Within the realm of biosensing, DNA analysis has become an indispensable research tool in medicine, enabling the investigation of relationships among genes, proteins, and drugs. Conventional DNA microarray technology uses multiple lasers and complex optics, resulting in expensive and bulky systems which are not suitable for point-of-care medical diagnostics. The immobilization of DNA probes across the microarray substrate also results in substantial spatial variation. To mitigate the above shortcomings, this thesis presents a set of techniques developed for the CMOS image sensor for point-of-care spectrally-multiplexed fluorescent DNA sensing and other fluorescence biosensing applications. First, a CMOS tunable-wavelength multi-color photogate (CPG) sensor is presented. The CPG exploits the absorption property of a polysilicon gate to form an optical filter, thus the sensor does not require an external color filter. A prototype has been fabricated in a standard 0.35μm digital CMOS technology and demonstrates intensity measurements of blue (450nm), green (520nm), and red (620nm) illumination. Second, a wide dynamic range CMOS multi-color image sensor is presented. An analysis is performed for the wide dynamic-range, asynchronous self-reset with residue readout architecture where photon shot noise is taken into consideration. A prototype was fabricated in a standard 0.35μm CMOS process and is validated in color light sensing. The readout circuit achieves a measured dynamic range of 82dB with a peak SNR of 46.2dB. Third, a low-power CMOS image sensor VLSI architecture for use with comparator based ADCs is presented. By eliminating the in-pixel source follower, power consumption is reduced, compared to the conventional active pixel sensor. A 64×64 prototype with a 10μm pixel pitch has been fabricated in a 0.35μm standard CMOS technology and validated experimentally. Fourth, a spectrally-multiplexed fluorescence contact imaging microsystem for DNA analysis is presented. The microsystem has been quantitatively modeled and validated in the detection of marker gene sequences for spinal muscular atropy disease and the E. coli bacteria. Spectral multiplexing enables the two DNA targets to be simultaneously detected with a measured detection limit of 240nM and 210nM of target concentration at a sample volume of 10μL for the green and red transduction channels, respectively.

Within the realm of biosensing, DNA analysis has become an indispensable research tool in medicine, enabling the investigation of relationships among genes, proteins, and drugs. Conventional DNA microarray technology uses multiple lasers and complex optics, resulting in expensive and bulky systems which are not suitable for point-of-care medical diagnostics. The immobilization of DNA probes across the microarray substrate also results in substantial spatial variation. To mitigate the above shortcomings, this thesis presents a set of techniques developed for the CMOS image sensor for point-of-care spectrally-multiplexed fluorescent DNA sensing and other fluorescence biosensing applications. First, a CMOS tunable-wavelength multi-color photogate (CPG) sensor is presented. The CPG exploits the absorption property of a polysilicon gate to form an optical filter, thus the sensor does not require an external color filter. A prototype has been fabricated in a standard 0.35μm digital CMOS technology and demonstrates intensity measurements of blue (450nm), green (520nm), and red (620nm) illumination. Second, a wide dynamic range CMOS multi-color image sensor is presented. An analysis is performed for the wide dynamic-range, asynchronous self-reset with residue readout architecture where photon shot noise is taken into consideration. A prototype was fabricated in a standard 0.35μm CMOS process and is validated in color light sensing. The readout circuit achieves a measured dynamic range of 82dB with a peak SNR of 46.2dB. Third, a low-power CMOS image sensor VLSI architecture for use with comparator based ADCs is presented. By eliminating the in-pixel source follower, power consumption is reduced, compared to the conventional active pixel sensor. A 64×64 prototype with a 10μm pixel pitch has been fabricated in a 0.35μm standard CMOS technology and validated experimentally. Fourth, a spectrally-multiplexed fluorescence contact imaging microsystem for DNA analysis is presented. The microsystem has been quantitatively modeled and validated in the detection of marker gene sequences for spinal muscular atropy disease and the E. coli bacteria. Spectral multiplexing enables the two DNA targets to be simultaneously detected with a measured detection limit of 240nM and 210nM of target concentration at a sample volume of 10μL for the green and red transduction channels, respectively.

Master's thesis is focused on capturing of low dynamic range images using common devices such as camera and its multiple exposure. The main part of thesis is dedicated to composing these images to HDR image, inclusive sequence of images of static scenes, but also dynamic ones. Next part describes tone mapping used for display HDR image on LDR monitors. Moreover, there is given design and implementation of application solving problems mentioned earlier. In the end, the implemented application is evaluated and the possible continuation of this work is stated.

