Imperfect refractive index matching in scanning laser optical tomography and a method for digital correction

Significance

Scanning laser optical tomography (SLOT) is a volumetric multi-modal imaging technique that is comparable to optical projection tomography and computer tomography. Image quality is crucially dependent on matching the refractive indexes (RIs) of the sample and surrounding medium, but RI matching often requires some effort and is never perfect.

Aim

Reducing the burden of RI matching between the immersion medium and sample in biomedical imaging is a challenging and interesting task. We aim at implementing a post processing strategy for correcting SLOT measurements that have errors caused by RI mismatch.

Approach

To better understand the problems with poorly matched Ris, simulated SLOT measurements with imperfect RI matching of the sample and medium are performed and presented here. A method to correct distorted measurements was developed and is presented and evaluated. This method is then applied to a sample containing fluorescent polystyrene beads and a sample made of olydimethylsiloxane with embedded fluorescent nanoparticles.

Results

From the simulations, it is evident that measurements with an RI mismatch larger than 0.02 and no correction yield considerably worse results compared to perfectly matched measurements. RI mismatches larger than 0.05 make it almost impossible to resolve finer details and structures. By contrast, the simulations imply that a measurement with an RI mismatch of up to 0.1 can still yield reasonable results if the presented correction method is applied. The experiments validate the simulated results for an RI mismatch of about 0.09.

Conclusions

The method significantly improves the SLOT image quality for samples with imperfectly matched Ris. Although the absolutely best imaging quality will be achieved with perfect RI matching, these results pave the way for imaging in SLOT with RI mismatches while maintaining high image quality.

Diagnostic efficacy of hand-held digital refractometer for determining total serum protein in indigenous sheep of Pakistan

The study was designed to ascertain the diagnostic efficacy of hand-held digital refractometer in determining total protein (TP). The Sipli sheep (n = 128) were grouped as per gender (females = 99, males = 29) and age (G1 = up till 1 year, n = 35; G2 = from 1 to 2 years, n = 63; G3 = above 2 years, n = 30). The results regarding the overall mean (±SE) values for the TPs attained through serum chemistry analyzer (TP1) and hand-held digital refractometer (TP2) were non-significantly (P≥0.05) different (59.2±1.6g/L and 59.8±0.5g/L, respectively). However, the reference intervals (RIs) were quite different for the two TPs being 45.1-95.7g/L and 57.0-67.0g/L for TP1 and TP2, respectively. Similar results were seen for gender-wise and group-wise results. On the contrary, the results regarding correlation coefficient and logilinear regression showed a negative correlation between the two TPs (r = -0.0244) with an adjusted r-square of 0.059 (5.9% probability). Furthermore, the three tests implied to assess the level of agreement between the two methods (Cronbach alpha, Intraclass correlation coefficient, and Bland & Altman test) revealed least agreement between the two methods. In a nutshell, the results of TP through digital refractometer were not in concordance with those attained through serum chemistry analyzer. However, it can cautiously be used if these results are compared with relevant corrected RIs.

Light Scattering Method for Aerosol Sizing Based on Machine Learning

Optical scattering has been widely used for aerosol sizing due to its noninvasive and real-time measurement. However, it is crucial to retrieve the particle size distribution (PSD) of aerosols without prior knowledge of the refractive index. Now, it has been a great challenge to measure the refractive index in situ. In this study, a novel PSD sensing method utilizing the light scattering angular spectrum (LSAS) and machine learning techniques is proposed to address this challenge. The complex nonlinear relationship between LSAS and PSD can be constructed while accounting for the refractive index of aerosols. A miniaturized prototype sensor is designed and tested on different sizes of aerosol samples. The experiment results showed that the maximum Kullback-Leibler divergence (DKL) of PSD is 0.07, which indicates that the sensing method can provide the ability for highly accurate aerosol PSD measurement without requiring prior knowledge of the refractive index. The compacted prototype sensor shows great potential for aerosol analysis in conventional field measurements outside the laboratory.

Intracapsular accommodation mechanism in terms of lens curvature gradient

The intracapsular accommodation mechanism (IAM) may be understood as an increase in the lens equivalent refractive index as the eye accommodates. Our goal was to evaluate the existence of an IAM by analysing observed changes in the inner curvature gradient of the lens. To this end, we fitted a gradient index and curvature lens model to published experimental data on external and nucleus geometry changes during accommodation. For each case analysed, we computed the refractive power and equivalent index for each accommodative state using a ray transfer matrix. All data sets showed an increase in the effective refractive index, indicating a positive IAM, which was stronger for older lenses. These results suggest a strong dependence of the lens equivalent refractive index on the inner curvature gradient.

An integrated model of the human cornea as a linear biaxial birefringent medium

A novel model of human corneal birefringence is presented. The cornea is treated as a homogeneous biaxial linear birefringent medium in which the values of the binormal axes angle and organization of the main refractive indices vary continuously from the apex to the limbus. In its central part, the angle between binormal axes is 35°, and para centrally, it smoothly increases to 83.7°. The values of the main refractive indices (nx, ny, nz) change, as well as their order, from nx < nz < ny to nz < nx < ny. The transition between these two states was described with a normal distribution (μ = 0.45, σ = 0.1). The presented model corresponds with the experimental results presented in the literature. To our knowledge, it is the first model that presents the anisotropic properties' distributions of the entire cornea. The presented model facilitates a better understanding of the corneal birefringence phenomenon directly related to its lamellar structure.

Quantitation of polyethylene glycol by size exclusion chromatography with charged aerosol, differential refractive index, and multi-angle light scattering detectors

Polyethylene glycol (PEG) has found tremendous applications in pharmaceutical products and has played a critical role in PEGylated drug modalities to improve pharmacokinetic properties and biological efficacy. The characterization and quantitation of PEGs are essential to control manufacture process and drug product quality. However, the assay value of PEG could change dramatically depending on the structures of the PEG and the detection techniques used. In this study, we developed a size exclusion chromatographic (SEC) method for quantitative PEG analysis, and we systematically evaluated the performance of three online detectors with different operating principles: a charged aerosol detector (CAD), a differential refractive index (dRI) detector, and a multi-angle light scattering detector (MALS). Fourteen PEG compounds covering a wide range of molecular weight (MW, 1 - 40 kDa) and molecular architectures (linear, branched, Y-shaped and multi-arm geometries) were evaluated by these three detection techniques. Our study revealed that the dRI showed the most universal responses among all the PEGs regardless of their molecular weight or geometries. In the contrast, CAD and MALS detector showed MW-dependent and semi-universal geometry-dependent responses. Another key finding is that the relative response factor for each multi-arm PEG in the CAD and the MALS were inversely correlated, suggesting both can be applied to qualitatively assess polymers of different architectures, including the ones with subtle differences in their core structures. The comparison of the three detectors not only provides the fundamental and comprehensive understanding of PEG quantitation but also enables the process development and control of high-quality PEGs in producing PEGylated therapeutics in the pharmaceutical industry.

