respect to the HS data. These differences were quantified in terms of the modulation transfer function in young, healthy eyes measured in infrared light to demonstrate the potential use of the system in visual optics studies.

Differentiating cancerous tissues from noncancerous tissues using single-fiber reflectance spectroscopy with different fiber diameters

Elastic light-scattering spectra acquired with single-fiber optical probes with diameters of 100, 200, 400, 600, 800, 1000, 1200, and 1500 μm were used to differentiate cancerous from noncancerous prostate tissues. The spectra were acquired ex vivo on 24 excised prostate tissue samples collected from four patients. For each probe, the spectra and histopathology results were compared in order to investigate the correlation between the core diameters of the single-fiber optical probe and successful differentiation between cancerous and noncancerous prostate tissues. The spectra acquired using probes with a fiber core diameter of 400 μm or smaller successfully differentiated cancerous from noncancerous prostate tissues. Next, the spectra were acquired from monosized polystyrene microspheres with a diameter of 5.00±0.01 μm to investigate the correlation between the core diameters of the probes and the Mie oscillations on the spectra. Monte Carlo simulations of the light distribution of the tissue phantoms were run to interrogate whether the light detected by the probes with different fiber core diameters was in the ballistic or diffusive regime. If the single-fiber optical probes detect light in the ballistic regime, the spectra can be used to differentiate between cancerous and noncancerous tissues.

Differences in forward angular light scattering distributions between M1 and M2 macrophages

The ability to distinguish macrophage subtypes noninvasively could have diagnostic potential in cancer, atherosclerosis, and diabetes, where polarized M1 and M2 macrophages play critical and often opposing roles. Current methods to distinguish macrophage subtypes rely on tissue biopsy. Optical imaging techniques based on light scattering are of interest as they can be translated into biopsy-free strategies. Because mitochondria are relatively strong subcellular light scattering centers, and M2 macrophages are known to have enhanced mitochondrial biogenesis compared to M1, we hypothesized that M1 and M2 macrophages may have different angular light scattering profiles. To test this, we developed an in vitro angle-resolved forward light scattering measurement system. We found that M1 and M2 macrophage monolayers scatter relatively unequal amounts of light in the forward direction between 1.6 deg and 3.2 deg with M2 forward scattering significantly more light than M1 at increasing angles. The ratio of forward scattering can be used to identify the polarization state of macrophage populations in culture.

Detecting structural information of scatterers using spatial frequency domain imaging

We demonstrate optical phantom experiments on the phase function parameter γ using spatial frequency domain imaging. The incorporation of two different types of scattering particles allows for control of the optical phantoms’ microscopic scattering properties. By laterally structuring areas with either TiO2 or Al2O3 scattering particles, we were able to obtain almost pure subdiffusive scattering contrast in a single optical phantom. Optical parameter mapping was then achieved using an analytical radiative transfer model revealing the microscopic structural contrast on a macroscopic field of view. As part of our study, we explain several correction and referencing techniques for high spatial frequency analysis and experimentally study the sampling depth of the subdiffusive parameter γ.

Airborne system for multispectral, multiangle polarimetric imaging

In this paper, we describe the design, fabrication, calibration, and deployment of an airborne multispectral polarimetric imager. The motivation for the development of this instrument was to explore its ability to provide information about water constituents, such as particle size and type. The instrument is based on four 16 MP cameras and uses wire grid polarizers (aligned at 0°, 45°, 90°, and 135°) to provide the separation of the polarization states. A five-position filter wheel provides for four narrow-band spectral filters (435, 550, 625, and 750 nm) and one blocked position for dark-level measurements. When flown, the instrument is mounted on a programmable stage that provides control of the view angles. View angles that range to ±65° from the nadir have been used. Data processing provides a measure of the polarimetric signature as a function of both the view zenith and view azimuth angles. As a validation of our initial results, we compare our measurements, over water, with the output of a Monte Carlo code, both of which show neutral points off the principle plane. The locations of the calculated and measured neutral points are compared. The random error level in the measured degree of linear polarization (8% at 435) is shown to be better than 0.25%.

Acceleration of Monte Carlo simulation of photon migration in complex heterogeneous media using Intel many-integrated core architecture

Over two decades, the Monte Carlo technique has become a gold standard in simulation of light propagation in turbid media, including biotissues. Technological solutions provide further advances of this technique. The Intel Xeon Phi coprocessor is a new type of accelerator for highly parallel general purpose computing, which allows execution of a wide range of applications without substantial code modification. We present a technical approach of porting our previously developed Monte Carlo (MC) code for simulation of light transport in tissues to the Intel Xeon Phi coprocessor. We show that employing the accelerator allows reducing computational time of MC simulation and obtaining simulation speed-up comparable to GPU. We demonstrate the performance of the developed code for simulation of light transport in the human head and determination of the measurement volume in near-infrared spectroscopy brain sensing.

