Operator-induced errors in Hartmann-Shack wavefront sensing:model eye study

Purpose: To evaluate the effects of instrument realignment and angular misalignment during the clinical determination of wavefront aberrations by simulation in model eyes. Setting: Aston Academy of Life Sciences, Aston University, Birmingham, United Kingdom. Methods: Six model eyes were examined with wavefront-aberration-supported cornea ablation (WASCA) (Carl Zeiss Meditec) in 4 sessions of 10 measurements each: sessions 1 and 2, consecutive repeated measures without realignment; session 3, realignment of the instrument between readings; session 4, measurements without realignment but with the model eye shifted 6 degrees angularly. Intersession repeatability and the effects of realignment and misalignment were obtained by comparing the measurements in the various sessions for coma, spherical aberration, and higher-order aberrations (HOAs). Results: The mean differences between the 2 sessions without realignment of the instrument were 0.020 μm ± 0.076 (SD) for Z3 - 1(P = .551), 0.009 ± 0.139 μm for Z3 1(P = .877), 0.004 ± 0.037 μm for Z4 0 (P = .820), and 0.005 ± 0.01 μm for HO root mean square (RMS) (P = .301). Differences between the nonrealigned and realigned instruments were -0.017 ± 0.026 μm for Z3 - 1(P = .159), 0.009 ± 0.028 μm for Z3 1 (P = .475), 0.007 ± 0.014 μm for Z4 0(P = .296), and 0.002 ± 0.007 μm for HO RMS (P = 0.529; differences between centered and misaligned instruments were -0.355 ± 0.149 μm for Z3 - 1 (P = .002), 0.007 ± 0.034 μm for Z3 1(P = .620), -0.005 ± 0.081 μm for Z4 0(P = .885), and 0.012 ± 0.020 μm for HO RMS (P = .195). Realignment increased the standard deviation by a factor of 3 compared with the first session without realignment. Conclusions: Repeatability of the WASCA was excellent in all situations tested. Realignment substantially increased the variance of the measurements. Angular misalignment can result in significant errors, particularly in the determination of coma. These findings are important when assessing highly aberrated eyes during follow-up or before surgery. © 2007 ASCRS and ESCRS.

Two-wavelength whole-field interferometry setup for thermal lens study

In this paper we present a new approach for thermal lens analysis using a two-wavelength DSPI (Digital Speckle Pattern Interferometry) setup for wavefront sensing. The employed geometry enables the sensor to detect wavefronts with small phase differences and inherent aberrations found in induced lenses. The wavefronts was reconstructed by four-stepping fringe evaluation and branch-cut unwrapping from fringes formed onto a diffusive glass. Real-time single-exposure contour interferograms could be obtained in order to get discernible and low-spacial frequency contour fringes and obtain low-noise measurements. In our experiments we studied the thermal lens effect in a 4% Er-doped CaO-Al2O3 glass sample. The diode lasers were tuned to have a contour interval of around 120 μm. The incident pump power was longitudinally and collinearly oriented with the probe beams. Each interferogram described a spherical-like wavefront. Using the ABCD matrix formalism we obtained the induced lens dioptric power from the thermal effect for different values of absorbed pump power. © 2012 Copyright SPIE.

Accommodative response to electrical stimulation of the sclera of peripheral cornea in cats and porcines