Assessing failure of transfer of passive immunity by gamma-glutamyl-transferase activity and serum refractometry in holstein-friesian calves affected by neonatal diarrhea

Hardly published data are available to diagnose the failure of transfer of passive immunity (FTPI) in calves affected by neonatal calf diarrhea (NCD). This study evaluated the diagnostic performance and differences among optical serum total protein (STP) concentration and gamma-glutamyl-transferase (GGT) activity for assessing FTPI in diarrheic Holstein Friesian calves. 72 diarrheic and 19 healthy Holstein Friesian calves aged 1 to 10 days were enrolled. Each calf underwent a complete clinical examination and dehydration assessment. The effect of dehydration status and age on the correlation between the two methods under study (STP and GGT) and the gold standard (Immunoglobulin G [IgG] measured with RID) was investigated with Spearman's correlation index R for ranks. Serum total protein concentration and GGT activity were analyzed by receiver operating characteristic (ROC) curve analysis to identify the optimal cut-off point to distinguish between diarrheic calves with or without FTPI, also considering the effects of dehydration and age. The results show that GGT activity was affected by the age of calves, while STP was influenced by dehydration. The cut-offs to distinguish calves with IgG < 10 g/L were < 52 g/L of STP in normohydrated calves, < 58 g/L of STP in dehydrated calves, and < 124 IU/L of GGT in calves with aged between 3 and 10 days. In nondehydrated diarrheic calves, the STP refractometer showed better diagnostic accuracy.In dehydrated calves aged between 3 and 10 days, however, its accuracy drops, and it is advisable to use GGT activity.

Refractive index of human articular cartilage varies with tissue structure and composition

Optical properties of biological tissues, such as refractive index, are fundamental properties, intrinsically linked to a tissue's composition and structure. This study aims to investigate the variation of refractive index (RI) of human articular cartilage along the tissue depth (via collagen fibril orientation and optical density) and integrity (based on Mankin and Osteoarthritis Research Society International (OARSI) scores). The results show the relationship between RI and PG content (p=0.042), collagen orientation (p=0.037), and OARSI score (p=0.072). When taken into account, the outcome of this study suggests that the RI of healthy cartilage differs from that of pathological cartilage (p=0.072). This could potentially provide knowledge on how progressive tissue degeneration, such as osteoarthritis, affects changes in cartilage RI, which can, in turn, be used as a potential optical biomarker of tissue pathology.

Correlations of multimode optical incidences in a turbulent biological tissue

In a turbulent biological tissue, field correlations at the observation plane are found when a multimode optical incidence is used. For different multimode structures, variations of the multimode field correlations are evaluated against the biological tissue turbulence parameters, i.e., the strength coefficient of the refractive-index fluctuations, fractal dimension, characteristic length of heterogeneity, and the small length-scale factor. Using a chosen multimode content, for specific biological tissue types of liver parenchyma (mouse), intestinal epithelium (mouse), upper dermis (human), and deep dermis (mouse), field correlations are evaluated versus the strength coefficient of the refractive-index fluctuations and small length-scale factor. Again, with a chosen multimode content, behavior of the field correlations is studied against the strength coefficient of the refractive-index fluctuations for various diagonal lengths and the transverse coordinate at the observation plane. Finally, the field correlation versus the strength coefficient of the refractive-index fluctuations is reported for different single modes, which are special cases of multimode excitation. This topic is being reported in the literature for the first time, to our knowledge, and the presented results can be employed in many important biological tissue applications.

Tapered Fiber Bioprobe Based on U-Shaped Fiber Transmission for Immunoassay

In this paper, a tapered fiber bioprobe based on Mach-Zehnder interference (MZI) is proposed. To retain the highly sensitive straight-tapered fiber MZI sensing structure, we designed a U-shaped transmission fiber structure for the collection of optical sensing signals to achieve a miniature-insert-probe design. The spectrum responses from the conventional straight-tapered fiber MZI sensor and our proposed sensor were compared and analyzed, and experimental results showed that our proposed sensor not only has the same sensing capability as the straight-tapered fiber sensor, but also has the advantages of being flexible, convenient, and less liquid-consuming, which are attributed to the inserted probe design. The tapered fiber bioprobe obtained a sensitivity of 1611.27 nm/RIU in the refractive index detection range of 1.3326-1.3414. Finally, immunoassays for different concentrations of human immunoglobulin G were achieved with the tapered fiber bioprobe through surface functionalization, and the detection limit was 45 ng/mL. Our tapered fiber bioprobe has the insert-probe advantages of simpleness, convenience, and fast operation. Simultaneously, it is low-cost, highly sensitive, and has a low detection limit, which means it has potential applications in immunoassays and early medical diagnosis.

Comparison of turbidometric immunoassay and brix refractometry to radial immunodiffusion for assessment of colostral immunoglobulin concentration in beef cattle

BACKGROUND

Colostral immunoglobulin G (IgG) concentration is critical to the attainment of adequate transfer of passive immunity in cattle, however, studies comparing available tools for measurement of colostral IgG concentration in beef cattle are limited.

OBJECTIVES

To report the agreement between 3 commercially available tests for evaluating IgG concentration in beef colostrum.

ANIMALS

Two hundred six beef-breed cows hospitalized for calving management or dystocia.

METHODS

Retrospective study to assess IgG of whole colostrum measured stall-side via turbidimetric immunoassay (TI) and brix refractometry (BRIX), compared to fat separated (FS) analysis via single radial-immunodiffusion (RID; reference standard), TI-FS and BRIX-FS. Test performance was assessed using Passing Bablock regression, Bland-Altman analysis, and area under the curve to determine optimal thresholds.

RESULTS

Correlation between RID and TI-FS, BRIX-FS, or BRIX was similar (Spearman's ρ = 0.717, 0.715, 0.716, respectively) but correlation for TI was poor (ρ = 0.586). Regression analysis identified a substantial constant (-214.75 [CI: -272.03 to -178.07]) and proportional (13.24 [CI: 11.81-15.37]) bias between the RID and TI-FS which was similar for TI. TI-FS concentrations of 28.47, 38.75, and 50.62 g/L, BRIX-FS of ≤21.9%, ≤24.0%, and ≤27.4%, and BRIX of ≤21.3%, ≤23.8%, and ≤26.4% indicated IgG concentrations <50, <100, and <150 g/L, respectively; appropriate cutoffs for TI could not be generated.

CONCLUSIONS AND CLINICAL IMPORTANCE

Both TI and TI-FS demonstrated a large constant and proportional bias compared to RID; BRIX and BRIX-FS were well correlated with RID and remain a reliable method for estimation of colostral IgG concentration in beef cattle.

Comparison of turbidometric immunoassay, refractometry, and gamma-glutamyl transferase to radial immunodiffusion for assessment of transfer of passive immunity in high-risk beef calves

BACKGROUND

Attainment of adequate transfer of passive immunity (TPI) is critical to health of calves; however, studies comparing available tools for measurement of TPI in individual beef animals are limited.

OBJECTIVES

To report agreement between 4 tests evaluating individual TPI status in beef calves.

ANIMALS

One hundred ninety-six beef calves born to cows and heifers presenting for calving management or dystocia.

METHODS

Retrospective study to assess serum immunoglobulin (IgG) concentrations via turbidimetric immunoassay (TI), gamma-glutamyl transferase (GGT), serum total protein (TP), and single radial immunodiffusion (RID; reference standard). Test agreement was evaluated using Passing-Bablok regression, Bland-Altman analysis, Cohen's kappa, and receiver operating characteristic (ROC) curves with and without covariate adjustment to determine optimal thresholds.

