Refractive Index Mismatch Research Articles

Optimized three-dimensional trapping of aerosols: the effect of immersion medium

Optical tweezers have proven to be indispensable micromanipulation tools especially in aqueous solutions. Because of the significantly larger spherical aberration induced by the refractive index mismatch, trapping aerosols has always been cumbersome if not impossible. We introduce a simple but very efficient method for optimized aerosol trapping at a desired depth. We show that a wise selection of the immersion medium and the mechanical tube length not only enables trapping of objects that are known to be untrappable but also provides a way to tune the trappable depth range.

Correction of depth-induced spherical aberration for deep observation using two-photon excitation fluorescence microscopy with spatial light modulator.

We demonstrate fluorescence imaging with high fluorescence intensity and depth resolution in which depth-induced spherical aberration (SA) caused by refractive-index mismatch between the medium and biological sample is corrected. To reduce the impact of SA, we incorporate a spatial light modulator into a two-photon excitation fluorescence microscope. Consequently, when fluorescent beads in epoxy resin were observed with this method of SA correction, the fluorescence signal of the observed images was ∼27 times higher and extension in the direction of the optical axes was ∼6.5 times shorter at a depth of ∼890 μm. Thus, the proposed method increases the depth observable at high resolution. Further, our results show that the method improved the fluorescence intensity of images of the fluorescent beads and the structure of a biological sample.

Deep-UV microsphere projection lithography.

In this Letter, we present a single-exposure deep-UV projection lithography at 254-nm wavelength that produces nanopatterns in a scalable area with a feature size of 80 nm. In this method, a macroscopic lens projects a pixelated optical mask on a monolayer of hexagonally arranged microspheres that reside on the Fourier plane and image the mask's pattern into a photoresist film. Our macroscopic lens shrinks the size of the mask by providing an imaging magnification of ∼1.86×10(4), while enhancing the exposure power. On the other hand, microsphere lens produces a sub-diffraction limit focal point-a so-called photonic nanojet-based on the near-surface focusing effect, which ensures an excellent patterning accuracy against the presence of surface roughness. Ray-optics simulation is utilized to design the bulk optics part of the lithography system, while a wave-optics simulation is implemented to simulate the optical properties of the exposed regions beneath the microspheres. We characterize the lithography performance in terms of the proximity effect, lens aberration, and interference effect due to refractive index mismatch between photoresist and substrate.

Adaptive optics stochastic optical reconstruction microscopy (AO-STORM) using a genetic algorithm.

The resolution of Single Molecule Localization Microscopy (SML) is dependent on the width of the Point Spread Function (PSF) and the number of photons collected. However, biological samples tend to degrade the shape of the PSF due to the heterogeneity of the index of refraction. In addition, there are aberrations caused by imperfections in the optical components and alignment, and the refractive index mismatch between the coverslip and the sample, all of which directly reduce the accuracy of SML. Adaptive Optics (AO) can play a critical role in compensating for aberrations in order to increase the resolution. However the stochastic nature of single molecule emission presents a challenge for wavefront optimization because the large fluctuations in photon emission do not permit many traditional optimization techniques to be used. Here we present an approach that optimizes the wavefront during SML acquisition by combining an intensity independent merit function with a Genetic algorithm (GA) to optimize the PSF despite the fluctuating intensity. We demonstrate the use of AO with GA in tissue culture cells and through ~50µm of tissue in the Drosophila Central Nervous System (CNS) to achieve a 4-fold increase in the localization precision.

Improving axial resolution in confocal microscopy with new high refractive index mounting media.