Visualization is the process of constructing methods, which are able to synthesize interesting and informative images from data sets, to simplify the process of interpreting the data. In this thesis a new approach to construct meteorological visualization methods using neural network technology is described. The methods are trained with examples instead of explicitely designing the appearance of the visualization. This approach is exemplified using two applications. In the fist the problem to compute an image of the sky for dynamic weather, that is taking account of the current weather state, is addressed. It is a complicated problem to tie the appearance of the sky to a weather state. The method is trained with weather data sets and images of the sky to be able to synthesize a sky image for arbitrary weather conditions. The method has been trained with various kinds of weather and images data. The results show that this is a possible method to construct weather visaualizations, but more work remains in characterizing the weather state and further refinement is required before the full potential of the method can be explored. This approach would make it possible to synthesize sky images of dynamic weather using a fast and efficient empirical method. In the second application the problem of computing synthetic satellite images form numerical forecast data sets is addressed. In this case a mode is trained with preclassified satellite images and forecast data sets to be able to synthesize a satellite image representing arbitrary conditions. The resulting method makes it possible to visualize data sets from numerical weather simulations using synthetic satellite images, but could also be the basis for algorithms based on a preliminary cloud classification. / Report code: LiU-Tek-Lic-2004:66.

One of the main objectives in digital imaging is to mimic the capabilities of the human eye, and perhaps, go beyond in certain aspects. However, the human visual system is so versatile, complex, and only partially understood that no up-to-date imaging technology has been able to accurately reproduce the capabilities of the it. The extraordinary capabilities of the human eye have become a crucial shortcoming in digital imaging, since digital photography, video recording, and computer vision applications have continued to demand more realistic and accurate imaging reproduction and analytic capabilities. Over decades, researchers have tried to solve the colour constancy problem, as well as extending the dynamic range of digital imaging devices by proposing a number of algorithms and instrumentation approaches. Nevertheless, no unique solution has been identified; this is partially due to the wide range of computer vision applications that require colour constancy and high dynamic range imaging, and the complexity of the human visual system to achieve effective colour constancy and dynamic range capabilities. The aim of the research presented in this thesis is to enhance the overall image quality within an image signal processor of digital cameras by achieving colour constancy and extending dynamic range capabilities. This is achieved by developing a set of advanced image-processing algorithms that are robust to a number of practical challenges and feasible to be implemented within an image signal processor used in consumer electronics imaging devises. The experiments conducted in this research show that the proposed algorithms supersede state-of-the-art methods in the fields of dynamic range and colour constancy. Moreover, this unique set of image processing algorithms show that if they are used within an image signal processor, they enable digital camera devices to mimic the human visual system s dynamic range and colour constancy capabilities; the ultimate goal of any state-of-the-art technique, or commercial imaging device.

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By utilizing a Research through Design approach this master thesis studies how technological changes might affect professionals working in the motion picture industry, specifically; how the advent of HDR (High Dynamic Range) affects the colorist. The research questions formulated are the following; (1) How can color grading in HDR be approached? (2) What effect can HDR have on visual modality? (3) What specific affordances can HDR offer the colorist? (4) How can HDR affect the creative space of the colorist? Three of the research questions are derived from the theoretical framework applied in this master thesis; starting with the social semiotic implementation of the term modality (models of reality), the Gibsonian term affordance (possibilities for action and meaning making) and its use in communications research, and lastly; the concept of creative space in motion picture production. Analytic autoethnography was used to generate primary data by documenting the process of color grading a 13-minute short film, and also performing semistructured interviews with four colorists. Amongst other findings, this study found that HDR offers a wider range of modality expression than SDR (Standard Dynamic Range); regarding several visual modality markers. Four HDR-specific affordances were formulated; (1) color expandability, (2) highlight differentiability, (3) tonal rangeability, (4) brightness disturbability. Relating to the concept of creative space; the colorists expressed a concern that they will have to create multiple versions when delivering HDR, but not get a bigger budget for it, therefore having less time to spend on other aspects of color grading.