RESULTS

Correlation between RID and test results varied: TI, ρ = 0.757; TP, ρ = 0.715; GGT: ρ = 0.413. For the TI compared to RID, regression analysis identified a constant (intercept = -0.51 [CI: -2.63, 3.05]) and proportional (slope = 1.87 [CI: 1.69, 2.08]) bias. Based on ROC, TI concentrations of ≤9.89 and ≤13.76 g/L, and TP concentrations of ≤5.5 and ≤6.0 g/dL, indicated IgG concentrations <18.0 and <25.0 g/L, respectively.

CONCLUSIONS AND CLINICAL IMPORTANCE

Within this cohort of calves, TI demonstrated the best correlation with RID; however, significant bias was identified which led to frequent underestimation of IgG concentration. Serum total protein demonstrated less correlation with RID but had less misclassification than TI. Both TI and TP demonstrated less correlation for calves that received colostrum replacement prompting clinical awareness of colostrum type when evaluating individual TPI in beef calves.

Chromatic dispersion of soft contact lens materials

PURPOSE

To investigate and evaluate the chromatic dispersion of various hydrogel and silicon hydrogel contact lens materials.

METHODS

Eighteen different soft contact lens materials with high and low water content in lens power of -1.00 DS were measured by one operator at temperature of 20 °C ± 0.5° soaked in ISO standard phosphate-buffered saline (PBS) and in their respective packaging solutions (PS). An analogue Abbe refractometer (Model Zuzi 320, AUXILAB, S.L., Navarra, Spain) was used for refractive index (RI) measurements at 5 different wavelengths. All contact lenses were presented in a random and masked order to the operator. The Bland-Altman method with 95 % limits of agreement (LoA) and coefficient of repeatability (CoR) was used to characterise the repeatability of refractive index measurements. The Abbe numbers for each material were calculated by entering the measured and interpolated refractive indices into the Abbe number equation. One-way ANOVA analysis was used to test if there were significant differences between the 5 different wavelengths (470 nm-680 nm) within each material. An unpaired t-test was used to determine if there were differences in refractive index or dispersion between packaging solution and PBS results.

RESULTS

Nelfilcon A (Dailies Aqua Comfort Plus) soaked in PS showed the best repeatability of all 18 examined soft contact lenses across all wavelengths with an average refractive index of 1.3848 for all 6 contact lenses with a standard deviation of 0.00064. The 95 % limits of agreement were between 1.3835 and 1.3860. The mean coefficient of repeatability for nelfilcon A was 0.00125. For contact lenses soaked in ISO Standard PBS comfilcon A (Biofinity) had the best repeatability. The average refractive index of all 6 contact lenses was 1.4041 with a standard deviation of 0.00031 and a coefficient of repeatability of 0.00060. The 95 % limits of agreement were between 1.4035 and 1.4047. The analysis with One-way ANOVA with multiple comparisons involving Holm-Sidak post-hoc, showed that there are significant differences (p < 0.001, Fratio = 376.2 between wavelengths and Fratio = 1559 between different refractive indices) in the refractive index of most common lens materials across the visible wavelength range. Based on unpaired t-test, there is no significant difference (p > 0.05) in the Abbe numbers of the tested lens materials whether they have been placed in the packaging solution or in standard PBS (p > 0.05, 95 % CI = -4.8070 to 5.8680, t = 0.2054). The Abbe numbers for the calculated contact lenses soaked in PS ranged between 43.7 and 89.9. For contact lenses stored in PBS the range was between 46.3 and 81.6.

CONCLUSION

There is a good repeatability between repeated RI measurements taken from the same lens and from the same material. The significant differences between the refractive indices across the 5 different wavelengths showed the presence of chromatic dispersion in the 18 evaluated soft contact lens materials. Furthermore, it could be shown that there is no significant difference in dispersion whether the contact lenses are soaked in standard PBS or in their respective packaging solutions. With no other published data available as a reference, absolute accuracy of the calculated Abbe numbers remains to be confirmed, however, this study did confirm that significant chromatic dispersion exists in soft contact lens materials.

Changes in serum total protein and immunoglobulin G concentrations and Brix percentages in neonatal Arabian foals from birth up to 21 days of age

The aim of this study was to evaluate changes in the serum immunoglobulin G (IgG) and serum total protein (STP) concentrations and serum Brix percentages of neonatal Arabian foals during first 3 weeks of life. Blood samples were collected from 12 apparently healthy foals by jugular venipuncture at birth and at 12-hours, 24-hours, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15 and 21 days of age. Serum IgG and STP concentrations and Brix percentages were measured by the radial immunodiffusion assay, and digital STP and Brix refractometers, respectively. Based on the serum IgG concentrations measured at 24 h, two foals were diagnosed with failure of transfer of passive immunity (FTPI). While IgG concentrations were determined using the data of foals with adequate transfer of passive immunity, other calculations were made using the data of all foals. The mean IgG concentration of the foals increased from birth (<200 mg/dl) to 12 (2068.5 mg/dl) and 24 h (2184.7 mg/dl), and progressively decreased up to 21 days of age (1318.5 mg/dl). The serum IgG concentrations at 12 h were highly correlated with each of the IgG concentrations measured over the 21-day period. The serum IgG and STP concentrations and Brix percentages of the foals diagnosed with FTPI at 12 h did not reach the adequate strata over time. These results suggest that foals can be reliably tested for passive immunity status at 12 h after birth.

Structure functions for optical waves in a complex medium of turbulent biological tissues

Although optical wave propagation is investigated based on the absorption and scattering in biological tissues, the turbulence effect can also not be overlooked. Here, the closed-form expressions of the wave structure function (WSF) and phase structure function (PSF) of plane and spherical waves propagating in biological tissue are obtained to help with future research on imaging, intensity, and coherency in turbulent biological tissues. This paper presents the effect of turbulent biological tissue on optical wave propagation to give a perception of the performance of biomedical systems that use optical technologies. The behavior of optical waves in different types of turbulent biological tissues such as a liver parenchyma (mouse), an intestinal epithelium (mouse), a deep dermis (mouse), and an upper dermis (human) are investigated and compared. It is observed that turbulence becomes more effective with an increase in the characteristic length of heterogeneity, propagation distance, and the strength of the refractive index fluctuations. However, an increase in the fractal dimension, wavelength, and small length scale factor has a smaller turbulence effect on the propagating optical wave. We envision that our results may be used to interpret the performance of optical medical systems operating in turbulent biological tissues.

Long Period Grating Mach-Zehnder Interferometer Based Immunosensor with Temperature and Bulk Refractive Index Compensation

A long period grating Mach-Zehnder interferometer (LPGMZI) that consists of two identical long period gratings (LPGs) in a single fibre was developed to measure immunoglobulin M (IgM). The measured spectrum has fringes due to the interference between the core mode and cladding mode. This immunosensor inherits the advantages of an LPG and has the potential to compensate for unwanted signal changes due to bulk refractive index (RI) and temperature fluctuations by analysing interference fringes and their envelope. The external RI was measured from 1.3384 to 1.3670 in two different cases: (i) only the connecting section between the two LPGs is immersed or (ii) the whole LPGMZI is immersed. The fringes shift with an external RI in both scenarios, whereas the envelope stays still in case (i) or shifts at the same rate as the fringes in case (ii). The LPGMZI was also characterised at different temperatures between 25 °C and 30 °C by placing the whole LPGMZI in a water bath. The fringes and envelope shift at the same rate with temperature. The LPGMZI platform was then used to create an IgM immunosensor. The connecting section between the two LPGs was functionalised with anti-IgM and immersed into solutions with IgM concentrations from 20 μg/mL to 320 μg/mL. The fringes shift with IgM concentration and the envelope remains static. The results from this work show that LPGMZI has the potential to compensate for the temperature and bulk RI fluctuations and perform as a portable biosensor platform.