Purpose: We have reported that the changes in the accommodative response to electrical stimulation of the branches of the ciliary nerves in cats. (Miyagawa et al, PLoS One, 2014). We have also reported that no robust accommodative responses to the electrical stimulations of the sclera of peripheral cornea (SSPC) were observed in enucleated porcine eyes (Mihashi et al, VPOptics, 2014). In this study, accommodative responses to SSPC stimulation in cats and porcines were investigated. Methods: Two eyes of two cats under anesthesia and after they were sacrificed were studied. Three enucleated porcine eyes obtained from a local slaughterhouse were also studied. Trains of biphasic pulses (current, 3 mA; duration, 2 ms/phase; frequency, 40 Hz) were applied using a tungsten electrode (0.3mm diameter) from several orientations. Wavefront sensing with a compact wavefront aberrometer (Uday et al J Cataract Refract Surg, 2013) were performed before and 4 s (cat) and 10 s (pig) after the stimulations and wavefront aberrations including spherical errors were analyzed over a 4-mm pupil area. Results: In the first cat under anesthesia, at three out of seven stimulus positions, 0.2 D hyperopic accommodative responses were observed and in two orientations, myopic responses were observed. For the other cat, weak accommodative responses including astigmatic changes were observed. In the sacrificed condition of the second cat, 0.1 D myopic response was observed for one stimulus orientation and the smaller responses were observed at six out of eight stimulus positions. No accommodative responses were elicited for the enucleated porcine eyes. Conclusions: In the anesthetized cats, electrical stimulation of the SSPC induced accommodative responses; the responses were unstable and weaker than the responses by the ciliary nerve stimulations we observed in our previous study. Small accommodative responses were observed after one of two cats had been sacrificed, but no accommodative responses were detected in the enucleated porcine eyes. Further studies are needed to confirm difference in the accommodation functions in the two species.

Enhancing the Visualization of the Peripheral Retina with Wide Field-of-View Optical Coherence Tomography

The goal of my Ph.D. thesis is to enhance the visualization of the peripheral retina using wide-field optical coherence tomography (OCT) in a clinical setting.

OCT has gain widespread adoption in clinical ophthalmology due to its ability to visualize the diseases of the macula and central retina in three-dimensions, however, clinical OCT has a limited field-of-view of 300. There has been increasing interest to obtain high-resolution images outside of this narrow field-of-view, because three-dimensional imaging of the peripheral retina may prove to be important in the early detection of neurodegenerative diseases, such as Alzheimer's and dementia, and the monitoring of known ocular diseases, such as diabetic retinopathy, retinal vein occlusions, and choroid masses.

Before attempting to build a wide-field OCT system, we need to better understand the peripheral optics of the human eye. Shack-Hartmann wavefront sensors are commonly used tools for measuring the optical imperfections of the eye, but their acquisition speed is limited by their underlying camera hardware. The first aim of my thesis research is to create a fast method of ocular wavefront sensing such that we can measure the wavefront aberrations at numerous points across a wide visual field. In order to address aim one, we will develop a sparse Zernike reconstruction technique (SPARZER) that will enable Shack-Hartmann wavefront sensors to use as little as 1/10th of the data that would normally be required for an accurate wavefront reading. If less data needs to be acquired, then we can increase the speed at which wavefronts can be recorded.

For my second aim, we will create a sophisticated optical model that reproduces the measured aberrations of the human eye. If we know how the average eye's optics distort light, then we can engineer ophthalmic imaging systems that preemptively cancel inherent ocular aberrations. This invention will help the retinal imaging community to design systems that are capable of acquiring high resolution images across a wide visual field. The proposed model eye is also of interest to the field of vision science as it aids in the study of how anatomy affects visual performance in the peripheral retina.

Using the optical model from aim two, we will design and reduce to practice a clinical OCT system that is capable of imaging a large (800) field-of-view with enhanced visualization of the peripheral retina. A key aspect of this third and final aim is to make the imaging system compatible with standard clinical practices. To this end, we will incorporate sensorless adaptive optics in order to correct the inter- and intra- patient variability in ophthalmic aberrations. Sensorless adaptive optics will improve both the brightness (signal) and clarity (resolution) of features in the peripheral retina without affecting the size of the imaging system.

The proposed work should not only be a noteworthy contribution to the ophthalmic and engineering communities, but it should strengthen our existing collaborations with the Duke Eye Center by advancing their capability to diagnose pathologies of the peripheral retinal.