Linear polarization optimized Stokes polarimeter based on four-quadrant detector

A four-quadrant detector (4QD) consists of four well-balanced detectors. We report on a Stokes polarimeter with optimal linear polarization measurements based on a 4QD. We turned the four intensity-detection channels into four polarization-analyzing channels by placing four polarizers and one quarter-wave plate in front of the individual detectors. An optimization method for the four polarization-analyzing channels is proposed to improve measurement accuracy. Considering applications in favor of linear polarization measurements instead of global optimization for all the possible states of polarization (SOP), we optimize the polarimeter first for the linear polarization components and then for the circular polarization component. The polarimeter is capable of simultaneous measurements of fast varying SOP with improved performance for the linear polarizations.

A drifter for measuring water turbidity in rivers and coastal oceans

A disposable instrument for measuring water turbidity in rivers and coastal oceans is described. It transmits turbidity measurements and position data via a satellite uplink to a processing server. The primary purpose of the instrument is to help document changes in sediment runoff from river catchments in North Queensland, Australia. The 'river drifter' is released into a flooded river and drifts downstream to the ocean, measuring turbidity at regular intervals. Deployment in the Herbert River showed a downstream increase in turbidity, and thus suspended sediment concentration, while for the Johnstone River there was a rapid reduction in turbidity where the river entered the sea. Potential stranding along river banks is a limitation of the instrument. However, it has proved possible for drifters to routinely collect data along 80 km of the Herbert River. One drifter deployed in the Fly River, Papua New Guinea, travelled almost 200 km before stranding.

POLVSM (Polarized Volume Scattering Meter) instrument: an innovative device to measure the directional and polarized scattering properties of hydrosols

An innovative instrument dedicated to the multispectral measurements of the directional and polarized scattering properties of the hydrosols, so-called POLVSM, is described. The instrument could be used onboard a ship, as a benchtop instrument, or at laboratory. The originality of the POLVSM concept relies on the use of a double periscopic optical system whose role is (i) to separate the plane containing the light source from the scattering plane containing the sample and the receiver and (ii) to prevent from any specularly reflected light within the sample chamber. As a result, a wide range of scattering angle, namely from 1° to 179°, is covered by the detector. Another originality of the instrument is to measure the Mueller scattering matrix elements, including the degree of polarization. A relevant calibration procedure, which could be of great interest as well for other instruments, is proposed to convert the raw data into physical units. The relative uncertainty in POLVSM data was determined at ± 4.3%. The analysis of measurements of the volume scattering function and degree of polarization performed under controlled conditions for samples dominated either by inorganic hydrosols or phytoplankton monospecific species showed a good consistency with literature, thus confirming the good performance of the POLVSM device. Comparisons of POLVSM data with theoretical calculations showed that Mie theory could reproduce efficiently the measurements of the VSF and degree of polarization for the case of inorganic hydrosols sample, despite the likely non sphericity of these particles as revealed by one of the element of the Mueller matrix. Our results suggested as well that a sophisticated modeling of the heterogeneous internal structure of living cells, or at least, the use of layered sphere models, is needed to correctly predict the directional and polarized effects of phytoplankton on the oceanic radiation. The relevance of performing angularly resolved measurements of the Mueller scattering elements to gain understanding on the mechanisms processes involved in the scattering of light by marine particles, which has important implications for ocean color remote sensing studies, is demonstrated.

Imaging in scattering media using correlation image sensors and sparse convolutional coding

Correlation image sensors have recently become popular low-cost devices for time-of-flight, or range cameras. They usually operate under the assumption of a single light path contributing to each pixel. We show that a more thorough analysis of the sensor data from correlation sensors can be used can be used to analyze the light transport in much more complex environments, including applications for imaging through scattering and turbid media. The key of our method is a new convolutional sparse coding approach for recovering transient (light-in-flight) images from correlation image sensors. This approach is enabled by an analysis of sparsity in complex transient images, and the derivation of a new physically-motivated model for transient images with drastically improved sparsity.