Wedged Fiber Optic Surface Plasmon Resonance Sensor for High-Sensitivity Refractive Index and Temperature Measurements

Here, we experimentally demonstrate a wedged fiber optic surface plasmon resonance (SPR) sensor enabling high-sensitivity temperature detection. The sensing probe has a geometry with two asymmetrical bevels, with one inclined surface coated with an optically thin film supporting propagating plasmons and the other coated with a reflecting metal film. The angle of incident light can be readily tuned through modifying the beveled angles of the fiber tip, which has a remarkable impact on the refractive index sensitivity of SPR sensors. As a result, we measure a high refractive index sensitivity as large as 8161 nm/RIU in a wide refractive index range of 1.333-1.404 for the optimized sensor. Furthermore, we carry out a temperature-sensitivity measurement by packaging the SPR probe into a capillary filled with n-butanol. This showed a temperature sensitivity reaching up to -3.35 nm/°C in a wide temperature range of 20 °C-100 °C. These experimental results are well in agreement with those obtained from simulations, thus suggesting that our work may be of significance in designing reflective fiber optic SPR sensing probes with modified geometries.

Quantifiable Effect of Interparticle Plasmonic Coupling on Sensitivity and Tuning Range for Wavelength-Mode LSPR Fiber Sensor Fabricated by Simple Immobilization Method

Herein a gold nanosphere (AuNS)-coated wavelength-mode localized surface plasmon resonance (LSPR) fiber sensor was fabricated by a simple and time-saving electrostatic self-assembly method using poly(allylamine hydrochloride). Based on the localized enhanced coupling effect between AuNSs, the LSPR spectrums of the AuNS monolayer with good dispersity and high density exhibited a favourable capability for refractive index (RI) measurement. Based on the results obtained from the optimization for AuNS distribution, sensing length, and RI range, the best RI sensitivity of the fiber modified by 100 nm AuNS reached up to about 2975 nm/RIU, with the surrounding RI range from 1.3322 to 1.3664. Using an 80 nm AuNS-modified fiber sensor, the RI sensitivity of 3953 nm/RIU was achieved, with the RI range increased from 1.3744 to 1.3911. The effect of sensing length to RI sensitivity was proven to be negligible. Furthermore, the linear relationship between the RI sensitivity and plasma resonance frequency of the bulk metal, which was dependent on the interparticle plasmon coupling effect, was quantified. Additionally, the resonance peak was tuned from 539.18 nm to 820.48 nm by different sizes of AuNSs-coated fiber sensors at a RI of 1.3322, which means the spectrum was extended from VIS to NIR. It has enormous potential in hypersensitive biochemistry detection at VIS and NIR ranges.

Quantitative phase imaging based on polarization encoding

Most optical characterization methods rely on measuring the complex optical fields emerging from the interaction between light and material systems. Nevertheless, inherent scattering and absorption cause ambiguities in both interferometric and noninterferometric attempts to measure phase. Here we demonstrate that the complete information about a probe optical field can be encoded into the states of polarization, and develop a topography measurement method by blindly varying the ambient refractive index surrounding the sample in a wedged cuvette, which is capable of simultaneously measuring the thickness and the ambient refractive index of the sample in real time, as well as extending the measurement range of the sample thickness. With the method, we have successfully measured the topography of a 136.7 µm thick coverslip by blindly changing the ambient refractive index by 0.001246, resulting in the thickest sample characterization ever achieved by quantitative phase imaging, to the best of our knowledge. An efficient and complete characterization of optical fields is critical for any high-resolution imaging approach and the technique demonstrated here should prove attractive for applications ranging from microscopy to remote sensing. Thanks to the high precision and fast response speed, this method may pave a new way for measuring the topography of the thick samples, such as biological tissues.

Spatial-Division Multiplexing Approach for Simultaneous Detection of Fiber-Optic Ball Resonator Sensors: Applications for Refractometers and Biosensors

Fiber-optic ball resonators are an attractive technology for refractive index (RI) sensing and optical biosensing, as they have good sensitivity and allow for a rapid and repeatable manufacturing process. An important feature for modern biosensing devices is the multiplexing capacity, which allows for interrogating multiple sensors (potentially, with different functionalization methods) simultaneously, by a single analyzer. In this work, we report a multiplexing method for ball resonators, which is based on a spatial-division multiplexing approach. The method is validated on four ball resonator devices, experimentally evaluating both the cross-talk and the spectral shape influence of one sensor on another. We show that the multiplexing approach is highly efficient and that a sensing network with an arbitrary number of ball resonators can be designed with reasonable penalties for the sensing capabilities. Furthermore, we validate this concept in a four-sensor multiplexing configuration, for the simultaneous detection of two different cancer biomarkers across a widespread range of concentrations.

DeepOrientation: convolutional neural network for fringe pattern orientation map estimation

Fringe pattern based measurement techniques are the state-of-the-art in full-field optical metrology. They are crucial both in macroscale, e.g., fringe projection profilometry, and microscale, e.g., label-free quantitative phase microscopy. Accurate estimation of the local fringe orientation map can significantly facilitate the measurement process in various ways, e.g., fringe filtering (denoising), fringe pattern boundary padding, fringe skeletoning (contouring/following/tracking), local fringe spatial frequency (fringe period) estimation, and fringe pattern phase demodulation. Considering all of that, the accurate, robust, and preferably automatic estimation of local fringe orientation map is of high importance. In this paper we propose a novel numerical solution for local fringe orientation map estimation based on convolutional neural network and deep learning called DeepOrientation. Numerical simulations and experimental results corroborate the effectiveness of the proposed DeepOrientation comparing it with a representative of the classical approach to orientation estimation called combined plane fitting/gradient method. The example proving the effectiveness of DeepOrientation in fringe pattern analysis, which we present in this paper, is the application of DeepOrientation for guiding the phase demodulation process in Hilbert spiral transform. In particular, living HeLa cells quantitative phase imaging outcomes verify the method as an important asset in label-free microscopy.

Study on a terahertz biosensor based on graphene-metamaterial

The interaction between the terahertz wave propagating in free space and the sample is weak, which leads to the weak signal of the sample, which cannot meet the detection needs of trace samples. In order to meet the detection of trace samples, a kind of metamaterial absorber (the basic unit of the absorber is composed of gold-high resistance silicon-aluminum three-layer structure) is designed, and the monolayer graphene is transferred on the surface of the metamaterial absorber to construct the graphene-metamaterial absorber heterostructure. The transmission spectrum of the resonant cavity is simulated and measured by terahertz time domain spectroscopy system, and the obvious resonance frequency shift is observed. The results show that the graphene-metamaterial absorber heterostructure can detect josamycin antibiotic solution with concentration of 0.02 mg/L (the mass of josamycin is 0.2 ng). Compared with using the same structure metamaterial absorber to detect josamycin antibiotics, the sensitivity is increased by an order of magnitude. Using graphene-metamaterial heterostructure to detect the relative change of heterostructure reflectivity caused by josamycin antibiotics can reach 40%. The research in this paper provides a new technical means for accurate and rapid detection in terahertz band.