the plenoptic sensor

In this thesis, we will introduce the innovative concept of a plenoptic sensor that can determine the phase and amplitude distortion in a coherent beam, for example a laser beam that has propagated through the turbulent atmosphere.. The plenoptic sensor can be applied to situations involving strong or deep atmospheric turbulence. This can improve free space optical communications by maintaining optical links more intelligently and efficiently. Also, in directed energy applications, the plenoptic sensor and its fast reconstruction algorithm can give instantaneous instructions to an adaptive optics (AO) system to create intelligent corrections in directing a beam through atmospheric turbulence. The hardware structure of the plenoptic sensor uses an objective lens and a microlens array (MLA) to form a mini “Keplerian” telescope array that shares the common objective lens. In principle, the objective lens helps to detect the phase gradient of the distorted laser beam and the microlens array (MLA) helps to retrieve the geometry of the distorted beam in various gradient segments. The software layer of the plenoptic sensor is developed based on different applications. Intuitively, since the device maximizes the observation of the light field in front of the sensor, different algorithms can be developed, such as detecting the atmospheric turbulence effects as well as retrieving undistorted images of distant objects. Efficient 3D simulations on atmospheric turbulence based on geometric optics have been established to help us perform optimization on system design and verify the correctness of our algorithms. A number of experimental platforms have been built to implement the plenoptic sensor in various application concepts and show its improvements when compared with traditional wavefront sensors. As a result, the plenoptic sensor brings a revolution to the study of atmospheric turbulence and generates new approaches to handle turbulence effect better.

Two roads to planet detection

One of the most exciting discoveries in astrophysics of the last last decade is of the sheer diversity of planetary systems. These include "hot Jupiters", giant planets so close to their host stars that they orbit once every few days; "Super-Earths", planets with sizes intermediate to those of Earth and Neptune, of which no analogs exist in our own solar system; multi-planet systems with planets smaller than Mars to larger than Jupiter; planets orbiting binary stars; free-floating planets flying through the emptiness of space without any star; even planets orbiting pulsars. Despite these remarkable discoveries, the field is still young, and there are many areas about which precious little is known. In particular, we don't know the planets orbiting Sun-like stars nearest to our own solar system, and we know very little about the compositions of extrasolar planets. This thesis provides developments in those directions, through two instrumentation projects.

The first chapter of this thesis concerns detecting planets in the Solar neighborhood using precision stellar radial velocities, also known as the Doppler technique. We present an analysis determining the most efficient way to detect planets considering factors such as spectral type, wavelengths of observation, spectrograph resolution, observing time, and instrumental sensitivity. We show that G and K dwarfs observed at 400-600 nm are the best targets for surveys complete down to a given planet mass and out to a specified orbital period. Overall we find that M dwarfs observed at 700-800 nm are the best targets for habitable-zone planets, particularly when including the effects of systematic noise floors caused by instrumental imperfections. Somewhat surprisingly, we demonstrate that a modestly sized observatory, with a dedicated observing program, is up to the task of discovering such planets.

We present just such an observatory in the second chapter, called the "MINiature Exoplanet Radial Velocity Array," or MINERVA. We describe the design, which uses a novel multi-aperture approach to increase stability and performance through lower system etendue, as well as keeping costs and time to deployment down. We present calculations of the expected planet yield, and data showing the system performance from our testing and development of the system at Caltech's campus. We also present the motivation, design, and performance of a fiber coupling system for the array, critical for efficiently and reliably bringing light from the telescopes to the spectrograph. We finish by presenting the current status of MINERVA, operational at Mt. Hopkins observatory in Arizona.

The second part of this thesis concerns a very different method of planet detection, direct imaging, which involves discovery and characterization of planets by collecting and analyzing their light. Directly analyzing planetary light is the most promising way to study their atmospheres, formation histories, and compositions. Direct imaging is extremely challenging, as it requires a high performance adaptive optics system to unblur the point-spread function of the parent star through the atmosphere, a coronagraph to suppress stellar diffraction, and image post-processing to remove non-common path "speckle" aberrations that can overwhelm any planetary companions.

To this end, we present the "Stellar Double Coronagraph," or SDC, a flexible coronagraphic platform for use with the 200" Hale telescope. It has two focal and pupil planes, allowing for a number of different observing modes, including multiple vortex phase masks in series for improved contrast and inner working angle behind the obscured aperture of the telescope. We present the motivation, design, performance, and data reduction pipeline of the instrument. In the following chapter, we present some early science results, including the first image of a companion to the star delta Andromeda, which had been previously hypothesized but never seen.

A further chapter presents a wavefront control code developed for the instrument, using the technique of "speckle nulling," which can remove optical aberrations from the system using the deformable mirror of the adaptive optics system. This code allows for improved contrast and inner working angles, and was written in a modular style so as to be portable to other high contrast imaging platforms. We present its performance on optical, near-infrared, and thermal infrared instruments on the Palomar and Keck telescopes, showing how it can improve contrasts by a factor of a few in less than ten iterations.