Propagation factors of cosine-Gaussian-correlated Schell-model beams in non-Kolmogorov turbulence

Based on the extended Huygens-Fresnel principle and second-order moments of the Wigner distribution function (WDF), we have studied the relative root-mean-square (rms) angular width and the propagation factor of cosine-Gaussian-correlated Schell-model (CGSM) beams propagating in non-Kolmogorov turbulence. It has been found that the CGSM beam has advantage over the Gaussian Schell-model (GSM) beam for reducing the turbulence-induced degradation, and this advantage will be more obvious for the beams with larger parameter n and spatial coherence δ or under the condition of stronger fluctuation of turbulence. The CGSM beam with larger parameter n or smaller spatial coherence δ will be less affected by the turbulence. In addition, the effects of the slope-parameter α, inner and outer scale and the refractive-index structure constant of the non-Kolmogorov's power spectrum on the propagation factor are also analyzed in detailed.

Optical parametrically gated microscopy in scattering media

High-resolution imaging in turbid media has been limited by the intrinsic compromise between the gating efficiency (removal of multiply-scattered light background) and signal strength in the existing optical gating techniques. This leads to shallow depths due to the weak ballistic signal, and/or degraded resolution due to the strong multiply-scattering background--the well-known trade-off between resolution and imaging depth in scattering samples. In this work, we employ a nonlinear optics based optical parametric amplifier (OPA) to address this challenge. We demonstrate that both the imaging depth and the spatial resolution in turbid media can be enhanced simultaneously by the OPA, which provides a high level of signal gain as well as an inherent nonlinear optical gate. This technology shifts the nonlinear interaction to an optical crystal placed in the detection arm (image plane), rather than in the sample, which can be used to exploit the benefits given by the high-order parametric process and the use of an intense laser field. The coherent process makes the OPA potentially useful as a general-purpose optical amplifier applicable to a wide range of optical imaging techniques.

Electromagnetic sinc Schell-model beams and their statistical properties

A class of electromagnetic sources with sinc Schell-model correlations is introduced. The conditions on source parameters guaranteeing that the source generates a physical beam are derived. The evolution behaviors of statistical properties for the electromagnetic stochastic beams generated by this new source on propagating in free space and in atmosphere turbulence are investigated with the help of the weighted superposition method and by numerical simulations. It is demonstrated that the intensity distributions of such beams exhibit unique features on propagating in free space and produce a double-layer flat-top profile of being shape-invariant in the far field. This feature makes this new beam particularly suitable for some special laser processing applications. The influences of the atmosphere turbulence with a non-Kolmogorov power spectrum on statistical properties of the new beams are analyzed in detail.

Phantom validation of Monte Carlo modeling for noncontact depth sensitive fluorescence measurements in an epithelial tissue model

Experimental investigation and optimization of various optical parameters in the design of depth sensitive optical measurements in layered tissues would require a huge amount of time and resources. A computational method to model light transport in layered tissues using Monte Carlo simulations has been developed for decades to reduce the cost incurred during this process. In this work, we employed the Monte Carlo method to investigate the depth sensitivity achieved by various illumination and detection configurations including both the traditional cone configurations and new cone shell configurations, which are implemented by convex or axicon lenses. Phantom experiments have been carried out to validate the Monte Carlo modeling of fluorescence in a two-layered turbid, epithelial tissue model. The measured fluorescence and depth sensitivity of different illumination–detection configurations were compared with each other. The results indicate excellent agreement between the experimental and simulation results in the trends of fluorescence intensity and depth sensitivity. The findings of this study and the development of the Monte Carlo method for noncontact setups provide useful insight and assistance in the planning and optimization of optical designs for depth sensitive fluorescence measurements.

Long-range polarimetric imaging through fog

We report an experimental implementation of long-range polarimetric imaging through fog over kilometric distance in real field atmospheric conditions. An incoherent polarized light source settled on a telecommunication tower is imaged at a distance of 1.3 km with a snapshot polarimetric camera including a birefringent Wollaston prism, allowing simultaneous acquisition of two images along orthogonal polarization directions. From a large number of acquisitions datasets and under various environmental conditions (clear sky/fog/haze, day/night), we compare the efficiency of using polarized light for source contrast increase with different signal representations (intensity, polarimetric difference, polarimetric contrast, etc.). With the limited-dynamics detector used, a maximum fourfold increase in contrast was demonstrated under bright background illumination using polarimetric difference image.