Optical Strain Gauge Prototype Based on a High Sensitivity Balloon-like Interferometer and Additive Manufacturing

An optical strain gauge based on a balloon-like interferometer structure formed by a bent standard single-mode fiber combined with a 3D printer piece has been presented and demonstrated, which can be used to measure displacement. The interferometer has a simple and compact size, easy fabrication, low cost, and is repeatable. The sensor is based on the interference between the core and cladding modes. This is caused by the fiber's curvature because when light propagates through the curved balloon-shaped interferometer region, a portion of it will be released from the core limitation and coupled to the cladding. The balloon has an axial displacement as a result of how the artwork was constructed. The sensor head is sandwiched between two cantilevers such that when there is a displacement, the dimension associated with the micro bend is altered. The sensor response as a function of displacement can be determined using wavelength shift or intensity change interrogation techniques. Therefore, this optical strain gauge is a good option for applications where structure displacement needs to be examined. The sensor presents a sensitivity of 55.014 nm for displacement measurements ranging from 0 to 10 mm and a strain sensitivity of 500.13 pm/μϵ.

High-fidelity intensity diffraction tomography with a non-paraxial multiple-scattering model

We propose a novel intensity diffraction tomography (IDT) reconstruction algorithm based on the split-step non-paraxial (SSNP) model for recovering the 3D refractive index (RI) distribution of multiple-scattering biological samples. High-quality IDT reconstruction requires high-angle illumination to encode both low- and high- spatial frequency information of the 3D biological sample. We show that our SSNP model can more accurately compute multiple scattering from high-angle illumination compared to paraxial approximation-based multiple-scattering models. We apply this SSNP model to both sequential and multiplexed IDT techniques. We develop a unified reconstruction algorithm for both IDT modalities that is highly computationally efficient and is implemented by a modular automatic differentiation framework. We demonstrate the capability of our reconstruction algorithm on both weakly scattering buccal epithelial cells and strongly scattering live C. elegans worms and live C. elegans embryos.

Simultaneous measurement of displacement and temperature using a balloon-like hybrid fiber sensor

A fiber sensor based on a silica capillary in a balloon-like shape for simultaneous measurement of displacement and temperature is proposed and experimentally demonstrated. The sensor is fabricated by splicing a segment of a hollow-core fiber between two single-mode fibers (SMF) and by creating a balloon shape with the capillary at the top-center position. The SMF-capillary-SMF configuration excites an antiresonant (AR) guidance, and the balloon shape enhances the Mach-Zehnder interferometer (MZI). Experimental results show that, for a balloon length of 4.0 cm and a capillary length of 1.2 cm, the AR is insensitive to displacement and its sensitivity to temperature is 14.3 pm/°C, while the MZI has a sensitivity to displacement of 1.68 nm/mm in the range between 0 and 5 mm and a sensitivity to temperature of 28.6 pm/°C, twice the value of the AR. The proposed fiber sensor has only one sensing element in one configuration, which makes it simple to fabricate as well as low cost.

Route to flexible metamaterial terahertz biosensor based on multi-resonance dips

A flexible terahertz (THz) metamaterial biosensor is theoretically and experimentally investigated. The metamaterial unit cell of the periodic structure array was simply composed of three non-overlapping cut wires with different length parameters on a flexible thin-film (parylene-C) to improve sensitivity. The biosensor sample was fabricated using a lithography process and characterized by a THz time-domain spectroscopy (TDS) system. The metamaterial exhibited multi-resonance dips in transmission spectrum at 0.6-2.0 THz, which can self-correct errors in biosensing. Numerical results show that the Q-factor, figure of merit (FOM) and sensitivity can change in dynamic ranges with the geometric parameters (space and width) of three-cut-wire metamaterial. When space distance was 40 µm and other parameters were default, the sensitivity, FOM and Q-factor reached 710 GHz/RIU (Refractive Index Unit), 9, and 20, respectively. Therefore, through proper design and preparation, the metamaterial can be applied to biochemical detection.

Advances in Waveguide Bragg Grating Structures, Platforms, and Applications: An Up-to-Date Appraisal

A Bragg grating (BG) is a one-dimensional optical device that may reflect a specific wavelength of light while transmitting all others. It is created by the periodic fluctuation of the refractive index in the waveguide (WG). The reflectivity of a BG is specified by the index modulation profile. A Bragg grating is a flexible optical filter that has found broad use in several scientific and industrial domains due to its straightforward construction and distinctive filtering capacity. WG BGs are also widely utilized in sensing applications due to their easy integration and high sensitivity. Sensors that utilize optical signals for sensing have several benefits over conventional sensors that use electric signals to achieve detection, including being lighter, having a strong ability to resist electromagnetic interference, consuming less power, operating over a wider frequency range, performing consistently, operating at a high speed, and experiencing less loss and crosstalk. WG BGs are simple to include in chips and are compatible with complementary metal-oxide-semiconductor (CMOS) manufacturing processes. In this review, WG BG structures based on three major optical platforms including semiconductors, polymers, and plasmonics are discussed for filtering and sensing applications. Based on the desired application and available fabrication facilities, the optical platform is selected, which mainly regulates the device performance and footprint.

Full-Stokes Retrieving and Configuration Optimization in a Time-Integration Imaging Polarimeter

A time-integration imaging polarimeter with continuous rotating retarder is presented, and its full-Stokes retrieving and configuration optimization are also demonstrated. The mathematical expression between the full-Stokes vector and the time-integration light intensities is derived. As a result, the state of polarization of incident light can be retrieved by only one matrix calculation. However, the modulation matrix deviates from the initial well-conditioned status due to time integration. Thus, we re-optimize the nominal angles for the special retardance of 132° and 90° with an exposure angle of 30°, which results in a reduction of 31.8% and 16.8% of condition numbers comparing to the original configuration, respectively. We also give global optimization results under different exposure angles and retardance of retarder; as a result, the 137.7° of retardance achieves a minimal condition number of 2.0, which indicates a well-conditioned polarimeter configuration. Besides, the frame-by-frame algorithm ensures the dynamic performance of the presented polarimeter. For a general brushless DC motor with a rotating speed of over 2000 rounds per minute, the speed of polarization imaging will achieve up to 270 frames per second. High precision and excellent dynamic performance, together with features of compactness, simplicity, and low cost, may give this traditional imaging polarimeter new life and attractive prospects.

Terahertz Metamaterial Sensor for Sensitive Detection of Citrate Salt Solutions

Citrate salts (CSs), as one type of organic salts, have been widely used in the food and pharmaceutical industries. Accurate and quantitative detection of CSs in food and medicine is very important for health and safety. In this study, an asymmetric double-opening ring metamaterial sensor is designed, fabricated, and used to detect citrate salts combined with THz spectroscopy. Factors that influence the sensitivity of the metamaterial sensor including the opening positions and the arrangement of the metal opening ring unit, the refraction index and the thickness of the analyte deposited on the metamaterial sensor were analyzed and discussed from electromagnetic simulations and THz spectroscopy measurements. Based on the high sensitivity of the metamaterial sensor to the refractive index of the analyte, six different citrate salt solutions with low concentrations were well identified. Therefore, THz spectroscopy combined with a metamaterials sensor can provide a new, rapid, and accurate detection of citrate salts.

