Single-Cell Optical Absorbance Characterization With High-Throughput Microfluidic Microscopy

Morphological changes in cells associated with disease states are often assessed using clinical microscopy. However, the changes in chemical composition of cells can also be used to detect disease conditions. Optical absorption measurements carried out on single cells using inexpensive sources, detectors can help assess the chemical composition of cells; thereby enable detection of diseases. In this article, we present a novel technique capable of simultaneously detecting changes in morphology and chemical composition of cells. The presented technique enables characterization of optical absorbance-based methods against microscopy for detection of disease states. Using the technique, we have been able to achieve a throughput of about 1000 cells per second. We demonstrate the proof-of-principle by detecting malaria in a given blood sample. The presented technique is capable of detecting very lower levels of parasitemia within time scales comparable to antigen-based rapid diagnostic tests.

Directional bilateral filters for smoothing fluorescence microscopy images

Images obtained through fluorescence microscopy at low numerical aperture (NA) are noisy and have poor resolution. Images of specimens such as F-actin filaments obtained using confocal or widefield fluorescence microscopes contain directional information and it is important that an image smoothing or filtering technique preserve the directionality. F-actin filaments are widely studied in pathology because the abnormalities in actin dynamics play a key role in diagnosis of cancer, cardiac diseases, vascular diseases, myofibrillar myopathies, neurological disorders, etc. We develop the directional bilateral filter as a means of filtering out the noise in the image without significantly altering the directionality of the F-actin filaments. The bilateral filter is anisotropic to start with, but we add an additional degree of anisotropy by employing an oriented domain kernel for smoothing. The orientation is locally adapted using a structure tensor and the parameters of the bilateral filter are optimized for within the framework of statistical risk minimization. We show that the directional bilateral filter has better denoising performance than the traditional Gaussian bilateral filter and other denoising techniques such as SURE-LET, non-local means, and guided image filtering at various noise levels in terms of peak signal-to-noise ratio (PSNR). We also show quantitative improvements in low NA images of F-actin filaments. (C) 2015 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License.

Optimum Parameter Selection in Sparse Reconstruction of Frequency-Domain Optical-Coherence Tomography Signals

For a multilayered specimen, the back-scattered signal in frequency-domain optical-coherence tomography (FDOCT) is expressible as a sum of cosines, each corresponding to a change of refractive index in the specimen. Each of the cosines represent a peak in the reconstructed tomogram. We consider a truncated cosine series representation of the signal, with the constraint that the coefficients in the basis expansion be sparse. An l(2) (sum of squared errors) data error is considered with an l(1) (summation of absolute values) constraint on the coefficients. The optimization problem is solved using Weiszfeld's iteratively reweighted least squares (IRLS) algorithm. On real FDOCT data, improved results are obtained over the standard reconstruction technique with lower levels of background measurement noise and artifacts due to a strong l(1) penalty. The previous sparse tomogram reconstruction techniques in the literature proposed collecting sparse samples, necessitating a change in the data capturing process conventionally used in FDOCT. The IRLS-based method proposed in this paper does not suffer from this drawback.

Robust Savitzky-Golay Filters

Local polynomial approximation of data is an approach towards signal denoising. Savitzky-Golay (SG) filters are finite-impulse-response kernels, which convolve with the data to result in polynomial approximation for a chosen set of filter parameters. In the case of noise following Gaussian statistics, minimization of mean-squared error (MSE) between noisy signal and its polynomial approximation is optimum in the maximum-likelihood (ML) sense but the MSE criterion is not optimal for non-Gaussian noise conditions. In this paper, we robustify the SG filter for applications involving noise following a heavy-tailed distribution. The optimal filtering criterion is achieved by l(1) norm minimization of error through iteratively reweighted least-squares (IRLS) technique. It is interesting to note that at any stage of the iteration, we solve a weighted SG filter by minimizing l(2) norm but the process converges to l(1) minimized output. The results show consistent improvement over the standard SG filter performance.

Patch-based and multiresolution optimum bilateral filters for denoising images corrupted by Gaussian noise

We propose optimal bilateral filtering techniques for Gaussian noise suppression in images. To achieve maximum denoising performance via optimal filter parameter selection, we adopt Stein's unbiased risk estimate (SURE)-an unbiased estimate of the mean-squared error (MSE). Unlike MSE, SURE is independent of the ground truth and can be used in practical scenarios where the ground truth is unavailable. In our recent work, we derived SURE expressions in the context of the bilateral filter and proposed SURE-optimal bilateral filter (SOBF). We selected the optimal parameters of SOBF using the SURE criterion. To further improve the denoising performance of SOBF, we propose variants of SOBF, namely, SURE-optimal multiresolution bilateral filter (SMBF), which involves optimal bilateral filtering in a wavelet framework, and SURE-optimal patch-based bilateral filter (SPBF), where the bilateral filter parameters are optimized on small image patches. Using SURE guarantees automated parameter selection. The multiresolution and localized denoising in SMBF and SPBF, respectively, yield superior denoising performance when compared with the globally optimal SOBF. Experimental validations and comparisons show that the proposed denoisers perform on par with some state-of-the-art denoising techniques. (C) 2015 SPIE and IS&T

