Multidimensional data reconstruction for two color fluorescence microscopy

We propose an iterative data reconstruction technique specifically designed for multi-dimensional multi-color fluorescence imaging. Markov random field is employed (for modeling the multi-color image field) in conjunction with the classical maximum likelihood method. It is noted that, ill-posed nature of the inverse problem associated with multi-color fluorescence imaging forces iterative data reconstruction. Reconstruction of three-dimensional (3D) two-color images (obtained from nanobeads and cultured cell samples) show significant reduction in the background noise (improved signal-to-noise ratio) with an impressive overall improvement in the spatial resolution (approximate to 250 nm) of the imaging system. Proposed data reconstruction technique may find immediate application in 3D in vivo and in vitro multi-color fluorescence imaging of biological specimens. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4769058]

A Huber-loss-driven clustering technique and its application to robust cell detection in confocal microscopy images

We address the problem of detecting cells in biological images. The problem is important in many automated image analysis applications. We identify the problem as one of clustering and formulate it within the framework of robust estimation using loss functions. We show how suitable loss functions may be chosen based on a priori knowledge of the noise distribution. Specifically, in the context of biological images, since the measurement noise is not Gaussian, quadratic loss functions yield suboptimal results. We show that by incorporating the Huber loss function, cells can be detected robustly and accurately. To initialize the algorithm, we also propose a seed selection approach. Simulation results show that Huber loss exhibits better performance compared with some standard loss functions. We also provide experimental results on confocal images of yeast cells. The proposed technique exhibits good detection performance even when the signal-to-noise ratio is low.

Point Spread Function Engineering for Super-Resolution Single-Photon and Multiphoton Fluorescence Microscopy

Super-resolution imaging techniques are of paramount interest for applications in bioimaging and fluorescence microscopy. Recent advances in bioimaging demand application-tailored point spread functions. Here, we present some approaches for generating application-tailored point spread functions along with fast imaging capabilities. Aperture engineering techniques provide interesting solutions for obtaining desired system point spread functions. Specially designed spatial filters—realized by optical mask—are outlined both in a single-lens and 4Pi configuration. Applications include depth imaging, multifocal imaging, and super-resolution imaging. Such an approach is suitable for fruitful integration with most existing state-of-art imaging microscopy modalities.

Modeling of agglomeration inside a droplet with nanosuspensions in an acoustic field

This short communication reports results of particle agglomeration details of an acoustically levitated nanosilica droplet. The droplet undergoes thermo-physical and morphological changes under external heating load (convective or radiative) forming different solid structures due to particle agglomeration. We report an agglomeration model based on population balance approach coupled with species and energy conservation equations in the liquid phase and compare it with the experimentally observed structure formations using high speed photography. The analysis is able to predict similar spherical bowl shaped morphologies as observed experimentally using scanning electron microscopy and laser induced fluorescence. (C) 2012 Elsevier Ltd. All rights reserved.

Synthesis and phase evolution in Nb/Si multilayers obtained by sequential laser ablation

The paper reports the synthesis of Nb/Si multilayers (48/27 nm) deposited on Si single crystal substrate by sequential laser ablation of elemental Nb and Si. Significant amount of Nb is found in the amorphous Si layer (similar to 25-35 at.% Nb). The Nb layer is found to be polycrystalline. The phase evolution of the multilayer has been studied by annealing at 600 degrees C for various times and carrying out cross sectional electron microscopic studies. We report the formation of amorphous silicide layer at the Nb/Si interface followed by the formation of the NbSi2 phase in the Si layer. Further annealing leads to the nucleation of hexagonal Nb5Si3 grains in amorphous silicide layers at Nb/NbSi2 interfaces. These results are different from those reported for sputter deposited multilayer. (C) 2013 Elsevier B. V. All rights reserved.