Effects of water salinity on the multi-angular polarimetric properties of light reflected from smooth water surfaces

Salinity is an important environmental factor regulating the aquatic system structure of lakes and other water bodies. Changes in salinity, which can be caused by human activities, can adversely impact the life of water organisms. The refractive index, which can be directly related to water salinity, also controls the polarimetric properties of light reflected from the water surface. In this study, polarimetric measurements of smooth water surfaces with different salinity content were performed at different viewing zenith angles in the wavelength range of 450-1000 nm in the specular reflection directions. The results show that the light reflected from the water surface (defined as reflectance factor) in one measurement direction can be replaced by the reflectance factor derived from polarimetric measurements, and if the polarizer absorptance is considered, the average relative difference is less than 3%. The degree of linear polarization (DOLP) was used to retrieve the refractive indices of water with different salinities based on the Fresnel reflection coefficient. The inverted refractive indices not only have high accuracy (uncertainty from 0.9% to 1.8%) but also have a very strong relationship with the water salinity content. Our study shows the possibility of estimating the variation in water salinity using multi-angular polarimetric measurements.

Real-time and high-sensitivity refractive index sensing with an arched optofluidic waveguide

Refractive index (RI) sensing plays an important role in analytical chemistry, medical diagnosis, and environmental monitoring. The optofluidic technique is considered to be an ideal tool for RI sensor configuration for its high integration, high sensitivity, and low cost. However, it remains challenging to achieve RI measurement in real time with high sensitivity and low detection limit (DL) simultaneously. In this work, we design and fabricate a RI sensor with an arched optofluidic waveguide by monitoring the power loss of the light passing through the waveguide, which is sandwiched by the air-cladding and the liquid-cladding under test, we achieve RI detection of the sample in real time and with high sensitivity. Furthermore, both numerical simulation and experimental investigation show that our RI sensor can be designed with different geometric parameters to cover multiple RI ranges with high sensitivities for different applications. Experimental results illustrate that our sensor is capable to achieve a superior sensitivity better than -19.2 mW/RIU and a detection limit of 5.21×10^-8 RIU in a wide linear dynamic range from 1.333 to 1.392, providing a promising solution for real-time and high-sensitivity RI sensing.

Dual-wavelength surface plasmon resonance holographic microscopy for simultaneous measurements of cell-substrate distance and cytoplasm refractive index

Studying the basic characteristics of living cells is of great significance in biological research. Bio-physical parameters, including cell-substrate distance and cytoplasm refractive index (RI), can be used to reveal cellular properties. In this Letter, we propose a dual-wavelength surface plasmon resonance holographic microscopy (SPRHM) to simultaneously measure the cell-substrate distance and cytoplasm RI of live cells in a wide-field and non-intrusive manner. Phase-contrast surface plasmon resonance (SPR) images of individual cells at wavelengths of 632.8 nm and 690 nm are obtained using an optical system. The two-dimensional distributions of cell-substrate distance and cytoplasm RI are then demodulated from the phase-contrast SPR images of the cells. MDA-MB-231 cells and IDG-SW3 cells are experimentally measured to verify the feasibility of this approach. Our method provides a useful tool in biological fields for dual-parameter detection and characterization of live cells.

A Review of Sensitivity Enhancement in Interferometer-Based Fiber Sensors

Optical fiber sensors based on an interferometer structure play a significant role in monitoring physical, chemical, and biological parameters in natural environments. However, sensors with high-sensitivity measurement still present their own challenges. This paper deduces and summarizes the methods of sensitivity enhancement in interferometer based fiber optical sensors, including the derivation of the sensing principles, key characteristics, and recently-reported applications.The modal coupling interferometer is taken as an example to derive the five terms related to the sensitivity: (1) the wavelength-dependent difference of phase between two modes/arms ∂ϕd/∂λ, (2) the sensor length Lw,A, (3) refractive index difference between two modes/arms Δneff,A, (4) sensing parameter dependent length change α, and (5) sensing parameter dependent refractive index change γ. The research papers in the literature that modulate these terms to enhance the sensing sensitivity are reviewed in the paper.

Sensors and Instruments for Brix Measurement: A Review

Quality assessment of fruits, vegetables, or beverages involves classifying the products according to the quality traits such as, appearance, texture, flavor, sugar content. The measurement of sugar content, or Brix, as it is commonly known, is an essential part of the quality analysis of the agricultural products and alcoholic beverages. The Brix monitoring of fruit and vegetables by destructive methods includes sensory assessment involving sensory panels, instruments such as refractometer, hydrometer, and liquid chromatography. However, these techniques are manual, time-consuming, and most importantly, the fruits or vegetables are damaged during testing. On the other hand, the traditional sample-based methods involve manual sample collection of the liquid from the tank in fruit/vegetable juice making and in wineries or breweries. Labour ineffectiveness can be a significant drawback of such methods. This review presents recent developments in different destructive and nondestructive Brix measurement techniques focused on fruits, vegetables, and beverages. It is concluded that while there exist a variety of methods and instruments for Brix measurement, traits such as promptness and low cost of analysis, minimal sample preparation, and environmental friendliness are still among the prime requirements of the industry.

Tomographic measurement of dielectric tensors at optical frequency

The dielectric tensor is a physical descriptor of fundamental light-matter interactions, characterizing anisotropic materials with principal refractive indices and optic axes. Despite its importance in scientific and industrial applications ranging from material science to soft matter physics, the direct measurement of the three-dimensional dielectric tensor has been limited by the vectorial and inhomogeneous nature of light scattering from anisotropic materials. Here, we present a dielectric tensor tomographic approach to directly measure dielectric tensors of anisotropic structures including the spatial variations of principal refractive indices and directors. The anisotropic structure is illuminated with a polarized plane wave with various angles and polarization states. Then, the scattered fields are holographically measured and converted into vectorial diffracted field components. Finally, by inversely solving a vectorial wave equation, the three-dimensional dielectric tensor is reconstructed. Using this approach, we demonstrate quantitative tomographic measurements of various nematic liquid-crystal structures and their fast three-dimensional non-equilibrium dynamics.

Dynamic spectroscopic imaging ellipsometry

A dynamic spectroscopic imaging ellipsometer (DSIE) employing a monolithic polarizing interferometer is described. The proposed DSIE system can provide spatio-spectral ellipsometric phase map data Δ(λ, x) dynamically at a speed of 30 Hz. We demonstrate the ultrafast mapping capability of the spectroscopic ellipsometer by measuring a patterned 8-inch full wafer with a spatial resolution of less than 50 × 50 µm² in an hour.

Computational multi-wavelength phase synthesis using convolutional neural networks [Invited]

Multi-wavelength digital holographic microscopy (MWDHM) provides indirect measurements of the refractive index for non-dispersive samples. Successive-shot MWDHM is not appropriate for dynamic samples and single-shot MWDHM significantly increases the complexity of the optical setup due to the need for multiple lasers or a wavelength tunable source. Here we consider deep learning convolutional neural networks for computational phase synthesis to obtain high-speed simultaneous phase estimates on different wavelengths and thus single-shot estimates of the integral refractive index without increased experimental complexity. This novel, to the best of our knowledge, computational concept is validated using cell phantoms consisting of internal refractive index variations representing cytoplasm and membrane-bound organelles, respectively, and a simulation of a realistic holographic recording process. Specifically, in this work we employed data-driven computational techniques to perform accurate dual-wavelength hologram synthesis (hologram-to-hologram prediction), dual-wavelength phase synthesis (unwrapped phase-to-phase prediction), direct phase-to-index prediction using a single wavelength, hologram-to-phase prediction, and 2D phase unwrapping with sharp discontinuities (wrapped-to-unwrapped phase prediction).

