Bright-field and fluorescence chip-scale microscopy for biological imaging

Optical microscopy is an essential tool in biological science and one of the gold standards for medical examinations. Miniaturization of microscopes can be a crucial stepping stone towards realizing compact, cost-effective and portable platforms for biomedical research and healthcare. This thesis reports on implementations of bright-field and fluorescence chip-scale microscopes for a variety of biological imaging applications. The term “chip-scale microscopy” refers to lensless imaging techniques realized in the form of mass-producible semiconductor devices, which transforms the fundamental design of optical microscopes.

Our strategy for chip-scale microscopy involves utilization of low-cost Complementary metal Oxide Semiconductor (CMOS) image sensors, computational image processing and micro-fabricated structural components. First, the sub-pixel resolving optofluidic microscope (SROFM), will be presented, which combines microfluidics and pixel super-resolution image reconstruction to perform high-throughput imaging of fluidic samples, such as blood cells. We discuss design parameters and construction of the device, as well as the resulting images and the resolution of the device, which was 0.66 µm at the highest acuity. The potential applications of SROFM for clinical diagnosis of malaria in the resource-limited settings is discussed.

Next, the implementations of ePetri, a self-imaging Petri dish platform with microscopy resolution, are presented. Here, we simply place the sample of interest on the surface of the image sensor and capture the direct shadow images under the illumination. By taking advantage of the inherent motion of the microorganisms, we achieve high resolution (~1 µm) imaging and long term culture of motile microorganisms over ultra large field-of-view (5.7 mm × 4.4 mm) in a specialized ePetri platform. We apply the pixel super-resolution reconstruction to a set of low-resolution shadow images of the microorganisms as they move across the sensing area of an image sensor chip and render an improved resolution image. We perform longitudinal study of Euglena gracilis cultured in an ePetri platform and image based analysis on the motion and morphology of the cells. The ePetri device for imaging non-motile cells are also demonstrated, by using the sweeping illumination of a light emitting diode (LED) matrix for pixel super-resolution reconstruction of sub-pixel shifted shadow images. Using this prototype device, we demonstrate the detection of waterborne parasites for the effective diagnosis of enteric parasite infection in resource-limited settings.

Then, we demonstrate the adaptation of a smartphone’s camera to function as a compact lensless microscope, which uses ambient illumination as its light source and does not require the incorporation of a dedicated light source. The method is also based on the image reconstruction with sweeping illumination technique, where the sequence of images are captured while the user is manually tilting the device around any ambient light source, such as the sun or a lamp. Image acquisition and reconstruction is performed on the device using a custom-built android application, constructing a stand-alone imaging device for field applications. We discuss the construction of the device using a commercial smartphone and demonstrate the imaging capabilities of our system.

Finally, we report on the implementation of fluorescence chip-scale microscope, based on a silo-filter structure fabricated on the pixel array of a CMOS image sensor. The extruded pixel design with metal walls between neighboring pixels successfully guides fluorescence emission through the thick absorptive filter to the photodiode layer of a pixel. Our silo-filter CMOS image sensor prototype achieves 13-µm resolution for fluorescence imaging over a wide field-of-view (4.8 mm × 4.4 mm). Here, we demonstrate bright-field and fluorescence longitudinal imaging of living cells in a compact, low-cost configuration.

The effect of the rotating double-prism wide-angle laser beam scanner on the beam shape

In this paper, we describe a wide-angle laser beam scanner and the rigorous result of the wide-angle laser beam scanner was obtained with the help of the vector refraction theory. Using the rigorous results, the distortion of the beam shape was discussed. The distortion of the beam shape is varying with the different relative angles of the double prisms. According to the conservation of the energy, the distribution of the laser intensity is changed too. (c) 2005 Elsevier GmbH. All rights reserved.

Research on a scanner for tilting orthogonal double prisms

The original scanner for tilting orthogonal double prisms is studied to test the tracking performance in intersatellite laser communications. With a reduction ratio of more than 100 times from the change rate of the angle of beam deviation to that of the tilting angle of each prism, the theoretical analysis performed, as well as the verification experiment, indicates that the scanner can meet the requirements of the scanning accuracy superior to 0.5 mu rad with the scanning range greater than 500 mu rad and can facilitate the mechanical structure design. (c) 2006 Optical Society of America.

