Hierarchical Mergence Approach to Cell Detection in Phase Contrast Microscopy Images

Phase contrast microscope is one of the most universally used instruments to observe long-term cell movements in different solutions. Most of classic segmentation methods consider a homogeneous patch as an object, while the recorded cell images have rich details and a lot of small inhomogeneous patches, as well as some artifacts, which can impede the applications. To tackle these challenges, this paper presents a hierarchical mergence approach (HMA) to extract homogeneous patches out and heuristically add them up. Initially, the maximum region of interest (ROI), in which only cell events exist, is drawn by using gradient information as a mask. Then, different levels of blurring based on kernel or grayscale morphological operations are applied to the whole image to produce reference images. Next, each of unconnected regions in the mask is applied with Otsu method independently according to different reference images. Consequently, the segmentation result is generated by the combination of usable patches in all informative layers. The proposed approach is more than simply a fusion of the basic segmentation methods, but a well-organized strategy that integrates these basic methods. Experiments demonstrate that the proposed method outperforms previous methods within our datasets

Synthesis of One-Dimensional And Two-Dimensional Carbon Based Nanomaterials

Particular physical and chemical properties of carbon based nanomaterials (CBNs) have promised and exhibited great applications in manufacturing various nanodevices such as electron field emitters, sensors, one-dimensional conductors, supercapacitors, reinforcing fibres, hydrogen storage devices, and catalyst support for fuel cells electrodes. Despite these amazing technical progresses, many challenges still remain in the development of synthesis methods suitable for commercial applications and fabricating novel functional nanostructures with complex architecture. In this Ph.D. thesis, one-dimensional (1D), two-dimensional (2D) carbon nanostructures, and 1D/2D hybrid of carbon nanostructures have been synthesized using various chemical vapour deposition (CVD) methods. The objective of this work is to explore the potential of various CVD methods, including specially-designed CVD techniques, such as modified spray pyrolysis, plasma enhanced CVD, and magnetron sputtering deposition. By making use of these innovative methods, high density regular and nitrogen-doped nanotubes, graphite nanosheets and assemblies have been successfully obtained on conducting and semiconducting substrates. For the modified spray pyrolysis method, systematic investigation of regular carbon nanotubes (CNTs) was conducted in terms of optimizing various experimental parameters such as hydrocarbon source, temperature, and catalyst in order to control the quality and structure of CBNs. Doping of nitrogen into carbon nanotubes was also systematically studied to enhance their electrical and mechanical properties. Interestingly, a novel structure of multi-branched nitrogen doped CNTs has been achieved by this modified spray pyrolysis method. By employing the plasma assisted CVD/sputtering hybrid system, selective growth of single and few walled CNTs have been realized. The device has also been able to produce 2D carbon nanostructures of nanosheets and a hybrid of nanosheets suspended on vertical aligned CNTs. Based on the magnetron sputtering deposition method, carbon nanowalls have been synthesized without any catalyst addition. Morphology, microstructure, and vibration properties of the CBNs were characterized by scanning electron microscopy, transmission electron microscopy, Raman spectroscopy, and X-ray photoelectron spectroscopy. Carbon nanomaterials, grown in high densities on conducting and semiconducting substrates, promise great potential in building various nanodevices with different electron conducting requirements. In addition, CBNs provide a very high surface area for the support of platinum particles for use in hydrogen fuel cell electrodes

Decoding Pixel-Level Image Features from Two-Photon Calcium Signals of Macaque Visual Cortex

Images of visual scenes comprise essential features important for visual cognition of the brain. The complexity of visual features lies at different levels, from simple artificial patterns to natural images with different scenes. It has been a focus of using stimulus images to predict neural responses. However, it remains unclear how to extract features from neuronal responses. Here we address this question by leveraging two-photon calcium neural data recorded from the visual cortex of awake macaque monkeys. With stimuli including various categories of artificial patterns and diverse scenes of natural images, we employed a deep neural network decoder inspired by image segmentation technique. Consistent with the notation of sparse coding for natural images, a few neurons with stronger responses dominated the decoding performance, whereas decoding of ar tificial patterns needs a large number of neurons. When natural images using the model pretrained on artificial patterns are decoded, salient features of natural scenes can be extracted, as well as the conventional category information. Altogether, our results give a new perspective on studying neural encoding principles using reverse-engineering decoding strategies