Evaluation of immunoturbidimetric rheumatoid factor method from Diagam on Abbott c8000 analyzer: comparison with immunonephelemetric method

Rheumatoid factor (RF) consists of autoantibodies and because of its heterogeneity its determination is not easy. Currently, nephelometry and Elisa method are considered as reference methods. Due to consolidation, many laboratories have fully automated turbidimetric apparatus, and specific nephelemetric systems are not always available. In addition, nephelemetry is more accurate, but time consuming, expensive, and requires a specific device, resulting in a lower efficiency. Turbidimetry could be an attractive alternative. The turbidimetric RF test from Diagam meets the requirements of accuracy and precision for optimal clinical use, with an acceptable measuring range, and could be an alternative in the determination of RF, without the associated cost of a dedicated instrument, making consolidation and saving blood possible.

Light focusing and two-dimensional imaging through scattering media using the photoacoustic transmission matrix with an ultrasound array

We implement the photoacoustic transmission matrix approach on a two-dimensional photoacoustic imaging system, using a 15 MHz linear ultrasound array. Using a black leaf skeleton as a complex absorbing structure, we demonstrate that the photoacoustic transmission matrix approach allows to reveal structural features that are invisible in conventional photoacoustic images, as well as to selectively control light focusing on absorbing targets, leading to a local enhancement of the photoacoustic signal.

Sensitivity analysis of multi-layered C-axis inclined zigzag zinc oxide thin-film resonators as viscosity sensors

This paper presents a theoretical analysis of a new zigzag C-axis inclined multi-layer ZnO thin-film bulk acoustic wave resonator (FBAR) as a viscosity sensor to monitor the lubrication performance of engine oil and other liquids. Free vibration and forced vibration for the FBAR loaded with liquids are analyzed. Equations necessary to calculate the sensitivity are derived. The numerical analysis shows that as the number of layers increases, the absolute sensitivity increases as well. The influences on the sensitivity of C-axis inclined angle, Q-factor, and thickness are also investigated. The results provide a foundation for further design of multi-layer FBAR viscosity sensors.

Fast volumetric phase-gradient imaging in thick samples

Oblique back-illumination microscopy (OBM) provides high resolution, sub-surface phase-gradient images from arbitrarily thick samples. We present an image formation theory for OBM and demonstrate that OBM lends itself to volumetric imaging because of its capacity for optical sectioning. In particular, OBM can provide extended depth of field (EDOF) images from single exposures, by rapidly scanning the focal plane with an electrically tunable lens. These EDOF images can be further enhanced by deconvolution. We corroborate our theory with experimental volumetric images obtained from transparent bead samples and mouse cortical brain slices.

High throughput full Stokes Fourier transform imaging spectropolarimetry

A complete full Stokes imaging spectropolarimeter is proposed. Four separate polarized spectra are fed into the Sagnac Fourier transform spectrometer without slit using different angle combinations of the polarized elements. The four polarized spectra are separated without spatial aliasing. And the system has a good performance to resist the instrument noise due to its high light throughput. The mathematical model for the approach is derived and an optimization of the retardance is discussed. For acquiring the four spectra simultaneously, an improved robust polarization modulator using aperture division is outlined. Then the system is discussed in detail including the imaging principle and spectral resolution. Lastly, two proven experiments are carried out and the experimental results in visible light are outlined.

Measurement of the time-resolved reflection matrix for enhancing light energy delivery into a scattering medium

Multiple scatterings occurring in a turbid medium attenuate the intensity of propagating waves. Here, we propose a method to efficiently deliver light energy to the desired target depth in a scattering medium. We measure the time-resolved reflection matrix of a scattering medium using coherent time-gated detection. From this matrix, we derive and experimentally implement an incident wave pattern that optimizes the detected signal corresponding to a specific arrival time. This leads to enhanced light delivery at the target depth. The proposed method will lay a foundation for efficient phototherapy and deep-tissue in vivo imaging in the near future.

Dependent and multiple scattering in transmission and backscattering optical coherence tomography

We use transmission and backscattering optical coherence tomography (OCT) to distinguish and quantify dependent and multiple scattering effects in turbid media. With transmission OCT the dependent scattering coefficients for a range of monodisperse silica particle suspensions are determined. An excellent agreement is observed between the measured dependent scattering coefficients and calculations based on Mie calculations, the Percus-Yevick radial distribution function, and coherent light scattering theory. Backscattering OCT measurements are fitted using the extended Huygens-Fresnel (EHF) model with the dependent scattering coefficients obtained from the transmission OCT measurements as input parameters. Good agreement between the EHF model and the backscattering OCT measurements is observed. For large particles, the rms scattering angle θrms obtained from the EHF fit is in fair agreement with θrms calculated from the transmission OCT data.