One of the large challenges in direct imaging is sensing and correcting the electric field in the focal plane to remove scattered light that can be much brighter than any planets. In the last chapter, we present a new method of focal-plane wavefront sensing, combining a coronagraph with a simple phase-shifting interferometer. We present its design and implementation on the Stellar Double Coronagraph, demonstrating its ability to create regions of high contrast by measuring and correcting for optical aberrations in the focal plane. Finally, we derive how it is possible to use the same hardware to distinguish companions from speckle errors using the principles of optical coherence. We present results observing the brown dwarf HD 49197b, demonstrating the ability to detect it despite it being buried in the speckle noise floor. We believe this is the first detection of a substellar companion using the coherence properties of light.

Remote sensing the vertical profile of cloud droplet effective radius, thermodynamic phase, and temperature

Cloud-aerosol interaction is a key issue in the climate system, affecting the water cycle, the weather, and the total energy balance including the spatial and temporal distribution of latent heat release. Information on the vertical distribution of cloud droplet microphysics and thermodynamic phase as a function of temperature or height, can be correlated with details of the aerosol field to provide insight on how these particles are affecting cloud properties and their consequences to cloud lifetime, precipitation, water cycle, and general energy balance. Unfortunately, today's experimental methods still lack the observational tools that can characterize the true evolution of the cloud microphysical, spatial and temporal structure in the cloud droplet scale, and then link these characteristics to environmental factors and properties of the cloud condensation nuclei. Here we propose and demonstrate a new experimental approach (the cloud scanner instrument) that provides the microphysical information missed in current experiments and remote sensing options. Cloud scanner measurements can be performed from aircraft, ground, or satellite by scanning the side of the clouds from the base to the top, providing us with the unique opportunity of obtaining snapshots of the cloud droplet microphysical and thermodynamic states as a function of height and brightness temperature in clouds at several development stages. The brightness temperature profile of the cloud side can be directly associated with the thermodynamic phase of the droplets to provide information on the glaciation temperature as a function of different ambient conditions, aerosol concentration, and type. An aircraft prototype of the cloud scanner was built and flew in a field campaign in Brazil. The CLAIM-3D (3-Dimensional Cloud Aerosol Interaction Mission) satellite concept proposed here combines several techniques to simultaneously measure the vertical profile of cloud microphysics, thermodynamic phase, brightness temperature, and aerosol amount and type in the neighborhood of the clouds. The wide wavelength range, and the use of multi-angle polarization measurements proposed for this mission allow us to estimate the availability and characteristics of aerosol particles acting as cloud condensation nuclei, and their effects on the cloud microphysical structure. These results can provide unprecedented details on the response of cloud droplet microphysics to natural and anthropogenic aerosols in the size scale where the interaction really happens.

Energy dissipation in depth-sensing indentation as a characteristic of the nanoscratch behavior of coatings

Wear behavior of coatings has usually been described in terms of mechanical properties such as hardness (H) and effective elastic modulus (E*). Alternatively, an energy approach appears as a promising analysis taking into account the influence of those properties. In a nanoindentation test, the dissipated energy depends not only on the hardness and elastic modulus, but also on the elastic recovery (W(e)). This work aims to establish a relation between plastic deformation energy (E(p)) during depth-sensing indentation method and the grooving resistance of coatings in nanoscratch tests. An energy dissipation coefficient (K(d)) was defined, calculated as the ratio of the plastic to the total deformation energy (E(p)/E(t)), which represents the energy dissipation of materials. Reactive depositions using titanium as the target and nitrogen and methane as reactive gases were obtained by triode magnetron sputtering, in order to assess wear and nanoindentation data. A topographical, chemical and microstructural characterization has been conducted using X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), wave dispersion spectroscopy (WDS), scanning electron (SEM) and atomic force microscopy (AFM) techniques. Nanoscratch results showed that the groove depth was well correlated to the energy dissipation coefficient of the coatings. On the other hand, a reduction in the coefficient was found when the elastic recovery was increased. (C) 2009 Elsevier B.V. All rights reserved.