Invertible dark-center diffraction of the metal film induced by femtosecond laser

We found reversible dark-center diffraction of the transmitted probe beam passing through the chromium film. which is induced by the pump femtosecond laser. The dark-center diffraction of I he transmitted probe beam appears and disappears with and without the pump beam. A view of diffractive optics with binary phase plate is put forward, which explains the reversible dark-center diffractive optical phenomenon. The pre-ablated hole on the metal film can be regarded as a uniform light filed without phase modulation, the Surrounding Circular part around the pre-ablated hole can be regarded as "phase modulated". Therefore, this diffraction optic view might be helpful for us to understand the phase change of the metal film introduced by the femtosecond laser pulse. (C) 2008 Elsevier B.V, All rights reserved.

A metal-mirror-based reflecting polarizing beam splitter

We theoretically investigated the design of a metal-mirror-based reflecting polarizing beam splitter (RPBS). The metal mirror is a silver slab, which is embedded in the substrate of a rectangular silica transmission grating. By using a modal analysis and rigorous coupled-wave analysis, an RPBS grating is designed for operation at 1550 nm. When it is illuminated in Littrow mounting, the transverse electric (TE) and transverse magnetic (TM) waves will be mainly reflected in the minus-first and zeroth orders, respectively. Moreover, a wideband RPBS grating is obtained by adopting the simulated annealing algorithm. The RPBS gratings exhibit high diffraction efficiencies (similar to 95%) and high extinction ratios over a certain angle and wavelength range, especially for the minus-first-order reflection. This kind of RPBS should be useful in practical optical applications.

La secuencia del Neolítico en La Rioja Alavesa desde su origen hasta las primeras edades del metal

Homenaje a Ignacio Barandiarán Maestu / coord. por Javier Fernández Eraso, Juan Santos Yanguas

The study of biological characteristics and heavy metal determination of Cd, Pb, Fe, V, Ni in the muscle, liver and gonad tissues of kingfish Scomberomorus commerson in the coastal waters of the Hormozagan Province (Persian Gulf)

Biological studies and heavy metal (Ni, v, Fe, Pb,Cd) determination in liver, gonad and muscle of Scomberomorus commerson were carried out from Oct 2006 to Sept 2007 in Hormozgan coastal waters. 599 Samples were gutted for reproduction and nutrition studies, fork length and weight were measured to nearest cm and g respectively. Meanwhile 40 samples were also investigated for heavy metal studies. All specimens were collected from two major landing sites (Bandar Lengeh & Bandar Abbas). Minimums & maximum fork length & weight were 29, 128 cm & 235 and 15350 g respectively.Isometric growth was shown according to our study and b was estimated 2.9 (overall), 2.91(male) & 2.89 (female). The average relative gut length was 0.52± 0.007 and it was determined that S. commerson is a carnivorous. More than 99 percent of gut content was different teleost fishes. Gastro somatic index had two peaks in Nov & Jan (before spawning) and with a decreased trend in July, the spawning period. Occurrence of empty stomach was estimated % 65.77. Maximum amount of condition factor was in Dec. Spawning season was started from June. The average of Absolute & relative fecundity (to weight unit) was 1217149±179315 and 178.2±15.58 respectively. Lm50% was estimated 75 cm for females. Sex ratio was 0.97: 1 (male: female). Chi- Square test showed no significant difference (p>0.05). Maximum amount of hepatosomatic index was estimated in March.Metal concentrations were determined using either Flame Atomic Absorption Spectroscopy (for Fe) or Graphite Furnace Atomic Absorption Spectroscopy (for Pb,Cd,Ni and V). The mean concentration (μg/g dry weight)of Pb,Cd,Ni,V and Fe in the liver were 0.0309, 0.0268, 0.0672, 0.0077, 2.5159 in the gonad 0.0440 ,0.0295, 0.1096, 0.0000, 1.4449 and in the muscle 0.0244, 0.0324, 0.0656, 0.0128, 1.6138 respectively. The maximum metal concentrations were below the maximum permissible limits for human consumption recommended by the USEPA, WHO and the UK. The results of Kendall's Tau-b correlation coefficient were as follows: The Liver tissue: There were significant positive linear relationships between accumulation of V, Fe, and Pb with Fork length, Pb and Fe with weight, GSI with Pb, Cd, V and 109 Fe, and a negative linear relationships between HSI with accumulation of V and Fe, Fork length, weight and GSI. The Gonad tissue: There were significant positive linear relationships between GSI with accumulation of Pb, Cd, Fe, Fork length and weight, a negative linear relationship between HSI with Fork length, weight and GSI. The Muscle tissue: There were significant positive linear relationships between accumulations of V, Fe with Fork length and weight factors and as well as GSI with Cd, V, Fe, Pb, Fork length and weight,a negative linear relationship between HSI with Fork length, weight, Cd, Fe and GSI. The results of Mann-Whitney U tests (P≤0.05) show that there were significant differences between summer and autumn from heavy metal contents in the studied tissues point of view. The only exceptions were for Ni in the liver, gonads and muscle and as well as there were significant differences between male and female from heavy metal contents in the studied tissues. The only exceptions were for Pb in muscle, Ni in liver, gonad and muscle, V in muscle, and Cd and Fe in gonads.