Three dimensional representation and analysis of individual bead and packed bed scale chromatography using X-ray computed tomography and focused ion beam microscopy

Understanding the detailed, internal geometry of chromatography bead and packed bed structure remains a challenge, which is addressed in this thesis by using tomographic techniques to both visualise and quantify microstructural characteristics at both scales. Two main approaches were investigated for the purposes of producing accurate representations: X-ray computed tomography and focused ion beam microscopy, both providing high-resolution capability for imaging geometric features, enabling comparison between material types and techniques when considering suitability for chromatography structural research. At the bead scale, X-ray computed tomography and focused ion beam microscopy were used for imaging and comparison of the three bead types, with optimal cubic pixel sizes of 32nm and 15nm achieved respectively. Despite the superior resolution attainable for focused ion beam microscopy, drawbacks of intensive preparation requirements and the necessity for physical slicing and thus destruction highlighted that pixel dimensions were not the only consideration for sub-micron tomographic imaging. Tortuosity, which impacts important performance metrics such as transfer rates, was found to be below 2 in all cases due to the high porosities exhibited, with average pore size greatly influenced by the overall resolution. At the packed bed scale, X-ray CT was the sole technique selected using two different systems, with one system only capable of sufficiently imaging the harder ceramic samples, albeit achieving an overall superior pixel size of 2.7µm. Optimisation of X-ray conditions was required for each different material and corresponding equipment in order to achieve 3D representations of sufficient quality; to both visually display the packed bed structure in addition to providing the capability of quantifying key metrics relating to chromatography geometries and thus performance. Porosity readings of approximately 35% were in agreement with values obtained using established techniques and values, with radial discrepancies identified that were expected due to wall-effects impacting packing densities. Two industrially relevant chromatography processing considerations were examined using X-ray CT: fouling and packed bed compression. Both scales were investigated for fouling, with individual beads imaged between cycles to measure the change in simulated diffusivity due to foulant impregnation. Compression of packed beds was imaged before, during and after excessive flow through columns, where visual and quantitative changes to aspects such as simulated permeability were compared between states. The values obtained in both of these studies based upon real systems were compared to changes in porosity and tortuosity factor by applying erosion-dilation to structure in an original state

SIMULTANEOUS SYNTHESIS AND SELF-ASSEMBLY OF INORGANIC NANOMATERIALS TOWARDS ACTIVE AND STABLE NANOCATALYSTS

Ph.DDOCTOR OF PHILOSOPH

Metal oxide, Mixed oxide, and hybrid metal@oxide nanocrystals : size-and shape-controlled synthesis and catalytic applications