Fourier domain multispectral multiple scattering low coherence interferometry

We have implemented multispectral multiple scattering low coherence interferometry (ms2/LCI) with Fourier domain data collection. The ms2/LCI system is designed to localize features with spectroscopic contrast with millimeter resolution up to 1 cm deep in scattering samples by using photons that have undergone multiple low-angle (forward) scattering events. Fourier domain detection both increases the data acquisition speed of the system and gives access to rich spectroscopic information, compared to the previous single channel, time-domain implementation. Separate delivery and detection angular apertures reduce collection of the diffuse background signal in order to isolate localized spectral features from deeper in scattering samples than would be possible with traditional spectroscopic optical coherence tomography. Light from a supercontinuum source is used to acquire absorption spectra of chromophores in the visible range within a tissue-like scattering phantom. An intensity modulation and digital lock-in detection scheme is implemented to mitigate relative intensity and spectral noise inherent in supercontinuum sources. The technical parameters of the system and comparative analysis are presented.

Degeneration of Fraunhofer diffraction on bacterial colonies due to their light focusing properties examined in the digital holographic microscope system

The degeneration of Fraunhofer diffraction conditions in the optical system with converging spherical wave illumination for bacteria species identification based on diffraction patterns is analyzed by digital holographic methods. The obtained results have shown that the colonies of analyzed bacteria species act as biological lenses with the time-dependent light focusing properties, which are characterized and monitored by means of phase retrieval from sequentially captured digital holograms. This significantly affects the location of Fraunhofer patterns observation plane, which is continuously shifted across optical axis in time.

A buoy for continuous monitoring of Suspended Sediment Dynamics

Knowledge of Suspended Sediments Dynamics (SSD) across spatial scales is relevant for several fields of hydrology, such as eco-hydrological processes, the operation of hydrotechnical facilities and research on varved lake sediments as geoarchives. Understanding the connectivity of sediment flux between source areas in a catchment and sink areas in lakes or reservoirs is of primary importance to these fields. Lacustrine sediments may serve as a valuable expansion of instrumental hydrological records for flood frequencies and magnitudes, but depositional processes and detrital layer formation in lakes are not yet fully understood. This study presents a novel buoy system designed to continuously measure suspended sediment concentration and relevant boundary conditions at a high spatial and temporal resolution in surface water bodies. The buoy sensors continuously record turbidity as an indirect measure of suspended sediment concentrations, water temperature and electrical conductivity at up to nine different water depths. Acoustic Doppler current meters and profilers measure current velocities along a vertical profile from the water surface to the lake bottom. Meteorological sensors capture the atmospheric boundary conditions as main drivers of lake dynamics. It is the high spatial resolution of multi-point turbidity measurements, the dual-sensor velocity measurements and the temporally synchronous recording of all sensors along the water column that sets the system apart from existing buoy systems. Buoy data collected during a 4-month field campaign in Lake Mondsee demonstrate the potential and effectiveness of the system in monitoring suspended sediment dynamics. Observations were related to stratification and mixing processes in the lake and increased turbidity close to a catchment outlet during flood events. The rugged buoy design assures continuous operation in terms of stability, energy management and sensor logging throughout the study period. We conclude that the buoy is a suitable tool for continuous monitoring of suspended sediment concentrations and general dynamics in fresh water bodies.

Spectral-domain low-coherence interferometry for phase-sensitive measurement of Faraday rotation at multiple depths

We describe a method for differential phase measurement of Faraday rotation from multiple depth locations simultaneously. A polarization-maintaining fiber-based spectral-domain interferometer that utilizes a low-coherent light source and a single camera is developed. Light decorrelated by the orthogonal channels of the fiber is launched on a sample as two oppositely polarized circular states. These states reflect from sample surfaces and interfere with the corresponding states of the reference arm. A custom spectrometer, which is designed to simplify camera alignment, separates the orthogonal channels and records the interference-related oscillations on both spectra. Inverse Fourier transform of the spectral oscillations in k-space yields complex depth profiles, whose amplitudes and phase difference are related to reflectivity and Faraday rotation within the sample, respectively. Information along a full depth profile is produced at the camera speed without performing an axial scan for a multisurface sample. System sensitivity for the Faraday rotation measurement is 0.86 min of arc. Verdet constants of clear liquids and turbid media are measured at 687 nm.

Aperiodic CrSc multilayer mirrors for attosecond water window pulses

Extending single attosecond pulse technology from currently sub-200 eV to the so called 'water window' spectral range may enable for the first time the unique investigation of ultrafast electronic processes within the core states of bio-molecules as proteins or other organic materials. Aperiodic multilayer mirrors serve as key components to shape these attosecond pulses with a high degree of freedom and enable tailored short pulse pump-probe experiments. Here, we report on chirped CrSc multilayer mirrors, fabricated by ion beam deposition with sub-angstrom precision, designed for attosecond pulse shaping in the 'water window' spectral range.