Individual grain boundary properties and overall performance of metal-organic-deposition coated conductors

We have investigated single grain boundaries (GBs) isolated in coated conductors produced by Metal-Organic Deposition (MOD). When a magnetic field is swept in the film plane, an angle-dependent crossover from boundary to grain limited critical current density Jc is found. In the force-free orientation, even at fields as high as 8 T, the GBs still limit Jc. We deduce that this effect is a direct consequence of GB meandering. We have employed these single GB results to explain the dependence of Jc of polycrystalline tracks on their width: in-plane measurements become flatter as the tracks are narrowed down. This result is consistent with the stronger GB limitation at field configurations close to force-free found from the isolated boundaries. Our study shows that for certain geometries even at high fields the effect of GBs cannot be neglected.

An experimental study of loss sources in a fan operating with continuous inlet stagnation pressure distortion

The viability of Boundary Layer Ingesting (BLI) engines for future aircraft propulsion is dependent on the ability to design robust, efficient engine fan systems for operation with continuously distorted inlet flow. A key step in this process is to develop an understanding of the specific mechanisms by which an inlet distortion affects the performance of a fan stage. In this paper, detailed full-annulus experimental measurements of the flow field within a low-speed fan stage operating with a continuous 60-degree inlet stagnation pressure distortion are presented. These results are used to describe the three-dimensional fluid mechanics governing the interaction between the fan and the distortion and to make a quantitative assessment of the impact on loss generation within the fan. A 5.3 percentage point reduction in stage total-to-total efficiency is observed as a result of the inlet distortion. The reduction in performance is shown to be dominated by increased loss generation in the rotor due to off-design incidence values at its leading edge, an effect which occurs throughout the annulus despite the localised nature of the inlet distortion. Increased loss generation in the stator row is also observed due to flow separations that are shown to be caused by whirl angle distortion at rotor exit. By addressing these losses, it should be possible to achieve improved efficiency in BLI fan systems. Copyright © 2012 by ASME.

An experimental study of loss sources in a fan operating with continuous inlet stagnation pressure distortion

The viability of boundary layer ingesting (BLI) engines for future aircraft propulsion is dependent on the ability to design robust, efficient engine fan systems for operation with continuously distorted inlet flow. A key step in this process is to develop an understanding of the specific mechanisms by which an inlet distortion affects the performance of a fan stage. In this paper, detailed full-annulus experimental measurements of the flow field within a low-speed fan stage operating with a continuous 60 deg inlet stagnation pressure distortion are presented. These results are used to describe the three-dimensional fluid mechanics governing the interaction between the fan and the distortion and to make a quantitative assessment of the impact on loss generation within the fan. A 5.3 percentage point reduction in stage total-to-total efficiency is observed as a result of the inlet distortion. The reduction in performance is shown to be dominated by increased loss generation in the rotor due to off-design incidence values at its leading edge, an effect that occurs throughout the annulus despite the localized nature of the inlet distortion. Increased loss in the stator row is also observed due to flow separations that are shown to be caused by whirl angle distortion at rotor exit. By addressing these losses, it should be possible to achieve improved efficiency in BLI fan systems. © 2013 by ASME.