Resolution, high signal intensity and elevated signal to noise ratio (SNR) are key issues for biologists who aim at studying the localisation of biological structures at the cellular and subcellular levels using confocal microscopy. The resolution required to separate sub-cellular biological structures is often near to the resolving power of the microscope. When optimally used, confocal microscopes may reach resolutions of 180 nm laterally and 500 nm axially, however, axial resolution in depth is often impaired by spherical aberration that may occur due to refractive index mismatches. Spherical aberration results in broadening of the point-spread function (PSF), a decrease in peak signal intensity when imaging in depth and a focal shift that leads to the distortion of the image along the z-axis and thus in a scaling error. In this study, we use the novel mounting medium CFM3 (Citifluor Ltd., UK) with a refractive index of 1.518 to minimize the effects of spherical aberration. This mounting medium is compatible with most common fluorochromes and fluorescent proteins. We compare its performance with established mounting media, harbouring refractive indices below 1.500, by estimating lateral and axial resolution with sub-resolution fluorescent beads. We show furthermore that the use of the high refractive index media renders the tissue transparent and improves considerably the axial resolution and imaging depth in immuno-labelled or fluorescent protein labelled fixed mouse brain tissue. We thus propose to use those novel high refractive index mounting media, whenever optimal axial resolution is required.

Goos-Hänchen shifts of Helmholtz solitons at nonlocal nonlinear interfaces

We address the nonlinear Goos-Hanchen shift of Helmholtz solitons at a nonlocal nonlinear interface between a Kerr medium and a nonlocal nonlinear medium. Based on the framework of the Helmholtz theory, we have demonstrated that the Goos-Hanchen shift depends on the angle of the incidence, the linear and nonlinear refractive index mismatch at the interface, the nonparaxial parameter and the degree of nonlocality. Interestingly, internal and external refraction can be introduced when the nonlinear refractive index mismatch is greater than a threshold value. The total reflection will occur when the degree of nonlocality exceeds a value.

Effects of refractive index mismatch in optical CT imaging of polymer gel dosimeters.

Proposing an image reconstruction technique, algebraic reconstruction technique-refraction correction (ART-rc). The proposed method takes care of refractive index mismatches present in gel dosimeter scanner at the boundary, and also corrects for the interior ray refraction. Polymer gel dosimeters with high dose regions have higher refractive index and optical density compared to the background medium, these changes in refractive index at high dose results in interior ray bending. The inclusion of the effects of refraction is an important step in reconstruction of optical density in gel dosimeters. The proposed ray tracing algorithm models the interior multiple refraction at the inhomogeneities. Jacob's ray tracing algorithm has been modified to calculate the pathlengths of the ray that traverses through the higher dose regions. The algorithm computes the length of the ray in each pixel along its path and is used as the weight matrix. Algebraic reconstruction technique and pixel based reconstruction algorithms are used for solving the reconstruction problem. The proposed method is tested with numerical phantoms for various noise levels. The experimental dosimetric results are also presented. The results show that the proposed scheme ART-rc is able to reconstruct optical density inside the dosimeter better than the results obtained using filtered backprojection and conventional algebraic reconstruction approaches. The quantitative improvement using ART-rc is evaluated using gamma-index. The refraction errors due to regions of different refractive indices are discussed. The effects of modeling of interior refraction in the dose region are presented. The errors propagated due to multiple refraction effects have been modeled and the improvements in reconstruction using proposed model is presented. The refractive index of the dosimeter has a mismatch with the surrounding medium (for dry air or water scanning). The algorithm reconstructs the dose profiles by estimating refractive indices of multiple inhomogeneities having different refractive indices and optical densities embedded in the dosimeter. This is achieved by tracking the path of the ray that traverses through the dosimeter. Extensive simulation studies have been carried out and results are found to be matching that of experimental results.

折射率不匹配引入的像差对共聚焦显微成像的影响

折射率不匹配引入的像差对共聚焦显微成像的影响

Deep Tissue Wavefront Estimation for Sensorless Aberration Correction

The multiple light scattering in biological tissues limits the measurement depth for traditional wavefront sensor. The attenuated ballistic light and the background noise caused by the diffuse light give low signal to noise ratio for wavefront measurement. To overcome this issue, we introduced a wavefront estimation method based on a ray tracing algorithm to overcome this issue. With the knowledge of the refractive index of the medium, the wavefront is estimated by calculating optical path length of rays from the target inside of the samples. This method can provide not only the information of spherical aberration from the refractive-index mismatch between the medium and biological sample but also other aberrations caused by the irregular interface between them. Simulations based on different configurations are demonstrated in this paper.