Simultaneous measurement of the microscopic dynamics and the mesoscopic displacement field in soft systems by speckle imaging

The constituents of soft matter systems such as colloidal suspensions, emulsions, polymers, and biological tissues undergo microscopic random motion, due to thermal energy. They may also experience drift motion correlated over mesoscopic or macroscopic length scales, e.g. in response to an internal or applied stress or during flow. We present a new method for measuring simultaneously both the microscopic motion and the mesoscopic or macroscopic drift. The method is based on the analysis of spatio-temporal cross-correlation functions of speckle patterns taken in an imaging configuration. The method is tested on a translating Brownian suspension and a sheared colloidal glass.

Transverse ionic mobility measured in a dynamic light scattering device

We describe here some novel experiments with a commercial dynamic light scattering device. By inserting a quarter-wave plate in the light beam of the HeNe laser used in the Malvern DLS 'Zetasizer', one can obtain right handed (RH) or left-handed (LH) circularly polarized light from the incoming horizontally polarized laser light. This RH vs LH light is used in the ionic mobility (ζ-potential) measuring mode to detect what we believe are phenomena related to transverse ionic mobility, i.e. speed of a particle (or portions of the particle) as a function of applied static electric field, in directions transverse to those fields, and which, we suggest, arise from surface impedence phenomena related to the (1) parity-biased mechanical flexing of charged molecular moieties at the surface of a chiral particle or of an achiral particle+chiral co-solvents, possibly driven by the electrophoresis field and (2) electro-optic effects (induced currents) arising from the interaction of chiral co-solvents upon the surface of charged colloid particles in the presence of a (high frequency) electric field. Fluctuations of structure induce currents which are chirally biased either in themselves (in a chiral particle) or which 'borrow' chirality from chiral co-solvents conditioning the local high frequency E-field, and advance or retard the scattered phase of RH or LH polarized light. In either case the 'differential mobility' observed is related to the relative extent of motion in internal portions of the colloid particle - i.e. 'floppiness' in the particle.

Photothermal lens spectrometry measurements in highly turbid media

We measured the photothermal lens signal in samples exhibiting high turbidity using a pump-probe scheme. We show that the photothermal lens signal properties remain nearly unchanged up to values of turbidity of 6 cm(-1) despite the signal reduction due to the decrease of excitation power associated to turbidity losses. The signal starts decreasing abruptly for values of turbidity larger than 6 cm(-1). Multiple light scattering yields a reduction of the temperature gradients, which results in a decrease of the effective signal. However, the signal-to-noise ratio remains above 50 for turbidity values of 9 cm(-1), which corresponds to a reduction of light transmission by more than four orders of magnitude. We report on the detection of the photothermal lens signal through a 2 mm layer of organic tissue with a signal-to-noise ratio of about 500. This technique appears promising for imaging applications in organic samples, which usually exhibit high turbidity for visible and near-infrared light.

Estimating the absorption coefficient of the bottom layer in four-layered turbid mediums based on the time-domain depth sensitivity of near-infrared light reflectance

Expanding our previously proposed "time segment analysis" for a two-layered turbid medium, this study attempted to selectively determine the absorption coefficient (μa) of the bottom layer in a four-layered human head model with time-domain near-infrared measurements. The difference curve in the temporal profiles of the light attenuation between an object and a reference medium, which are obtained from Monte Carlo simulations, is divided into segments along the time axis, and a slope for each segment is calculated to obtain the depth-dependent μa(μaseg). The reduced scattering coefficient (μs') of the reference is determined by curve fitting with the temporal point spread function derived from the analytical solution of the diffusion equation to the time-resolved reflectance of the object. The deviation of μaseg from the actual μa is expressed by a function of the ratio of μaseg in an earlier time segment to that in a later segment for mediums with different optical properties and thicknesses of the upper layers. Using this function, it is possible to determine the μa of the bottom layer in a four-layered epoxy resin-based phantom. These results suggest that the method reported here has potential for determining the μa of the cerebral tissue in humans.