Note: A resonating reflector-based optical system for motion measurement in micro-cantilever arrays

A robust, compact optical measurement unit for motion measurement in micro-cantilever arrays enables development of portable micro-cantilever sensors. This paper reports on an optical beam deflection-based system to measure the deflection of micro-cantilevers in an array that employs a single laser source, a single detector, and a resonating reflector to scan the measurement laser across the array. A strategy is also proposed to extract the deflection of individual cantilevers from the acquired data. The proposed system and measurement strategy are experimentally evaluated and demonstrated to measure motion of multiple cantilevers in an array. (C) 2015 AIP Publishing LLC.

Dispersible crystalline nanobundles of YPO4 and Ln (Eu, Tb)-doped YPO4: rapid synthesis, optical properties and bio-probe applications

Undoped and Ln(3+) (Eu and Tb)-doped crystalline nanobundles of YPO4 were prepared by a facile microwave-assisted route with water as a solvent and without using any surfactant. TEM investigations reveal that the as-prepared powder consists of lenticular-shaped nanobundles (similar to 100 nm in diameter) made of very small nanorods with diameter less than 10 nm and length varying from 20 to 50 nm. Each nanorod in turn is single crystalline, as revealed by HRTEM imaging. The as-prepared nanobundles are easily dispersible in various solvents, especially water, without any surface functionalization, which is critical for various bio-probe applications like cell and tissue imaging. The Eu- and Tb-doped YPO4 nanobundles show good photoluminescence properties and were further evaluated for their use as fluorescent biolabels. Our results show that HeLa cells labelled with Eu- and Tb-doped YPO4 nanobundles show bright red (Eu) and green (Tb) intracellular luminescence under a confocal microscope. Concentration-and time-dependent MTT cell viability assays show that the nanobundles show low toxicity towards cells which makes them promising in bioimaging field.

Wide-Range Thermometry at Micro/Nano Length Scales with In2O3 Octahedrons as Optical Probes

We report the temperature-dependent photoluminescence and Raman spectra of In2O3 octahedrons synthesized by an evaporation condensation process. The luminescence obtained here is due to the defect-related deep level emission, which shows highly temperature-dependent behavior in 83-573 K range. Both the position as well as the intensity varies with temperature. Similarly, Raman spectroscopy in 83-303 K range shows temperature-dependent variation in peak intensity but no change in the peak position. Interestingly, the variation of intensity for different peaks is consistent with Placzek theory which invokes the possibility of temperature sensing. We demonstrate the reversibility of peak intensity with temperature for consecutive cycles and excellent stability of the octahedrons toward cryogenic temperature sensing. Overall, both the temperature-dependent photoluminescence and Raman spectra can be explored to determine temperature in the cryogenic range at micro/nano length scales. As an example, we evaluate the temperature-dependent Raman spectra of WO3 that undergoes a phase transition around 210 K and temperature-dependent luminescence of Rhodamine 6G (Rh6G) where intensity varies with temperature.

Diffractive Optical Analysis for Refractive Index Sensing using Transparent Phase Gratings

We report the implementation of a micro-patterned, glass-based photonic sensing element that is capable of label-free biosensing. The diffractive optical analyzer is based on the differential response of diffracted orders to bulk as well as surface refractive index changes. The differential read-out suppresses signal drifts and enables time-resolved determination of refractive index changes in the sample cell. A remarkable feature of this device is that under appropriate conditions, the measurement sensitivity of the sensor can be enhanced by more than two orders of magnitude due to interference between multiply reflected diffracted orders. A noise-equivalent limit of detection (LoD) of 6 x 10(-7) was achieved with this technique with scope for further improvement.

Effect of laser irradiation on optical properties of Ge12Sb25Se63 amorphous chalcogenide thin films

The change in photo-induced optical properties in thermally evaporated Ge12Sb25Se63 chalcogenide thin film under 532-nm laser illumination has been reported in this paper. The structure and composition of the film have been examined by X-ray diffraction and energy dispersive X-ray analysis, respectively. The optical properties such as refractive index, extinction coefficient and thickness of the films have been determined from the transmission spectra based on inverse synthesis method and the optical band gap has been derived from optical absorption spectra using the Tauc plot. It has been found that the mechanism of the optical absorption is due to allowed indirect transition. The optical band gap increases by 0.05 eV causing photo-bleaching mechanism, while refractive index decreases because of reduction in structural disordering. Deconvolution of Raman and X-ray photoelectron spectra into several peaks provides different structural units, which supports the optical photo-bleaching.