Mode Analysis for Equilateral-Triangle-Resonator Microlasers with Metal Confinement Layers

Mode characteristics are analyzed for electrically injected equilateral-triangle-resonator (ETR) semiconductor microlasers, which are laterally confined by insulating barrier SiO2 and electrode metals Ti-Au. For the ETR without metal layers, the totally confined mode field patterns are derived based on the reflection phase shifts, and the Q-factors are calculated from the far-field emission of the analytical near field distribution, which are agreement very well with the numerical results of the finite-difference time-domain (FDTD) simulation. The polarization dependence reflections for light rays incident on semiconductor-SiO2 -Ti-Au multi-layer structures are accounted in considering the confinement of TE and TM modes in the ETR with the metal layers. The reflectivity will greatly reduce with a Ti layer between SiO2 and Au for light rays with incident angle less than 30 especially for the TE mode, even the thickness of the Ti layer is only 10 nm. If the ETR is laterally confined by SiO2-Au layers without the Ti layer, the Fabry-Perot type modes with an incident angle of zero on one side of the ETR can also have high Q-factor. The FDTD simulation for the ETR confined by metal layers verifies the above analysis based on multi-layer reflections. The output spectra with mode intervals of whispering-gallery modes and Fabry-Perot type modes are observed from different ETR lasers with side length of 10 m, respectively.

Phase-separation suppression in GaN-rich side of GaNP alloys grown by metal-organic chemical vapor deposition

The GaN-rich side of GaNP ternary alloys has been successfully synthesized by light-radiation heating and low-pressure metal-organic chemical vapor deposition. X-ray diffraction (XRD) rocking curves show that the ( 0002) peak of GaNP shifts to a smaller angle with increasing P content. From the GaNP photoluminescence (PL) spectra, the red shifts from the band-edge emission of GaN are determined to be 73, 78 and 100 meV, respectively, in the GaNP alloys with the P contents of 1.5%, 5.5% and 7.5%. No PL peak or XRD peak related to GaP is observed, indicating that phase separation induced by the short-range distribution of GaP-rich regions in the GaNP layer has been effectively suppressed. The phase-separation suppression in the GaNP layer is associated with the high growth rate and the quick cooling rate under the given growth conditions, which can efficiently restrain the accumulation of P atoms in the GaNP layer.

Laterally confined modes in wet-etched, metal-coated, quantum-dot-inserted pillar microcavities

We report the fabrication and the measurement of microcavities whose optical eigenmodes were discrete and were well predicted by using the model of the photonic dot with perfectly reflected sidewalls. These microcavities were consisted of the semiconductor pillar fabricated by the simple wet-etched process and successive metal coating. Angle-resolved photoluminescence spectra demonstrate the characteristic emission of the corresponding eigenmodes, as its pattern revealed by varying both polar (0) and azimuthal (45) angles. It is shown that the metal-coated sidewalls can provide an efficient way to suppress the emission due to the leaking modes in these pillar microcavities.

The microstructure of hydrogenated microcrystalline silicon thin films studied by small-angle x-ray scattering

The microstructures of hydrogenated microcrystalline silicon (tic-Si: H) thin films, prepared by plasma-enhanced chemical vapor deposition (PECVD), hot wire CVD(HWCVD) and plasma assisted HWCVD (PE-HWCVD), have been analyzed by the small angle x-ray scattering(SAXS) measurement. The SAXS data show that the microstructures of the μ c-Si: H films display different characteristics for different deposition techniques. For films deposited by PECVD, the volume fraction of micro-voids and mean size are smaller than those in HWCVD sample. Aided by suitable ion-bombardment, PE-HWCVD samples show a more compact structure than the HWCVD sample. The microstructure parameters of the μ c-Si: H thin films deposited by two-steps HWCVD and PE-HWCVD with Ar ions are evidently improved. The result of 45° tilting SAXS measurement indicates that the distribution of micro-voids in the film is anisotropic. The Fouriertransform infrared spectra confirm the SAXS data.

GaN1-xPx ternary alloys with high P composition grown by metal-organic chemical vapor deposition

GaN1-xPx ternary alloys with high P compositions were deposited on sapphire substrates by means of metal-organic chemical vapor deposition. Depth profiles of the elements indicate that the maximum P/N composition ratio is about 17% and a uniform distribution of the P atoms in the alloys is achieved. 2theta/omega XRD spectra demonstrate that the (0002) peak of the GaN1-xPx alloys shifts to smaller angle with increasing P composition. From the photoluminescence (PL) spectra, the red shifts to the bandedge emission of GaN are determined to be 73, 78, 100 and 87 meV for the GaN1-xPx alloys with the P/N composition ratios of 3%, 11%, 15% and 17%, respectively. No PL peak related to GaP is observed, indicating that the phase separation between GaN and GaP is well suppressed in our GaN1-xPx samples. (C) 2003 Elsevier Science B.V. All rights reserved.