AFM cantilever with integrated piezoelectric thin film for micro-actuation

This work presents micro-actuation of atomic force microscopy (AFM) cantilevers using piezoelectric Zinc Oxide (ZnO) thin film. In tapping mode AFM, the cantilever is driven near its resonant frequency by an external oscillator such as piezotube or stack of piezoelectric material. Use of integrated piezoelectric thin film for AFM cantilever eliminates the problems like inaccurate tuning and unwanted vibration modes. In this work, silicon AFM cantilevers were sputter deposited with ZnO piezoelectric film along with top and bottom metallic electrodes. The self-excitation of the ZnO coated AFM cantilever was studied using Laser Doppler Vibrometer (LDV). At its resonant frequency (227.11 kHz), the cantilever displacement varies linearly with applied excitation voltage. We observed an increase in the actuation response (131nm/V) due to improved quality of ZnO films deposited at 200 degrees C.

Feasibility of laser-induced breakdown spectroscopy for the study of the temporal distribution of trace elements trapped in snow collected from greater himalayan range

The potential merit of laser-induced breakdown spectroscopy (LIBS) has been demonstrated for detection and quantification of trace pollutants trapped in snow/ice samples. In this technique, a high-power pulsed laser beam from Nd:YAG Laser (Model no. Surelite III-10, Continuum, Santa Clara, CA, USA) is focused on the surface of the target to generate plasma. The characteristic emissions from laser-generated plasma are collected and recorded by a fiber-coupled LIBS 2000+ (Ocean Optics, Santa Clara, CA, USA) spectrometer. The fingerprint of the constituents present in the sample is obtained by analyzing the spectral lines by using OOI LIBS software. Reliable detection of several elements like Zn, Al, Mg, Fe, Ca, C, N, H, and O in snow/ice samples collected from different locations (elevation) of Manali and several snow samples collected from the Greater Himalayan region (from a cold lab in Manali, India) in different months has been demonstrated. The calibration curve approach has been adopted for the quantitative analysis of these elements like Zn, Al, Fe, and Mg. Our results clearly demonstrate that the level of contamination is higher in those samples that were collected in the month of January in comparison to those collected in February and March.

A study on pulsed laser deposited metallic spin valves

In the recent past conventional Spin Valve (SV) structures are gaining growing interest over Tunneling Magneto-resistance (TMR) because of its preference due to low RA product in hard disc read head sensor applications. Pulsed Laser Deposited (PLD) SV and Pseudo Spin Valve (PSV) samples are grown at room temperature with moderately high MR values using simple FM/NM/FM/AFM structure. Although PLD is not a popular technique to grow metallic SVs because of expected large intermixing of the interfaces, particulate formation, still by suitably adjusting the deposition parameters we could get exchange bias (EB) as well as 2-3% MR of these SVs in the Current In Plane (CIP) geometry. Exchange Bias, which sets in even without applying magnetic field during deposition observed by using SQUID magnetometry as well as by MR measurements. Angular variation of the MR reveals four-fold anisotropy of the hard layer (Co) which becomes two-fold in presence of an adjacent AFM layer.

Nanoindentation studies on waveguides inscribed in chalcogenide glasses using ultrafast laser

Optical straight waveguides are inscribed in GeGaS and GeGaSSb glasses using a high repetition-rate sub-picosecond laser. The mechanical properties of the glasses in the inscribed regions, which have undergone photo induced changes, have been evaluated by using the nanoindentation technique. Results show that the hardness and elastic modulus of the photo-modified glasses are significantly lower as compared to the other locations in the waveguide, which tend to be similar to those of the unexposed areas. The observed mechanical effects are found to correlate well with the optical properties of the waveguides. Further, based on the results, the minimum threshold values of hardness and elastic modulus for the particular propagation mode of the waveguide (single or multi), has been established.

Electron microscopy of microstructural transformation in electrodeposited Ni-rich, Ag-Ni film

Ag-Ni films were electrodeposited over a Cu substrate. Structural characterization revealed a fibrous microstructure with an amorphous structure for the as-deposited film. Isothermal annealing at 400 degrees C of the film inside transmission electron microscope led to amorphous-to-crystalline transition along with the evolution of nano-sized particles in the microstructure. The crystalline phase was Ni-Ag solid solution. The relative volume fraction of the nano-sized particles increased gradually with time. There was however no detectable decomposition of solid solution phase till about 4 h of annealing. Beyond 4 h phase separation initiated and pure Ag and Ni phases formed in the film. This study provides a methodology by which microstructural engineering of as-electrodeposited amorphous Ag-Ni films can be conducted to isolate a particular microstructure in order to tap specific potentially usable functionalities. (C) 2013 Elsevier B.V. All rights reserved.