Structural and optical characterization of nonpolar (10-10) m-InN/m-GaN epilayers grown by PAMBE

Plasma-assisted molecular beam epitaxy growth of (10-10) m-InN/(10-10) m-GaN was carried out on bare (10-10) m-sapphire substrate. The high resolution X-ray diffraction studies confirmed the orientation of the as-grown films. Nonpolar InN layer was grown at different growth temperatures ranging from 390 degrees C to 440 degrees C and the FWHM of rocking curve revealed good quality film at low temperatures. An in-plane relationship was established for the hetrostructures using phi-scan and a perfect alignment was found for the epilayers. Change of morphology of the films grown at different temperatures was observed using an atomic force microscopy technique showing the smoothest film grown at 400 degrees C. InN optical band gap was found to be vary from 0.79-0.83 eV from absorption spectra. The blue-shift of absorption edge was found to be induced by excess background electron concentration. (C) 2015 Elsevier B.V. All rights reserved.

Triarylborane conjugated dicyanovinyl chromophores: intriguing optical properties and colorimetric anion discrimination

Three new triarylborane conjugated dicyanovinyl chromophores (Mes(2)B-pi-donor-DCV); donor: N-methyldiphenylamine (1) and triphenylamine (2 and 3 with two BMes(2) substitutions]) of type A-D-A (acceptor-donor- acceptor) are reported. Compounds 1-3 exhibit intense charge transfer (CT) absorption bands in the visible region. These absorption peaks are combination CT bands of the amine donor to both the BMes(2) and DCV units. This inference was supported by theoretical studies. Compound 1 shows weak fluorescence compared to 2 and 3. The discrimination of fluoride and cyanide ions is essential in the case of triarylborane (TAB) based anion sensors as a similar response is given towards both the anions. Anion binding studies of 1, 2 and 3 showed that fluoride ions bind selectively to the boron centre and block the corresponding CT transition (donor to BMes(2)) leaving the other CT transition to be red shifted. On the other hand, cyanide ions bind with both the receptor sites and stop both the CT transition processes and hence a different colorimetric response was noted. The binding of F-/CN- induces colour changes in the visible region of the electronic spectra of 2 and 3, which allows for the naked-eye detection of F- and CN- ions. The anion binding mechanisms are established using NMR titration experiments.

Structural and Optical Modification in Bi doped As40S60 Thin Films.

The influence of substitution of Bi atom instead of S atoms on the structural and optical properties of thin films of As40S60 are reported. The density is found to be increased with the addition Bi heavy metal into As2S3. The amorphous to polycrystalline structure of the bulk sample is observed for Bi more than 7%. The glass transition temperature is found to be decreased with addition of Bi. The absorption edge shifts to shorter wavelength, thereby decreasing optical band gap of BixAs(40)S(60-x) (x= 0,2 and 4% here) film. The optical parameter change is discussed from the stand point of chemical bonds formed in the films and related to the defect states produced due to incorporation of Bi atoms in place of chalcogenide S atoms.

Effect of Te Addition into As2Se3 Thin Film: Optical Property Study by FTIR and XPS.

In the present work, we report the effect of Te deposition onto As2Se3 film which affects the optical properties. The Te/As2Se3 film was illuminated with 532 nm laser to study the photo induced diffusion. The prepared As2Se3, Te/As2Se3 films were characterized by X-ray diffraction which show a completely amorphous nature. On the basis of optical transmission data carried out by Fourier Transform infrared Spectroscopy, a non direct transition was found for these films. The optical bandgap is found to be decreased with Te deposition and photo darkening phenomena is observed for the diffused film. The change in the optical constants are also supported by the corresponding change in different types of bonds which are being analyzed by X-ray photoelectron spectroscopy.

Evaporation-Condensation Synthesis and Optical Property of In(2)O(3)Octahedrons

Synthesis of In2O3 octahedrons is carried out successfully by heating Indium metal pieces in air ambient. The sample is characterized by scanning electron microscopy (SEM), Energy dispersive X-ray spectroscope (EDS), X-ray diffraction (XRD) and Raman spectroscopy. The as-prepared In2O3 octahedrons are highly crystalline and exhibit body centered cubic structure. Room temperature and temperature (293-453K) dependence photoluminescence reveals a deep levelbroad emission of yellowish-orange spectra centered around 605 nm. The emission is due to the presence of defect levels in the band gap of materials.