ClearSee: a rapid optical clearing reagent for whole-plant fluorescence imaging.

Imaging techniques for visualizing and analyzing precise morphology and gene expression patterns are essential for understanding biological processes during development in all organisms. With the aid of chemical screening, we developed a clearing method using chemical solutions, termed ClearSee, for deep imaging of morphology and gene expression in plant tissues. ClearSee rapidly diminishes chlorophyll autofluorescence while maintaining fluorescent protein stability. By adjusting the refractive index mismatch, whole-organ and whole-plant imaging can be performed by both confocal and two-photon excitation microscopy in ClearSee-treated samples. Moreover, ClearSee is applicable to multicolor imaging of fluorescent proteins to allow structural analysis of multiple gene expression. Given that ClearSee is compatible with staining by chemical dyes, the technique is useful for deep imaging in conjunction with genetic markers and for plant species not amenable to transgenic approaches. This method is useful for whole imaging for intact morphology and will help to accelerate the discovery of new phenomena in plant biological research.

Toward optical-tweezers-based force microscopy for airborne microparticles.

Optical tweezers have found widespread application in biological and colloidal physics for the measurement of pN forces over nanometer to micrometer length scales. Similar aerosol-phase measurements of interparticle force have not been reported in spite of the potential to better resolve particle coagulation kinetics. Various refractive index mismatches in the beam path as well as the need to explicitly account for gravity and inertial particle motion provide a number of challenges that must be overcome to make such measurements tractable. In this regard, we demonstrate schemes by which the particle position and trap stiffness may be unambiguously measured using bright-field microscopy with resolution comparable with analogous condensed-phase measurements. Moreover, some of the challenges of working with highly dynamic aqueous particles are introduced and exploited to observe size-dependent phenomena in aerosol optical tweezers. Notably, when combined with cavity-enhanced Raman spectroscopy, this provides a unique opportunity to explore trapping forces over a continuum of particle size and refractive index. It is expected that the methods developed will provide a basis for the measurement of pairwise interaction forces in aerosol optical tweezers while providing a probe of fundamental airborne particle trapping dynamics.

Further Closing the Resolution Gap: Integrating Cryo-Soft X-Ray and Light Microscopies

Further Closing the Resolution Gap: Integrating Cryo-Soft X-Ray and Light Microscopies

Methods to calibrate and scale axial distances in confocal microscopy as a function of refractive index.

Accurate distance measurement in 3D confocal microscopy is important for quantitative analysis, volume visualization and image restoration. However, axial distances can be distorted by both the point spread function (PSF) and by a refractive-index mismatch between the sample and immersion liquid, which are difficult to separate. Additionally, accurate calibration of the axial distances in confocal microscopy remains cumbersome, although several high-end methods exist. In this paper we present two methods to calibrate axial distances in 3D confocal microscopy that are both accurate and easily implemented. With these methods, we measured axial scaling factors as a function of refractive-index mismatch for high-aperture confocal microscopy imaging. We found that our scaling factors are almost completely linearly dependent on refractive index and that they were in good agreement with theoretical predictions that take the full vectorial properties of light into account. There was however a strong deviation with the theoretical predictions using (high-angle) geometrical optics, which predict much lower scaling factors. As an illustration, we measured the PSF of a correctly calibrated point-scanning confocal microscope and showed that a nearly index-matched, micron-sized spherical object is still significantly elongated due to this PSF, which signifies that care has to be taken when determining axial calibration or axial scaling using such particles.