Effects of osmolality and solutes on the morphology of red blood cells according to three-dimensional refractive index tomography

Phosphate-buffered saline (PBS) and Alsever's solution (AS) are frequently used as media in blood-related studies, while 0.9% normal saline (NS) is frequently used in transfusion medicine. Despite the frequent use, the effects of these solutions on the shape and volume of red blood cells (RBCs) have not been reported. We collected blood samples from five healthy adults and used three-dimensional refractive index tomography to investigate the changes in the morphology of RBCs caused by changes in osmolality and solutes at the single-cell level. After diluting 2 μL of RBCs 200-fold with each solution (PBS, AS, and 0.9% NS), 40 randomly selected RBCs were microscopically observed. RBC shape was measured considering sphericity, which is a dimensionless quantity ranging from 0 (flat) to 1 (spherical). RBCs in plasma or AS showed a biconcave shape with a small sphericity, whereas those in 0.9% NS or PBS showed a spherical shape with a large sphericity. Moreover, we confirmed that sodium chloride alone could not elicit the biconcave shape of RBCs, which could be maintained only in the presence of an osmotic pressure-maintaining substance, such as glucose or mannitol. Although 0.9% NS solution is one of the most commonly used fluids in hematology and transfusion medicine, RBCs in 0.9% NS or PBS are not biconcave. Therefore, as the debate on the use of NS continues, future clinical studies or applications should consider the effect of glucose or mannitol on the shape of RBCs.

Optical properties of biochemical compositions of microalgae within the spectral range from 300 to 1700 nm

The optical properties of biochemical compositions of microalgae are vital for the improvement of biosensor design, photobioreactor design, biofuel, and biophotonics techniques. A combination method using both the double optical pathlength transmission method (DOPTM) and the ellipsometry method (EM) is called DOPTM-EM, and it is used to acquire the optical constants of protein, lipid, and carbohydrate of Haematococcus pluvialis, Nannochloropsis sp., and Spirulina in both a solid state and a solution state within the visible and near-infrared spectral range. For different types of microalgae, the refractive indices of protein and carbohydrate in the solid state are similar to each other, but show an observed difference from lipid in the solid state. The refractive indices of protein and carbohydrate in the solution state presents a visible distinction in the researched spectral range. The absorption indices of protein, lipid, and carbohydrate in the solid state for these three types of microalgae are close to each other in the spectral range of 300-500 nm. However, an observed difference is shown in the spectral range of 500-1700 nm. For ease of application, the refractive index of biochemical composition of microalgae was fitted based on the Sellmeier equation. We believe this work can provide a reference to obtain the optical properties of biomaterial with high accuracy.

Probing bio-tissue films by optical internal reflectivity: modeling and measurements

In this paper, we develop a detailed theoretical model for the optical reflectivity of a bio-tissue film confined between two flat interfaces based on the anomalous-diffraction approximation. We consider bio-tissue films consisting of a few layers of spheroidal cells surrounded by extracellular medium. We explore numerically the predictions of our model and compare them with simple effective medium theories, sometimes used as a first attempt to understand the optical properties of biological media. Then, we fit the model to experimental reflectivity-versus-angle-of-incidence curves of confined whole-blood films measured in an internal reflection configuration. Measurements were performed by confining a drop of fresh blood between a prism and a coverslip. Our experimental results show that it is possible to measure the coherent reflectance with small enough error to infer microstructural parameters with a good precision. The errors in measuring the coherent reflectance depend on the reflectivity magnitude. For instance, for a reflectivity of about 0.3 the error is below 2%, and the refractive indices of cells and surrounding medium can be obtained with a precision better than 1%. These results also indicate that the present model can readily be used to figure out the physical changes experienced at the microscale in bio-tissue films during a physicochemical process.

Determination of protein concentration in downstream biomanufacturing processes by in-line index of refraction

Protein concentration determination is a necessary in-process control for the downstream operations within biomanufacturing. As production transitions from batch mode to an integrated continuous bioprocess paradigm, there is a growing need to move protein concentration quantitation from off-line to in-line analysis. One solution to fulfill this process analytical technology need is an in-line index of refraction (IoR) sensor to measure protein concentration in real time. Here the performance of an IoR sensor is evaluated through a series of experiments to assess linear response, buffer matrix effects, dynamic range, sensor-to-sensor variability, and the limits of detection and quantitation. The performance of the sensor was also tested in two bioprocessing scenarios, ultrafiltration and capture chromatography. The implementation of this in-line IoR sensor for real-time protein concentration analysis and monitoring has the potential to improve continuous bioprocess manufacturing.

Imaging-based spectrometer-less optofluidic biosensors based on dielectric metasurfaces for detecting extracellular vesicles

Biosensors are indispensable tools for public, global, and personalized healthcare as they provide tests that can be used from early disease detection and treatment monitoring to preventing pandemics. We introduce single-wavelength imaging biosensors capable of reconstructing spectral shift information induced by biomarkers dynamically using an advanced data processing technique based on an optimal linear estimator. Our method achieves superior sensitivity without wavelength scanning or spectroscopy instruments. We engineered diatomic dielectric metasurfaces supporting bound states in the continuum that allows high-quality resonances with accessible near-fields by in-plane symmetry breaking. The large-area metasurface chips are configured as microarrays and integrated with microfluidics on an imaging platform for real-time detection of breast cancer extracellular vesicles encompassing exosomes. The optofluidic system has high sensing performance with nearly 70 1/RIU figure-of-merit enabling detection of on average 0.41 nanoparticle/µm2 and real-time measurements of extracellular vesicles binding from down to 204 femtomolar solutions. Our biosensors provide the robustness of spectrometric approaches while substituting complex instrumentation with a single-wavelength light source and a complementary-metal-oxide-semiconductor camera, paving the way toward miniaturized devices for point-of-care diagnostics.

Application of digital holographic tomography in antitumor effect of cantharides complex on 4T1 breast cancer cells

The study focuses on a methodology providing noninvasive monitoring and evaluation of the antitumor effect of traditional Chinese medicine, cantharides complex (canth), on 4T1 breast tumor cells. Digital holographic tomography (DHT) and developed data post-processing algorithms were used for quantitative estimation of changes in optical and morphological parameters of cells. We calculated and compared data on the refractive index, thickness, and projected area of 4T1 breast tumor cells in control untreated specimens and those treated with doxorubicin hydrochloride (DOX), canth, and their combinations. Post-treatment changes in cellular morphology recorded by DHT demonstrated that the two drugs led to noticeably different morphological changes in cells that can be presumably associated with different pathways of their death, apoptosis, or necrosis. The effect of combined treatment with these two drugs strongly depended on their relative concentrations and could lead to changes characteristic either for DOX or for canth; however, being more profound than those obtained when using each drug solely. The results obtained by DHT are in a good correspondence with commonly used cell viability analysis and immunofluorescent analysis of changes in cellular cytoskeleton.