KDP/PEDOT: PSS mixture as a new alternative in the fabrication of pressure sensing devices

In this work we studied the mixture of poly(3,4-ethylenedioxythiophene): poly(styrenesulfonate) (PEDOT:PSS), a commercial polymer, with monobasic potassium phosphate (KDP), a piezoelectric salt, as a possible novel material in the fabrication of a low cost, easy-to-make,flexible pressure sensing device. The mixture between KDP and PEDOT: PSS was painted in a flexible polyester substrate and dried. Afterwards, I x V curves were carried out. The samples containing KDP presented higher values of current in smaller voltages than the PEDOT: PSS without KDP. This can mean a change in the chain arrays. Other results showed that the material responds to directly applied pressure to the sample that can be useful to sensors fabrication. (c) 2008 Elsevier B.V. All rights reserved.

In silico analysis of candidate genes involved in light sensing and signal transduction pathways in soybean

Several aspects of photoperception and light signal transduction have been elucidated by studies with model plants. However, the information available for economically important crops, such as Fabaceae species, is scarce. In order to incorporate the existing genomic tools into a strategy to advance soybean research, we have investigated publicly available expressed sequence tag ( EST) sequence databases in order to identify Glycine max sequences related to genes involved in light-regulated developmental control in model plants. Approximately 38,000 sequences from open-access databases were investigated, and all bona fide and putative photoreceptor gene families were found in soybean sequence databases. We have identified G. max orthologs for several families of transcriptional regulators and cytoplasmic proteins mediating photoreceptor-induced responses, although some important Arabidopsis phytochrome-signaling components are absent. Moreover, soybean and Arabidopsis gene-family homologs appear to have undergone a distinct expansion process in some cases. We propose a working model of light perception, signal transduction and response-eliciting in G. max, based on the identified key components from Arabidopsis. These results demonstrate the power of comparative genomics between model systems and crop species to elucidate several aspects of plant physiology and metabolism.

Quorum sensing detected by atomic force microscopy imaging of corrals surrounding multicellular arrangement of bacteria

Connectivity of the glycocalyx covering of small communities of Acidithiobacillus ferrooxidans bacteria deposited on hydrophilic mica plates was imaged by atomic force microscopy. When part of the coverage was removed by water rinsing, an insoluble structure formed by corrals surrounding each individual bacterium was observed. A collective ring structure with clustered bacteria (>= 3) was observed, which indicates that the bacteria perceived the neighborhood in order to grow a protective structure that results in smaller production of exopolysaccharides material. The most surprising aspect of these collective corral structures was that they occur at a low bacterial cell density. The deposited layers were also analyzed by confocal Raman microscopy and shown to contain polysaccharides, protein, and glucoronic acid.

Phosphatidylinositol phospholipase C mediates carbon sensing and vegetative nuclear duplication rates in Aspergillus nidulans

In this work, we disrupted one of three putative phosphatidylinositol phospholipase C genes of Aspergillus nidulans and studied its effect on carbon source sensing linked to vegetative mitotic nuclear division. We showed that glucose does not affect nuclear division rates during early vegetative conidial germination (6-7 h) in either the wild type or the plcA-deficient mutant. Only after 8 h of cultivation on glucose did the mutant strain present some decrease in nuclear duplication. However, decreased nuclear division rates were observed in the wild type when cultivated in media amended with polypectate, whereas our plcA-deficient mutant did not show slow nuclear duplication rates when grown on this carbon source, even though it requires induction and secretion of multiple pectinolytic enzymes to be metabolized. Thus, plcA appears to be directly linked to high-molecular-weight carbon source sensing.