Transmission electron microscopy study of Ni-rich, Ag-Ni nanowires

Present work provides an electrodeposition based methodology for synthesizing Ni-rich, Ag-Ni nanowires using an alumina template. Ag-Ni system shows negligible solid solubility in the bulk. Detailed structural and compositional characterization of as-synthesized nanowires using transmission electron microscopy technique revealed a two phase microstructure. Regions along and near the nanowire axis contained crystalline Ag-Ni solid solution phase with Ag-rich composition. Whereas, regions away from the axis and near the nanowire boundary predominantly contained nanocrystalline Ni-rich, Ni-Ag solid solution phase. (C) 2013 Elsevier B. V. All rights reserved.

Visualization of coherent structures in turbulent subsonic jet using planar laser induced fluorescence of acetone

In this paper, we present the molecular density distribution measurement in turbulent nitrogen jet (Re approximate to 3 x 10(3)), using acetone as molecular tracer. The tracer was seeded in the nitrogen jet by purging through the liquid acetone at ambient temperature. Planar laser sheet of 266 nm wavelength from frequency quadrupled, Q-switched, Nd:YAG laser was used as an excitation source. Emitted fluorescence images of jet flow field were recorded on CMOS camera. The dependence of planar laser induced fluorescence (PLIF) intensity on acetone vapor density was used to convert PLIF image of nitrogen jet into the density image on pixel-by-pixel basis. Instantaneous quantitative density image of nitrogen jet, seeded with acetone, was obtained. The arrowhead-shaped coherent turbulent structures were observed in the present work. It was found that coherent structures were non-overlapping with separate boundaries. Breaking of coherent structures into turbulence was clearly observed above four times jet width.

Determination of electric field at and near the focus of a cylindrical lens for applications in fluorescence microscopy

We present an explicit computable integral solution of the electric field generated at the focal region of a cylindrical lens. This representation is based on vectorial diffraction theory and further enables the computation of the system point spread function of a cylindrical lens. It is assumed that there is no back-scattering and the contribution from the evanescent field is negligible. Stationary phase approximation along with the Fresnel transmission coefficients are employed for evaluating the polarization dependent electric field components. Studies were carried out to determine the polarization effects and to calculate the system resolution. The effect of s -, p - and randomly polarized light is studied on the fixed sample (electric dipole is fixed in space). Proposed approach allows better understanding of electric field effects at the focus of a cylindrical aplanatic system. This opens up future developments in the field of fluorescence microscopy and optical imaging. (C) 2013 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License.

Continuous beam of laser-cooled Yb atoms

We demonstrate the launching of laser-cooled Yb atoms in a continuous atomic beam. The continuous cold beam has significant advantages over the more-common pulsed fountain, which was also demonstrated by us recently. The cold beam is formed in the following steps: i) atoms from a thermal beam are first Zeeman-slowed to a small final velocity; ii) the slowed atoms are captured in a two-dimensional magneto-optic trap (2D-MOT); and iii) atoms are launched continuously in the vertical direction using two sets of moving-molasses beams, inclined at +/- 15 degrees to the vertical. The cooling transition used is the strongly allowed S-1(0) -> P-1(1) transition at 399 nm. We capture about 7x10(6) atoms in the 2D-MOT, and then launch them with a vertical velocity of 13m/s at a longitudinal temperature of 125(6) mK. Copyright (C) EPLA, 2013

Generation of extended light-sheets for single and multi-photon fluorescence microscopy

We theoretically propose and computationally demonstrate the generation of extended light-sheet for fluorescence microscopy. This is made possible by the introduction of a specially designed double-window spatial filter that allows the light to pass through the periphery and center of a cylindrical lens. When illuminated with a plane wave, the proposed filter results in an extended depth-of-focus along with side-lobes which are due to other interferences in the transverse focal plane. Computational studies show a maximum extension of light-sheet by 3.38 times for single photon excitation and 3.68 times for multiphoton excitation as compared to state-of-art single plane illumination microscopy system. This technique may facilitate the study of large biological specimens (such as Zebrafish embryo and tissue) with high spatial resolution and reduced photobleaching. (C) 2013 AIP Publishing LLC.