Refractive Index Mismatch Can Misindicate Anomalous Diffusion in Single‐Focus Fluorescence Correlation Spectroscopy

Fluorescence correlation spectroscopy (FCS) is often used to study diffusion in complex media, wherein the refractive index usually differs from that of the immersion medium. This paper assesses the effect of this refractive index mismatch. Confocal single‐focus and two‐focus fluorescence correlation spectroscopy (2fFCS) is used to probe the diffusion of tagged dextran tracers in water, dilute dextran solutions, acrylamide monomer solutions, polyacrylamide polymer solutions, and a cross linked polyacrylamide hydrogel. In these experiments, both the refractive index and the potential topological constraint and thermodynamic interaction to the probe‐diffusion are varied, and pairs of samples with same refractive indexes but different compositions are compared. Whereas 2fFCS shows no anomalous diffusion in any of them, single‐focus FCS indicates anomalous diffusion. In particular, the values of the stretching exponent of the fluorescence autocorrelation function, which is often interpreted to reflect the extent of anomaly of diffusion, do not vary systematically with the extent of topological or thermodynamic complexity of the different matrixes, but with their refractive index. This shows that apparent anomalous diffusion in FCS is at risk to be the result of refractive index mismatch rather than reflecting truly complex diffusion. image

Method for refractive index measurement of nanoparticles.

A new method of measuring the refractive indices of nanoparticles has been proposed based on refractive index matching between nanoparticles and surrounding organic solvents. By finding the most transparent point of the transmittance spectrum, the refractive index of the nanoparticles is equal to that of the solvents at the corresponding wavelength. Utilizing a Rayleigh scattering model, the effects of refractive index mismatching (Δn) on the transmittance are investigated under different conditions. Some criteria for getting highly transparent nanoparticle dispersion and accurate refractive index measurements are suggested, which can support practical applications for nanomaterials in optical and optoelectronic applications.

Hybrid model of light propagation in random media based on the time-dependent radiative transfer and diffusion equations

Numerical modeling of light propagation in random media has been an important issue for biomedical imaging, including diffuse optical tomography (DOT). For high resolution DOT, accurate and fast computation of light propagation in biological tissue is desirable. This paper proposes a space–time hybrid model for numerical modeling based on the radiative transfer and diffusion equations (RTE and DE, respectively) in random media under refractive-index mismatching. In the proposed model, the RTE and DE regions are separated into space and time by using a crossover length and the time from the ballistic regime to the diffusive regime, ρDA~10/μt′ and tDA~20/vμt′ where μt′ and v represent a reduced transport coefficient and light velocity, respectively. The present model succeeds in describing light propagation accurately and reduces computational load by a quarter compared with full computation of the RTE.

SU‐E‐T‐294: Simulations to Investigate the Feasibility of ‘dry’ Optical‐CT Imaging for 3D Dosimetry

Purpose:To perform simulations investigating the feasibility of “dry” optical‐CT, and determine optimal design and scanning parameters for a novel dry tank telecentric optical‐CT 3D dosimetry system. Such a system would have important advantages in terms of practical convenience and reduced cost.Methods:A Matlab based ray‐tracing simulation platform, ScanSim, was used to model a telecentric system with a polyurethane dry tank, cylindrical dosimeter, and surrounding fluid. This program's capabilities were expanded for the geometry and physics of dry scanning. To categorize the effects of refractive index (RI) mismatches, simulations were run for several dosimeter (RI = 1.5−1.48) and fluid (RI = 1.55−1.33) combinations. Additional simulations examined the effect of increasing gap size (1–5mm) between the dosimeter and tank wall, and of changing the telecentric lens tolerance (0.5°−5°). The evaluation metric is the usable radius; the distance from the dosimeter center where the measured and true doses differ by less than 2%.Results:As the tank/dosimeter RI mismatch increases from 0–0.02, the usable radius decreases from 97.6% to 50.2%. The fluid RI for matching is lower than either the tank or dosimeter RI. Changing gap sizes has drastic effects on the usable radius, requiring more closely matched fluid at large gap sizes. Increasing the telecentric tolerance through a range from 0.5°–5.0° improved the usable radius for every combination of media.Conclusion:Dry optical‐CT with telecentric lenses is feasible when the dosimeter and tank RIs are closely matched (<0.01 difference), or when data in the periphery is not required. The ScanSim tool proved very useful in situations when the tank and dosimeter have slight differences in RI by enabling estimation of the optimal choice of RI of the small amount of fluid still required. Some spoiling of the telecentric beam and increasing the tolerance helps recover the usable radius.