Le contrôle de la taille et de la morphologie de nanocristaux d’oxydes métalliques simples, d’oxydes mixtes et d’oxydes métalliques hybrides est un sujet de grand intérêt. La dépendance de leur propriétés physio-chimiques avec leurs taille et morphologies, génèrent une variété de leur applications dans plusieurs domaines. Cependant, le dévellopement des nanocristaux en controllant la taille, la forme, l’assemblage et l’homogénéité de la composition chimique pour l’optimisation de propriété spécifiques demandent la combinaison de nombreux parametres de synthèse. Les trois différentes approches ont été développées dans le cadre de la thèse pour la synthèse d’une variété de nouveaux nanomatériaux d’oxydes simples, d’oxydes mixtes et d’oxydes métalliques hybrides dont la taille et la forme ont été bien controllées. Ces méthodes ont été nommées comme des méthodes solvo-hydrothermiques assistées par des molécules structurantes à l’état monophasique (eau ou eau/éthanol) et à l’état biphasique (eau-toluène). Nos approches de synthèse ont permi de préparer des nanocristaux des oxydes de métaux de transition (V, Cr, Mn, Co, Ni, In), et des terres rares (Sm, Ce, La, Gd, Er, Ti, Y, Zr), ainsi que des oxydes métalliques mixtes (tungstate, orthovanadate, molybdate). Ces nanomatériaux sont sous forme colloïdale mono-dispersée qui présente une cristallinité élevée. La taille et la forme de tels nanocristaux peuvent facilement être contrôlées par une simple variation des paramètres de synthèse telle que la concentration de précurseurs, la nature de la molécule structurante, la température et le temps de réaction. A large variété de techniques a été utilisée pour la caracterisation de ces nanomatériaux telles que TEM/HRTEM, SEM, SAED, EDS, XRD, XPS, FTIR, TGA-DTA, UV-vis, photoluminescence, BET. Les propriétés catalytiques de ces matériaux ont aussi été étudiées. Dans ce travail, le contrôle de la cinétique de croissance des nucléides ainsi que le mécanisme gouvernant la forme qui conduit à la taille et la morphologie finale du nanocrystal ont été proposé. L’effet de la taille et de la forme des nanoparticules d’oxyde métallique hybrides sur les propriétés catalytiques pour la réaction d’oxydation du CO et la photo-dégradation du bleue de méthylène a été aussi étudié. Car les catalyseurs existant actuellement à base de métaux nobles sont très couteux et en plus très sensibles à l’empoisonnement par le gas H2S ou les émissions polluantes de SOx. L’activité catalytique des nanocristaux d’oxydes métallique hybrides Cu@CeO2 de formes cubiques dans l’oxydation de CO et de Ag@TiO2 de formes de ceinture dans la photo dégradation du bleue de méthylène ont montré la dépendance de la taille et la forme des nanocristaux avec leur propriétés catalytiques.The ability to finely control the size and shape of metal oxide, mixed metal oxide, hybrid metal/oxide nanocrystals has become an area of great interest, as many of their physical and chemical properties are highly dependent on morphology, and the more technological applications will be possible for their use. Large-scale synthesis of such high-quality nanocrystals is the first and key step to this area of science. A tremendous effort has recently been spent in attempt to control these novel properties through manipulation of size, shape, structure, and composition. Flexibly nanocrystal size/shape control for both monodisperse single and multiple-oxide nanomaterial systems, however, remains largely empirical and still presents a great challenge. In this dissertation, new synthetic approaches have been developed and described for the synthetic design of a series of colloidal monodisperse metal oxide, mixed metal oxide, hybrid metal-oxide nanocrystals with controlled size and shape. These materials were generally characterized using TEM/HRTEM, SEM, SAED, EDS, XRD, XPS, FTIR, TGA-DTA, UV-vis, photoluminescence, BET techniques. Effect of the size and shape of these obtained hybrid metal-oxide nanocrystals on the catalytic properties is illustrated. We have developed three different new surfactant-assistant pathways for the large-scale synthesis of three types of nanomaterials including metal oxide, mixed metal oxide, hybrid noble-metal-oxide colloidal monodisperse nanocrystals. Namely, the solvo-hydrothermal surfactant-assisted methods in one-phase (water or water/ethanol) and two-phase (water-toluene) systems were used for the synthesis of metal oxide (transition metal-V, Cr, Mn, Co, Ni, In and rare earth-Sm, Ce, La, Gd, Er, Ti, Y, Zr) and mixed metal oxide (tungstate, orthovanadate, molybdate). The seed-media growth with the assistant of bifunctional surfactant was used for the synthesis of hybrid noble metal@oxide (Ag@TiO2, (Cu or Ag)@CeO2, Au/tungstate, Ag/molybdate, etc.) nanocrystals. A significant feature of our synthetic approaches was pointed out that most resulting nanocrystal products are monodisperse, high crystallinity, uniform shape, and narrow distribution. The size and shape of such nanocrystals can be controlled easily by simple tuning the reaction parameters such as the concentration of precursors and surfactants, the nature of surfactant, the temperature and time of synthetic reaction. The prepared nanocrystals with the functional surface were used as the building blocks for the self-assembly into hierarchical mesocrystal microspheres. The effective ways how to control the growth kinetics of the nuclei and the shape-guiding mechanisms leading to the manipulation of morphology of final products were proposed. Our current approaches have several conveniences including used nontoxic and inexpensive reagents (most using inorganic metal salts as starting precursors instead of expensive and toxic metallic alkoxides or organometallics), relatively mild conditions, high-yield, and large-scale production; in some causes, water or ethanol was used as environmentally benign reaction solvent. Catalytic activity and selectivity are governed by the nature of the catalyst surface, making shaped nanocrystals ideal substrates for understanding the influence of surface structure on heterogeneous catalysis at the nanoscale. Finally, this work was concentrated on demonstration of heterogeneous catalytic activity of hybrid metal-oxide nanomaterials (Cu@CeO2, Ag@TiO2) as a typical example. We synthesized the high-crystalline titanium oxide and cerium oxide nanocrystals with control over their shape and surface chemistry in high yield via the aqueous surfactant-assist method. The novel hybrid metal-oxide nanocrystals were produced by the depositing noble metal ion (Cu, Ag, Au) precursors on the pre-synthesized oxide seeds via seed-mediated growth. The catalytic activity of these metal-oxide nanohybrids of Cu@CeO2 nanocubes for CO oxidation conversion and Ag@TiO2 nanobelts for Methylene Blue photodegradation with size/shape-dependent properties were verified

