Automatic detection of fluorescein tear breakup sequence

Dry Eye Syndrome is a common disease in the western world, with effects from uncomfortable itchiness to permanent damage to the ocular surface. Almost 5 million Americans over 50 years old suffer from dry eye. A conservative estimate shows that approximately 17 million Americans have contact lens related dry eye -one of the main factors to contact lens discontinuation. In addition, the incidence of the disease is on the rise. Nevertheless, there is still no gold standard test that can reliably detect dry eye. One of the most commonly used tests by clinicians to detect dry eye is the Fluorescein Break Up Time (FBUT). However, results vary a lot between clinicians. Other tests such as observing the tear meniscus height are also performed regularly by the clinicians but not necessarily in conjunction with the FBUT test. Therefore there is a real need for a reliable, robust and operator-dependent method to evaluate dry eye. To our knowledge, no previous research has been conducted on automatic evaluation of dry eye in fluorescein images. In this thesis, we present new algorithms to automatically detect various dryness signs and make a number of original contributions. The first problem we address is how to detect the dry areas in fluorescein videos of the anterior of the eye, which are captured using a portable camera. We present a new multi-step algorithm which first locates the iris in each image in the video, then aligns the images according to the location of the iris and finally analyzes the aligned video to find the regions of dryness. We produce a novel segmentation result called dryness image, which depicts the various degrees of tear film thinning over the corneal surface. Then, we demonstrate through experiments that there is a large variation in the estimated Break Up Time (BUT) between clinicians and no ground-truth can be defined. To overcome that, we define a new value based on the clinical definitions of the BUT. These definitions are converted to image processing properties and an estimate of the BUT is computed using temporal analysis of the aligned video. We demonstrate that our new value is in the accepted range of the BUT values provided by the clinicians. We present an extension to the dryness algorithm, which is based on transforming the video to a volume by considering each video frame as a slice in a 3D volume. On a volume, a temporal monotonic constraint can be applied between pixels in consecutive slices. The constraint enforces the clinical definition of tear film thinning over time -the amount of fluid cannot increase while not blinking. The constraint is applied directly into the cost function and the whole volume is segmented simultaneously using graph-cuts. As a consequence, the approach is more robust and less sensitive to alignment errors. Finally, we generalize the idea and explain how monotonic constraints can be applied to other imaging modalities. In the last part of the thesis, we develop a new algorithm to evaluate the tear meniscus height and shape using graph-cuts. We formulate the segmentation problem using asymmetric cost functions and demonstrate its power and usefulness for the task. The asymmetry induces which directional moves are permitted in the minimization process and thus produces a result that adheres to the known shape properties of the tear meniscus. The iterative algorithm provides simultaneously the best segmentation result and shape prior of the meniscus

Quantitative imaging of the complexity in liquid bubbles' evolution reveals the dynamics of film retraction

The dynamics and stability of thin liquid films have fascinated scientists over many decades. Thin film flows are central to numerous areas of engineering, geophysics, and biophysics and occur over a wide range of length, velocity, and liquid properties scales. In spite of many significant developments in this area, we still lack appropriate quantitative experimental tools with the spatial and temporal resolution necessary for a comprehensive study of film evolution. We propose tackling this problem with a holographic technique that combines quantitative phase imaging with a custom setup designed to form and manipulate bubbles. The results, gathered on a model aqueous polymeric solution, provide an unparalleled insight into bubble dynamics through the combination of full-field thickness estimation, three-dimensional imaging, and fast acquisition time. The unprecedented level of detail offered by the proposed methodology will promote a deeper understanding of the underlying physics of thin film dynamics

Quantitative imaging of the complexity in liquid bubbles’ evolution reveals the dynamics of film retraction

Thin liquid films: Seeing bubbles in a better light A procedure for imaging the complex fluid dynamics in bubbles could greatly assist efforts to understand and exploit thin liquid films in applications ranging through medicine, industrial chemistry and engineering. Thin liquid films are ubiquitous in nature, found in such varied systems as soap bubbles, biological membranes, detergents, oils, insulation, foods and geological magma. Researchers in Italy led by Biagio Mandracchia at the Institute of Applied Science and Intelligent Systems in Naples, devised a novel holographic phase imaging technique to watch bubbles as they form, develop, burst and retract. The researchers built customized apparatus to create and manipulate the bubbles. The unprecedented level of detail being revealed offers deeper understanding of the physics underlying thin film behavior. Insights into the complex fluid dynamics within bubbles could advance thin film technology for many applications

Investigating graphene-based devices towards sensing applications.