Optimized goniometer for determination of the scattering phase function of suspended particles: simulations and measurements

We present simulations and measurements with an optimized goniometer for determination of the scattering phase function of suspended particles. We applied the Monte Carlo method, using a radially layered cylindrical geometry and mismatched boundary conditions, in order to investigate the influence of reflections caused by the interfaces of the glass cuvette and the scatterer concentration on the accurate determination of the scattering phase function. Based on these simulations we built an apparatus which allows direct measurement of the phase function from ϑ=7  deg to ϑ=172  deg without any need for correction algorithms. Goniometric measurements on polystyrene and SiO2 spheres proved this concept. Using the validated goniometer, we measured the phase function of yeast cells, demonstrating the improvement of the new system compared to standard goniometers. Furthermore, the scattering phase function of different fat emulsions, like Intralipid, was determined precisely.

Light Sheet Tomography (LST) for in situ imaging of plant roots

The production of crops capable of efficient nutrient use is essential for addressing the problem of global food security. The ability of a plant's root system to interact with the soil micro-environment determines how effectively it can extract water and nutrients. In order to assess this ability and develop the fast and cost effective phenotyping techniques which are needed to establish efficient root systems, in situ imaging in soil is required. To date this has not been possible due to the high density of scatterers and absorbers in soil or because other growth substrates do not sufficiently model the heterogeneity of a soil's microenvironment. We present here a new form of light sheet imaging with novel transparent soil containing refractive index matched particles. This imaging method does not rely on fluorescence, but relies solely on scattering from root material. We term this form of imaging Light Sheet Tomography (LST). We have tested LST on a range of materials and plant roots in transparent soil and gel. Due to the low density of root structures, i.e. relatively large spaces between adjacent roots, long-term monitoring of lettuce root development in situ with subsequent quantitative analysis was achieved.

Target detection in turbid medium using polarization-based range-gated technology

Range-gated technology is well known for its good reliability, large field of view (FOV) and low cost in target detection through scattering or turbid medium. However, the tail-gating technology suffers from low signal-to-noise ratio in high turbidity levels due to superposition of photons multiply scattered from the medium and that reflected from the target. In this paper, polarization properties of multiply scattered photons emerging from the turbid medium are studied. Results demonstrate that diffusive photons are almost completely depolarized with no diattenuation and retardance. We combined the tail-gated technology with polarization detection method to effectively image in high level of turbidity. This approach showed about two times enhancement in image contrast as compared with the conventional range-gated technology.

Recipes to make organic phantoms for diffusive optical spectroscopy

Three recipes are presented to make tissue constituent-equivalent phantoms of water and lipids. Different approaches to prepare the emulsion are proposed. Nature phantoms are made using no emulsifying agent, but just a professional disperser; instead Agar and Triton phantoms are made using agar or Triton X-100, respectively, as agents to emulsify water and lipids. Different water-to-lipid ratios ranging from 30% to 70% by mass were tested. A broadband time-resolved diffuse optical spectroscopy system was used to characterize the phantoms in terms of optical properties and composition. For some water/lipid ratios the emulsion fails or the phantom has limited lifetime, but in most cases the recipes provide phantoms with a high degree of homogeneity [coefficient of variation (CV) of 4.6% and 1.5% for the absorption and reduced scattering coefficient, respectively] and good reproducibility (CV of 8.3% and 12.4% for absorption and reduced scattering coefficient, respectively).

Identification of the physical mechanism of generation of coherent N2(+) emissions in air by femtosecond laser excitation

Recently, amplification of harmonic-seeded radiation generated through femtosecond laser filamentation in air has been observed, giving rise to coherent emissions at wavelengths corresponding to transitions between different vibrational levels of the electronic B(2)Σ(u)(+) and X(2)Σ(g)(+) states of molecular nitrogen ions [Phys. Rev. A. 84, 051802(R) (2011)]. Here, we carry out systematic investigations on its physical mechanism. Our experimental results do not support the speculation that such excellent coherent emissions could originate from nonlinear optical processes such as four-wave mixing or stimulated Raman scattering, leaving stimulated amplification of harmonic seed due to the population inversion generated in molecular nitrogen ions the most likely mechanism.

High contrast ballistic imaging using femtosecond optical Kerr gate of tellurite glass

We investigated the ballistic imaging technique using femtosecond optical Kerr gate of a tellurite glass. High contrast images of an object hidden behind turbid media were obtained. Compared to the conventional femtosecond optical Kerr gate using fused quartz, the optical Kerr gate using tellurite glass has more capacity to acquire high quality images of the object hidden behind a high optical density turbid medium. The experimental results indicated that the tellurite glass is a good candidate as the optical Kerr material for the ballistic imaging technique due to its large optical nonlinearity.