Electron photoemission in plasmonic nanoparticle arrays: analysis of collective resonances and embedding effects

We theoretically study the characteristics of photoelectron emission in plasmonic nanoparticle arrays. Nanoparticles are partially embedded in a semiconductor, forming Schottky barriers at metal/semiconductor interfaces through which photoelectrons can tunnel from the nanoparticle into the semiconductor; photodetection in the infrared range, where photon energies are below the semiconductor band gap (insufficient for band-to-band absorption in semiconductor), is therefore possible. The nanoparticles are arranged in a sparse rectangular lattice so that the wavelength of the lattice-induced Rayleigh anomalies can overlap the wavelength of the localized surface plasmon resonance of the individual particles, bringing about collective effects from the nanoparticle array. Using full-wave numerical simulations, we analyze the effects of lattice constant, embedding depth, and refractive index step between the semiconductor layer and an adjacent transparent conductive oxide layer. We show that the presence of refractive index mismatch between media surrounding the nanoparticles disrupts the formation of a narrow absorption peak associated with the Rayleigh anomaly, so the role of collective lattice effects in the formation of plasmonic resonance is diminished. We also show that 5 to 20-times increase of photoemission can be achieved on embedding of nanoparticles without taking into account dynamics of ballistic electrons. The results obtained can be used to increase efficiency of plasmon-based photodetectors and photovoltaic devices. The results may provide clues to designing an experiment where the contributions of surface and volume photoelectric effects to the overall photocurrent would be defined.

IR transparent hot pressed Mg-α/β-Sialon:Ba2+ ceramics

IR transparent Mg-α/β-Sialon:Ba2+ ceramics were fabricated by the hot press sintering method. The influence of BaCO3 addition to Si3N4–MgO–AlN system on transparency, microstructures and mechanical properties were investigated. Reactions between the mixed powders were analyzed from differential thermogravimetric (DTG) curve and formation of Celsian (BaAl2Si2O8) was observed at 1175°C. The α-Sialon phase in sintered bodies was increased with BaCO3 addition due to the excess liquid phase that allows Mg2+ diffusion in α-Si3N4 lattice to give higher α-Sialon phase as revealed from XRD patterns. To minimize the light scattering by mismatch of refractive indices between the Sialon phase and glassy phase, barium ion was introduced to match the refractive index of glassy phase to Sialon phase. The study of electron spin resonance (ESR) spectra shows that unpaired electrons affect the IR transmittance in Sialon ceramics. Weak ESR spectrum was shown for the IR transparent BaCO3 added Sialon ceramics. The highest light transmission was observed around 78% in IR region (2500nm), and had better transparency than previously reported Sialon ceramics. The fabricated Sialon ceramics had high hardness of 21.4GPa and fracture toughness of 5.4MPam1/2.

Transmission of nonparaxial nonlocal lattice solitons at nonlinear interfaces

We report on transmission of nonparaxial nonlocal lattice solitons at an arbitrary angle of incidence to the interface separating two nonlinear media with transverse periodic modulation of the refractive index. The energy distribution of solitons in two media can be varied by the degree of nonlocality, the nonlinear refractive index mismatch parameter at the interface, the nonparaxial parameter, the angle of incidence and the lattice parameters. Importantly, the modulation period and depth can introduce different regimes of soliton propagation in the media including refraction and trapping.