Graphene is a novel material that has exceptional electrical properties. In this work the graphene-based devices were developed towards three applications. Graphene-glass electrodes were fabricated and characterised towards understanding the electrochemical nature of graphene. It was shown that graphene could serve as an electrochemical electrode towards use as a sensing platform due to its fast electron transfer characteristics and thus exhibited potential as a platform for electrochemical sensing of electroactive species. Further, the Graphene-on-Glass electrodes were shown to be used as a working electrode to create a reversible electrochromic device where the optical transparency of the Graphene was modulated, and the electrochemical characteristics of the Graphene device were examined. A proof-of-concept detection for the presence of a biomarker for Sepsis was developed. Large-area, functionalised graphene was shown to able to electronically sense the presence of the binding events of the Anti-PCT antibody, PCT molecule and differentiate from their bulk solution. The device was able to detect the presence of PCT over the medically relevant range.. This sensor combines the exceptional electrical properties of graphene leading to high sensitivity, which when functionalized also yields high specificity as a sensor platform and offers a new route for diagnosis of Sepsis electronically in real time measurements. Lastly, a hybrid graphene FET array that is embedded under microfluidic channels was developed. The effect of water on the device was measured and the utility of such devices towards sensing in aqueous media is discussed. Further, it is shown that the microfluidic channels of varying widths are able to transport water along the graphene FET array, such that individual graphene strips can sense them. This measurement scheme is extremely useful and can be adapted to a host of other sensing applications which would benefit from dynamic and precise control on the detection of the analyte

Novel approaches for image analysis of in vitro epithelial cultures with application to silver nanoparticle toxicity

A novel imaging approach was developed for the purpose of counting cells from phase contrast microscopy images of laboratory grown (in vitro} cultures of epithelial cells. Validation through comparison with standard laboratory cell counting techniques showed this approach provided consistent and comparable results, whilst overcoming limitations of these existing techniques, such as operator variability and sample destruction. The imaging approach was subsequently applied to investigate the effects of silver nanoparticles (AgNP} on H400 oral keratinocytes. Concurrent investigations into antimicrobial effects of AgNP were performed on Escherichia coli, Staphylococcus aureus and Streptococcus mutans to provide models for Gram-positive and Gram-negative infection, and to compare with the literature and oral keratinocyte toxicity. It was found that AgNP elicit size-, dose- and time-dependent growth inhibition in both human cells and bacteria, although bacterial inhibition was not achieved without significant cytotoxicity at the same concentrations

Presbyopia:Effectiveness of correction strategies

Presbyopia is a global problem affecting over a billion people worldwide. The prevalence of unmanaged presbyopia is as high as 50% of those over 50 years of age in developing world populations due to a lack of awareness and accessibility to affordable treatment, and is even as high as 34% in developed countries. Definitions of presbyopia are inconsistent and varied, so we propose a redefinition that states “presbyopia occurs when the physiologically normal age-related reduction in the eye's focusing range reaches a point, when optimally corrected for distance vision, that the clarity of vision at near is insufficient to satisfy an individual's requirements”. Presbyopia is inevitable if one lives long enough, but intrinsic and extrinsic risk factors including cigarette smoking, pregnancy history, hyperopic or astigmatic refractive error, ultraviolet radiation, female sex (although accommodation is similar to males), hotter climates and some medical conditions such as diabetes can accelerate the onset of presbyopic symptoms. Whilst clinicians can ameliorate the symptoms of presbyopia with near vision spectacle correction, bifocal and progressive spectacle lenses, monovision, translating or multifocal contact lenses, monovision, extended depth of focus, multifocal (refractive, diffractive and asymmetric designs) or ‘accommodating’ intraocular lenses, corneal inlays, scleral expansion, laser refractive surgery (corneal monovision, corneal shrinkage, corneal multifocal profiles and lenticular softening), pharmacologic agents, and electro-stimulation of the ciliary muscle, none fully overcome presbyopia in all patients. While the restoration of natural accommodation or an equivalent remains elusive, guidance is gives on presbyopic correction evaluation techniques

Fabrication et caractérisation de nano-rubans de graphène par gravure électronique directe