Radial angular filter arrays for angle-resolved scattering spectroscopy

The radial angular filter array (RAFA) consists of a series of radially-distributed micro-machined channels, where the long axes of the channels converge at a focal point. The high aspect ratio of each channel provides a means to reject photons with trajectories outside the acceptance angle of the channel. The output of the RAFA represents the angular distribution of photons emitted from the focal point. A series of RAFAs were designed, fabricated, and tested to evaluate the impact of device geometry, inter-channel cross talk, achromaticity, and channel leakage on device performance. As an application example, an RAFA was used together with an imaging spectrometer to capture angle-resolved spectra of turbid samples.

Nuclear morphology measurements with angle-resolved low coherence interferometry for application to cell biology and early cancer detection

The study of intact, living cells using non-invasive optical spectroscopic methods offers the opportunity to assess cellular structure and organization in a way that is not possible with commonly used cell biology imaging techniques. We have developed a novel spectroscopic technique for diagnosing disease at the cellular level based on using low-coherence interferometry (LCI) to detect the angular distribution of scattered light. Angle-resolved LCI (a/LCI) combines the ability of LCI to isolate scattering from sub-surface tissue layers with the ability of light scattering spectroscopy to obtain structural information on sub-wavelength scales. In application to examining cellular structure, a/LCI enables quantitative measurements of changes in the size and texture of cell nuclei. These quantitative measurements are characteristic of different pathological states. The capabilities of a/LCI were demonstrated using a clinical system that can be applied in endoscopic surveillance of esophageal tissue, producing high sensitivity and specificity for detecting dysplastic tissues in vivo. Experiments with in vitro cell samples also show the utility of a/LCI in observing structural changes due to environmental stimuli as well as detecting apoptosis due to chemotherapeutic agents.

The relationship between turbidity of mouth-rinsed water and oral health status

OBJECTIVES

The purpose of this study was to examine the relationship between turbidity of mouth rinsed water and oral health status such as dental and periodontal conditions, oral hygiene status, flow rate of saliva and oral bacteria.

MATERIALS AND METHODS

Subjects were 165 patients who visited the Dental Hospital, Tokyo Medical and Dental University. Oral health status, including dental and periodontal conditions, oral hygiene status and flow rate of saliva, was clinically examined. The turbidity was measured with a turbidimeter. Quantification of Fusobacterium spp, Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola and total bacteria levels was performed using real-time PCR. The Pearson correlation and multiple regression analysis were used to explore the associations between the turbidity and oral health parameters.

RESULTS

The turbidity showed significant correlations with the number of decayed teeth and deep pockets, the plaque index, extent of tongue coating and Fusobacterium spp, P. gingivalis, T. forsythia, T. denticola and total bacteria levels. In a multiple regression model, the turbidity was negatively associated with the flow rate of saliva and positively associated with the total number of bacteria (p < 0.001).

CONCLUSION

Current findings suggested that turbidity of mouth rinsed water could be used as an indicator to evaluate oral health condition and the amount of bacteria in the oral cavity. In addition, the turbiditimeter appeared as a simple and objective device for screening abnormality of oral health condition at chair side as well as community-based research.

The use of long-term on-line turbidity measurements for the calculation of urban stormwater pollutant concentrations, loads, pollutographs and intra-event fluxes

This paper presents one of the largest databases on the quality of urban wet weather discharges measured since the development of continuous in-sewer water quality sensors in the late 1990s. Five years of continuous turbidity measurements enabled the validation of 263 and 239 rainfall events, respectively on two experimental catchments in Lyon (France), Chassieu (185 ha separate sewer) and Ecully (245 ha combined sewer). Except for high rainfall events of summer and second half of winter, analysis of database representativeness showed that all seasons were relatively well represented. As a first analysis of the database, traditional tools used in the urban drainage field were applied to assess: i) statistics and analysis of distributions of TSS and COD events loads and event mean concentrations (EMCs) and ii) the correlations between these statistics and events characteristics and iii) M(V) curves describing the intra-event mass distribution. Results showed that: i) EMCs and loads were approximately log-normally distributed, with a clear impact from wastewater contribution in Ecully, ii) EMCs are not correlated with storm event characteristics, whereas loads have shown significant correlation with key storm event variables such as total event volume, rainfall depth, maximum rainfall intensity and discharge and iii) M(V) curves dynamic could be classified in three categories, however with no clear correlation with storm event characteristics. The visual analysis of continuous time series of TSS and COD pollutographs, derived from turbidity time series showed that event pollutographs were highly variable, due to complex interacting processes during and between events, and suggests that further progress in knowledge and modelling of urban wet weather pollutant loads and pollutographs should be based on more detailed analyses of continuous time series rather, than on the traditional single event approach.