Growth and structure of CaCO3

Organisms often employ non-classical crystallisation mechanisms to create the remarkable materials that are biominerals. These materials often surpass their synthetic counterparts in terms of physical properties, morphologies and structural organisation. The non-classical mechanisms employed include the controlled formation, transition and release of amorphous precursor material, and the oriented attachment/ nucleation of nano sized particulates. Combined, these strategies are capable of generating hierarchically ordered superstructures. Both of these mechanisms operate under ambient conditions in a physically delimited environment of body fluids, which enables precise regulation of the solution composition. This thesis describes a range of biomimetic studies which have investigated key aspects in the formation and structural organization of calcium carbonate. Of interest were the influence of additives and physical confinement on the formation and transformation of amorphous calcium carbonate (ACC). The studies revealed that both of these factors play key roles in controlling ACC crystallisation. Additives which inhibit crystallisation in solution can accelerate transformation of ACC in the solid state. This effect was observed for all of the larger molecules examined, while the small molecules retarded crystallisation in both solution and the solid state. Investigation of ACC crystallisation in confinement, in turn, demonstrated that ACC dehydrates prior to crystallizing even in solution, and that nucleation of the first crystal phase in solution must occur by dissolution/ reprecipitation. Studies were also performed to characterise the “ammonia diffusion method” which is widely used in the precipitation of calcium carbonate. Despite this, virtually nothing is known about the changes in solution conditions which occur during this process. The analysis showed that the supersaturation remains relatively high and constant throughout most of the process, which potentially enables multiple nucleation events to occur in a single experiment. These results were then used to develop a one pot method which offers comparable reaction conditions. Finally, Bragg coherent diffraction imaging (BCDI) was used to characterise calcite crystals precipitated on self-assembled monolayers (SAM), where these provide a mimic of the organic matrices used to control crystallisation in organisms. Initial observations of the growth and dissolution of calcite by BCDI allowed the visualization of the 3D dislocation network present within a single crystal. Examination of crystals grown on SAMs, in contrast, showed that a build-up strain causes the formation of a single dislocation loop, where this is correlated with the morphological development of the crystal

Trends in Infectious Diseases

This book gives a comprehensive overview of recent trends in infectious diseases, as well as general concepts of infections, immunopathology, diagnosis, treatment, epidemiology and etiology to current clinical recommendations in management of infectious diseases, highlighting the ongoing issues, recent advances, with future directions in diagnostic approaches and therapeutic strategies. The book focuses on various aspects and properties of infectious diseases whose deep understanding is very important for safeguarding human race from more loss of resources and economies due to pathogens

Plasma-Catalysis for Environmental and Energy-Related Applications

Plasma catalysis has been a topic of research for many years due to its potential for applications in a wide range of chemical, environmental, and energy-related processes. Non-thermal plasma offers an unconventional way to initiate chemical reactions in gas and in liquid due to the energetic electrons generated in the plasma; however, it suffers from low selectivity. The coupling of plasma with catalysis can steer the reactions in the desired direction, thus ensuring improved selectivity towards the target products and reducing unwanted ones. Environmental applications of plasma catalysis have been focused on the removal of various air and water pollutants, while energy applications include hydrogen, syngas and ammonia production.This Special Issue demonstrates plasma catalysis as a solution to environmental problems caused by the greenhouses gases CO2 and CH4, which can be converted to value-added products and fuels, air pollution with stable polycyclic aromatic hydrocarbons and volatile organic compounds, and water pollution with pharmaceutical products