Le graphène est l'un des candidats les plus prometteurs pour la fabrication des futurs dispositifs électroniques. Ses remarquables propriétés électroniques découlent de sa structure atomique et sont caractérisés par un gaz bidimensionnel d'électrons à l'échelle macroscopique et des états moléculaires à l'échelle nanométrique. Cette thèse a pour but de structurer le graphène sur une large gamme d'échelle de longueurs pour produire des nano rubans de graphène (GNR) connectés à des électrodes de graphène. Les trois principaux objectifs sont (i) produire, contacter et structurer des GNR jusqu'à une largeur de 10 nm et une longueur de plusieurs centaines de nanomètres, (ii) planifier toutes les étapes de ce processus tout en minimisant la contamination pour obtenir, à terme, des échantillons compatibles avec l'ultravide et (iii) graver des GNRs tout en préservant la qualité cristallographique du graphène et minimisant son amorphisation. La première partie est dédiée à la caractérisation du graphène monocouche par des analyses topographiques AFM et spectroscopiques Raman. Nous montrons que ces techniques sont limitées, l'une, par une faible reproductibilité de la mesure de la hauteur apparente et l'autre, par une faible sensibilité aux défauts peu denses. Cependant, l'origine de l'instabilité de la mesure AFM a été identifiée comme résultant de la présence d'un ménisque d'eau. Des conditions de fonctionnement stable ont été trouvées et conduisent à des mesures de hauteur apparente reproductibles. Pour augmenter le signal Raman dû aux défauts dans le graphène, nous avons suivi l'évolution de l'intensité du signal dans le voisinage de nano-bâtonnets d'or cristallins placés près des bords du graphène. Une seconde partie décrit en détail comment nous avons directement gravé des GNR dans le graphène en utilisant un faisceau électronique de faible énergie (1-20 keV) en présence de vapeur d'eau. Nous montrons que la gravure induite par un faisceau électronique (EBIE) produit des GNRs de moins de 20 nm de large et longs de plusieurs centaines de nanomètres ou des tranchées longues de plusieurs micromètres permettant d'isoler un GNR du feuillet de graphène. Une attention particulière a été portée à la caractérisation de la qualité structurale des bords des GNR. La microscopie électronique en transmission avec correcteur d'aberrations montre que le graphène est intact à moins de 2 nm d'un bord de découpe EBIE. La dernière partie est dédiée à l'application de cette technique EBIE prometteuse pour fabriquer des GNR contactés électriquement dans un dispositif à effet de champ. Nous montrons que des dispositifs de graphène sur silice sont amorphisés de manière significative par des électrons rétrodiffusés. Un nouveau dispositif a été conçu et réalisé qui consiste à suspendre localement le graphène et a permis de fabriquer des GNR (typiquement 30x200 nm) connectés par des électrodes sur un substrat possédant une grille arrière. Ce travail ouvre la voie pour la mesure de transport électronique dans des GNR et, au-delà sur des structures plus complexes basées sur les GNRs. Il constitue la première étape vers une technologie atomique intégrée pour des dispositifs d'électronique moléculaire à base de graphène.Graphene is one of the most promising candidates to build future electronic devices. Its peculiar electronic properties derive from its atomic structure and are characterized by a two-dimensional electron gas at macroscopic scale and molecular states at the nanometer scale. This thesis work aims at patterning graphene monolayer over this entire range of length scales to produce arbitrarily shaped graphene nanoribbons (GNR) continuously connected to graphene pads. The three main objectives consist in (i) producing, contacting and patterning graphene monolayer down to features size of about 10 nm for a ribbon length of several hundreds of nanometers, (ii) integrating all steps while minimizing contamination to ultimately reach UHV-compatible samples and (iii) etching GNRs while preserving the high crystallinity of graphene and minimizing its amorphization. The first part will focus on the characterization of the graphene monolayer itself by ambient AFM topography and Raman spectroscopy. We show that these techniques suffer from a poor reproducibility of the height measurement and a limited sensitivity to low defect density. However, the source of AFM instabilities is identified as the presence of a water meniscus. Stable operating conditions are found and yield reproducible height measurements. In order to enhance the Raman signal of defects in graphene, we investigate the intensity evolution near crystalline gold nanorods placed close to graphene edges. The second part describes in detail how GNR can be etched directly in graphene using a low energy (1-20 keV) electron beam in the presence of water vapor. We show that electron beam induced etching (EBIE) can produce < 20 nm-wide GNRs with length of hundreds of nanometers or micrometer-long trenches to isolate the GNR form the graphene sheet. A particular attention is paid to the characterization of the structural quality of the GNR edges. A spherical aberration corrected TEM analysis demonstrates that the graphene lattice is intact at less than 2 nm from the EBIE-cut edges. The last part is dedicated to the application of our promising EBIE method to the fabrication of contacted GNR electronic field-effect devices. We show that graphene devices supported on silica are significantly amorphized by backscattered electrons. A new design of devices made of locally suspended graphene is proposed and makes it possible to produce GNRs (typically 30x200 nm) connected to electrodes on a back-gated substrate. This work opens the way to electrical transport measurements of GNR and, beyond, GNR-based complex structures and constitutes the first step towards an integrated atomic technology of molecular graphene devices

Astigmatism and Pseudoaccommodation in Pseudophakic Eyes

noAdvanced IOLs with circumferential zones of different power provide pseudoaccommodation. We investigated the potential for power variation with meridian, namely astigmatism, to provide pseudo-accommodation. With appropriate power and axis orientations, acceptable pseudo-accommodation can be achieved

Microelectromechanical Systems and Devices

The advances of microelectromechanical systems (MEMS) and devices have been instrumental in the demonstration of new devices and applications, and even in the creation of new fields of research and development: bioMEMS, actuators, microfluidic devices, RF and optical MEMS. Experience indicates a need for MEMS book covering these materials as well as the most important process steps in bulk micro-machining and modeling. We are very pleased to present this book that contains 18 chapters, written by the experts in the field of MEMS. These chapters are groups into four broad sections of BioMEMS Devices, MEMS characterization and micromachining, RF and Optical MEMS, and MEMS based Actuators. The book starts with the emerging field of bioMEMS, including MEMS coil for retinal prostheses, DNA extraction by micro/bio-fluidics devices and acoustic biosensors. MEMS characterization, micromachining, macromodels, RF and Optical MEMS switches are discussed in next sections. The book concludes with the emphasis on MEMS based actuators