Attenuation of Pseudomonas aeruginosa virulence by quorum sensing inhibitors

Traditional treatment of infectious diseases is based on compounds that kill or inhibit growth of bacteria. A major concern with this approach is the frequent development of resistance to antibiotics. The discovery of communication systems (quorum sensing systems) regulating bacterial virulence has afforded a novel opportunity to control infectious bacteria without interfering with growth. Compounds that can override communication signals have been found in the marine environment. Using Pseudomonas aeruginosa PAO1 as an example of an opportunistic human pathogen, we show that a synthetic derivate of natural furanone compounds can act as a potent antagonist of bacterial quorum sensing. We employed GeneChip((R)) microarray technology to identify furanone target genes and to map the quorum sensing regulon. The transcriptome analysis showed that the furanone drug specifically targeted quorum sensing systems and inhibited virulence factor expression. Application of the drug to P.aeruginosa biofilms increased bacterial susceptibility to tobramycin and SDS. In a mouse pulmonary infection model, the drug inhibited quorum sensing of the infecting bacteria and promoted their clearance by the mouse immune response.

Wavefront analysis and modulation transfer function of three multifocal intraocular lenses

Purpose: To evaluate wavefront performance and modulation transfer function (MTF) in the human eye aft er the implantation of diffractive or refractive multifocal intraocular lenses (IOLs). Materials and Methods: This was a prospective, interventional, comparative, nonrandomized clinical study. Uncorrected distance and near visual acuity, and wavefront analysis including MTF curves (iTrace aberrometer, Tracey Technologies, Houston, TX, USA) were measured in 60 patients aft er bilateral IOL implantation with 6 months of follow-up. Forty eyes received the diffractive ReSTOR (Alcon), 40 eyes received the refractive ReZoom (Advanced Medical Optics) and 40 eyes, the Tecnis ZM900 (Advanced Medical Optics). The comparison of MTF and aberration between the intraocular lenses was performed using analysis of variance (ANOVA), followed by the Dunn test when necessary. Results: The mean uncorrected distance visual acuity was similar in all three groups of multifocal IOLs. The ReSTOR group provided better uncorrected near visual acuity than the ReZoom group (P < 0.001), but similar to the Tecnis group. Spherical aberration was significantly higher in the ReZoom group (P = 0.007). Similar MTF curves were found for the aspheric multifocal IOL Tecnis and the spheric multifocal IOL ReSTOR, and both performed better than the multifocal IOL ReZoom in a 5 mm pupil (P < 0.001 at all spatial frequencies). Conclusions: Diffractive IOLs studied presented similar MTF curves for a 5 mm pupil diameter. Both diffractive IOLs showed similar spherical aberration, which was significantly better with the full-diffractive IOL Tecnis than with the refractive IOL ReZoom.

Wavefront Analysis, Contrast Sensitivity, and Depth of Focus After Cataract Surgery With Aspherical Intraocular Lens Implantation

PURPOSE: To determine whether implantation of an aspherical intraocular lens (IOL) results in reduced ocular aberrations and improved contrast sensitivity after cataract surgery without critical reduction of depth of focus. DESIGN: Double-blinded, randomized, prospective study. METHODS: In an intraindividual study of 25 patients with bilateral cataract, an aspherical IOL (Akreos Advanced Optic [AO]; Bausch & Lomb, Inc., Rochester, New York, USA) was implanted in one eye and a spherical IOL (Akreos Fit; Bausch & Lomb, Inc) in the fellow eye. Higher-order aberrations with a 5- and 6-mm pupil were measured with a dynamic retinoscopy aberrometer at 1 and 3 months after surgery. Uncorrected and best-corrected visual acuity and contrast sensitivity under mesopic and photopic conditions also were measured. Distance-corrected near and intermediate visual acuity were studied as a measurement of depth of focus. RESULTS: There was no statistically significant difference between eyes in uncorrected and best-corrected visual acuity at I and 3 months after surgery. There was a statistically significant between-group difference in contrast sensitivity under photopic conditions at 12 cycles per degree and under mesopic conditions at all spatial frequencies. The Akreos AO group obtained statistically significant lower values of higher-order aberrations and spherical aberration with 5- and 6-mm pupils compared with the Akreos Fit group (P < .05). There was no significant difference in distance-corrected near and intermediate visual acuity between both groups. CONCLUSIONS: Aspherical aberration-free Akreos AO IOL induced significantly less higher-order aberrations and spherical aberration than the Akreos Fit. Contrast sensitivity was better under mesopic conditions with the Akreos AO with similar results of depth of focus. (Am J Ophthalmol 2010;149:383-389. (C) 2010 by Elsevier Inc. All rights reserved.)