Terahertz refractive index-based morphological dilation for breast carcinoma delineation

This paper reports investigations led on the combination of the refractive index and morphological dilation to enhance performances towards breast tumour margin delineation during conserving surgeries. The refractive index map of invasive ductal and lobular carcinomas were constructed from an inverse electromagnetic problem. Morphological dilation combined with refractive index thresholding was conducted to classify the tissue regions as malignant or benign. A histology routine was conducted to evaluate the performances of various dilation geometries associated with different thresholds. It was found that the combination of a wide structuring element and high refractive index was improving the correctness of tissue classification in comparison to other configurations or without dilation. The method reports a sensitivity of around 80% and a specificity of 82% for the best case. These results indicate that combining the fundamental optical properties of tissues denoted by their refractive index with morphological dilation may open routes to define supporting procedures during breast-conserving surgeries.

Optimizing illumination in three-dimensional deconvolution microscopy for accurate refractive index tomography

In light transmission microscopy, axial scanning does not directly provide tomographic reconstruction of specimen. Phase deconvolution microscopy can convert a raw intensity image stack into a refractive index tomogram, the intrinsic sample contrast which can be exploited for quantitative morphological analysis. However, this technique is limited by reconstruction artifacts due to unoptimized optical conditions, which leads to a sparse and non-uniform optical transfer function. Here, we propose an optimization method based on simulated annealing to systematically obtain optimal illumination schemes that enable artifact-free deconvolution. The proposed method showed precise tomographic reconstruction of unlabeled biological samples.

Establishing NDRE dynamic models of winter wheat under multi-nitrogen rates based on a field spectral sensor

Field spectral sensors provide real-time, reliable, quantitative monitoring of crop growth. Fitting the continuous growth in the entire growing period from the measurements of limited frequency is helpful to the comparative analysis of interannual growth and fertilizer management in the field. To exploit this capacity, our work presents a model that uses the normalized difference red edge (NDRE) index derived from the field spectral sensor for real-time monitoring of the canopy growth of winter wheat in the whole growing period. We developed this model from experiments in three counties in Hebei province, China, where we obtained the near-infrared and red edge reflectance, grain yield, and canopy parameters for eight growth stages and for various nitrogen (N) rates. Given the correlation between effective accumulated temperature and crop growth, we used the growing degree-days as an adjustment parameter to develop models for dynamic monitoring of the NDRE of the winter wheat canopy during the entire growing period. The results show that high determination coefficients (R²=0.89 to 0.96) are obtained from all models based on relative NDRE and effective accumulative temperature (independent of N fertilization rates). The model based on the rational function is the best of all models tested, with the accuracy for normal and high N fertilization rates being slightly greater than that for low N fertilization rates. Therefore, a relative-NDRE model with the accumulative growing degree-days since sowing could allow monitoring canopy NDRE of winter wheat at any time, which could be helpful for overcoming the shortage of incomparable growth derived from the differences of sensing date, sowing date, and fertilizer, etc.

Improved 3D cellular morphometry of Caenorhabditis elegans embryos using a refractive index matching medium

Cell shape change is one of the driving forces of animal morphogenesis, and the model organism Caenorhabditis elegans has played a significant role in analyzing the underlying mechanisms involved. The analysis of cell shape change requires quantification of cellular shape descriptors, a method known as cellular morphometry. However, standard C. elegans live imaging methods limit the capability of cellular morphometry in 3D, as spherical aberrations generated by samples and the surrounding medium misalign optical paths. Here, we report a 3D live imaging method for C. elegans embryos that minimized spherical aberrations caused by refractive index (RI) mismatch. We determined the composition of a refractive index matching medium (RIMM) for C. elegans live imaging. The 3D live imaging with the RIMM resulted in a higher signal intensity in the deeper cell layers. We also found that the obtained images improved the 3D cell segmentation quality. Furthermore, our 3D cellular morphometry and 2D cell shape simulation indicated that the germ cell precursor P4 had exceptionally high cortical tension. Our results demonstrate that the RIMM is a cost-effective solution to improve the 3D cellular morphometry of C. elegans. The application of this method should facilitate understanding of C. elegans morphogenesis from the perspective of cell shape changes.

A Refractive Index Study of a Diverse Set of Polymeric Materials by QSPR with Quantum-Chemical and Additive Descriptors

Predicting the activities and properties of materials via in silico methods has been shown to be a cost- and time-effective way of aiding chemists in synthesizing materials with desired properties. Refractive index (n) is one of the most important defining characteristics of an optical material. Presented in this work is a quantitative structure–property relationship (QSPR) model that was developed to predict the refractive index for a diverse set of polymers. A number of models were created, where a four-variable model showed the best predictive performance with R² = 0.904 and Q²_LOO = 0.897. The robustness and predictability of the best model was validated using the leave-one-out technique, external set and y-scrambling methods. The predictive ability of the model was confirmed with the external set, showing the R²_ext = 0.880. For the refractive index, the ionization potential, polarizability, 2D and 3D geometrical descriptors were the most influential properties. The developed model was transparent and mechanistically explainable and can be used in the prediction of the refractive index for new and untested polymers.

Optical reflectivity of an interface with random refractive-index-contrast patterns

We develop simple models for the optical reflectivity of an interface in optical contact with random media consisting of discrete volumes of arbitrary form and different refractive indices. Examples of interest are surfaces sprinkled with microdroplets or an interface with biological cells adhered to it at random locations. We focus our attention to the case of internal reflectivity, in which the incidence medium has a larger refractive index than the refractive indices at the other side of the interface. Assuming an incident plane wave, we provide simple approximate expressions for the surface's coherent reflectance and for the surface's total reflectance. We compare predictions of the surface coherent-reflectance model with numerical simulations. Then we use the surface's reflectance models to interpret experimental measurements obtained with an optical prism and a thin vegetable tissue adhered to its base. In general, the surface reflectivity can be used to determine fractional contact area between the interface and microdroplets or biological cells and infer their refractive indices with an accuracy of about 0.5%.

Critical assessment of relevant methods in the field of biosensors with direct optical detection based on fibers and waveguides using plasmonic, resonance, and interference effects

Direct optical detection has proven to be a highly interesting tool in biomolecular interaction analysis to be used in drug discovery, ligand/receptor interactions, environmental analysis, clinical diagnostics, screening of large data volumes in immunology, cancer therapy, or personalized medicine. In this review, the fundamental optical principles and applications are reviewed. Devices are based on concepts such as refractometry, evanescent field, waveguides modes, reflectometry, resonance and/or interference. They are realized in ring resonators; prism couplers; surface plasmon resonance; resonant mirror; Bragg grating; grating couplers; photonic crystals, Mach-Zehnder, Young, Hartman interferometers; backscattering; ellipsometry; or reflectance interferometry. The physical theories of various optical principles have already been reviewed in detail elsewhere and are therefore only cited. This review provides an overall survey on the application of these methods in direct optical biosensing. The "historical" development of the main principles is given to understand the various, and sometimes only slightly modified variations published as "new" methods or the use of a new acronym and commercialization by different companies. Improvement of optics is only one way to increase the quality of biosensors. Additional essential aspects are the surface modification of transducers, immobilization strategies, selection of recognition elements, the influence of non-specific interaction, selectivity, and sensitivity. Furthermore, papers use for reporting minimal amounts of detectable analyte terms such as value of mass, moles, grams, or mol/L which are difficult to compare. Both these essential aspects (i.e., biochemistry and the presentation of LOD values) can be discussed only in brief (but references are provided) in order to prevent the paper from becoming too long. The review will concentrate on a comparison of the optical methods, their application, and the resulting bioanalytical quality.