Recentes estudos sugerem a existência de sinapses elétricas mediadas por junções gap entre fotorreceptores na retina de vertebrados. Neste trabalho, descrevemos um modelo computacional dos circuitos primário e secundário mediados pelos bastonetes da retina de vertebrados. O modelo é composto pelas seguintes populações de células: bastonetes, cones, células bipolares dos bastonetes, células bipolares dos cones, células amácrinas do tipo AII e células ganglionares. As células do modelo estão acopladas entre si por sinapses químicas e elétricas segundo padrões realísticos de convergência e divergência. As sinapses elétricas ocorrem entre os bastonetes, entre os bastonetes e os cones, entre as células amácrinas AII e entre as células bipolares dos cones e a células amácrinas AII. O modelo assume que um estímulo luminoso de baixa intensidade, simulando condições escotópicas, atinge todos os bastonetes da camada receptora, porém menos da metade deles é excitada. A resposta dos bastonetes excitados é controlada por uma fotocorrente cuja amplitude pode ser alterada para simular estímulos de diferentes intensidades dentro da faixa escotópica. O modelo é utilizado para investigar os efeitos dos diferentes graus de acoplamento elétrico entre as células receptoras e entre as células amácrinas AII, além do efeito de diferentes valores de condutância do canal Ih ativado pela hiperpolarização nos bastonetes, sobre a faixa dinâmica da retina. Os resultados das simulações mostram que, para valores realísticos da condutância do canal Ih, a faixa dinâmica medida na camada receptora é maximizada para o índice de conectividade crítico para que haja percolação de ligação. No entanto, quando a faixa dinâmica é medida para as células bipolares ou ganglionares o valor máximo é obtido para um índice de conectividade subcrítico. Este resultado é conseqüência da alta convergência de sinapses químicas entre os bastonetes e células bipolares. / Recent studies suggest the existence of electrical synapses (gap junctions) connecting photoreceptors in the vertebrate retina. In this work we describe a computer model of the primary and secondary rod pathways in the vertebrate retina. The model is composed of the following cell populations: rods, cones, rod bipolar cells, cone bipolar cells, AII amacrine cells and ganglion cells. Cells of the model are connected via chemical as well as electrical synapses according to realistic convergence and divergence factors. There are electrical synapses between rods, rods and cones, AII amacrine cells, and cone bipolar cells and AII amacrine cells. The model assumes that low intensity stimuli simulating scotopic conditions reach all rods in the receptor array but less than half of them are excited. The excited rods response is controlled by a photocurrent waveform whose amplitude can be manipulated to simulate stimuli of different intensities within the scotopic range. The model is used to investigate the effects of different degrees of coupling among photoreceptors and among AII amacrine cells, as well as values of rod hyperpolarization activated current Ih on the dynamic range of the retina. Results show that for realistic values of Ih conductance the dynamic range of the rod array is maximized at the critical connectivity degree for bond percolation. However, the dynamic range of the rod bipolar and ganglion cells is maximized for a photoreceptor connectivity degree below the critical value. The latter result is a consequence of the high convergence of chemical synapses from rods to rod bipolar cells.

Teoricamente, conexões por sinapses elétricas entre neurônios poderiam levar ao aumento da faixa de resposta dinâmica da rede neural. A faixa de resposta dinâmica de uma rede de neurônios pode ser definida como a faixa de valores de intensidade dos estímulos de entrada para a qual o conjunto de neurônios produz resposta antes de atingir a saturação. Em um cenário biológico, propôs-se que junções gap entre células ganglionares da retina aumentariam a faixa dinâmica da retina. O teste experimental dessa proposta apresenta várias dificuldades, o que torna a modelagem computacional uma alternativa metodológica para o estudo do papel das sinapses elétricas na faixa dinâmica da camada ganglionar da retina. O objetivo deste trabalho foi a construção de um modelo biologicamente plausível da camada ganglionar da retina da salamandra, submetida a sinais de entrada realísticos conforme evidências experimentais e com a inclusão de sinapses elétricas conectando suas células, para estudar in silico os possíveis efeitos dessas sinapses elétricas sobre a faixa dinâmica da camada ganglionar. A camada ganglionar foi modelada como uma rede bidimensional cujos neurônios foram modelados pelo formalismo de Hodgkin-Huxley. Cada neurônio recebeu um de dois tipos de entrada sináptica, transiente ou sustentada. Avaliou-se o efeito da inibição pré-sináptica das células ganglionares e o efeito de diferentes padrões de conectividade mediados pelas sinapses elétricas. Os resultados sugerem que o acoplamento elétrico aumenta a sensibilidade do sistema e altera o ponto de saturação, mas não necessariamente aumenta a faixa dinâmica. / Theoretically, connections by electrical synapses between neurons could lead to an increase in their dynamic range. The dynamic range of a network of neurons can be defined as the range of input stimuli values for which the network responds before saturation. In a biological scenario, it is hypothesized that gap junctions between retinal ganglion cells may increase the dynamic range of the retina. However, the experimental testing of this hypothesis presents several difficulties, which makes computational modeling a methodological alternative to study the role of electrical synapses on the dynamic range of the ganglion cell layer of the retina. In this work we constructed a biologically plausible computational model of the ganglion cell layer of the salamander retina. A bidimensional network was built with cells modeled by the Hodgkin-Huxley formalism connected via gap junctions and subject to realistic inputs constrained by experimental evidence, to study in silico the effects of gap junctions on the dynamic range of the model. We studied the effect of different gap junction-mediated connectivity patterns, input type combinations (transient, sustained and mixed between the two) and presynaptic inhibition on the dynamic range. Our results suggest that gap junction coupling increases the network\'s sensitivity and alters the saturation point but not necessarily increases the dynamic range.

La plupart des capteurs inertiels MEMS commerciaux comportent une masse d’épreuve et des moyens de transductions issus d’une même couche de silicium. Il en découle des compromis forts, notamment pour la détection capacitive : une couche épaisse permet d’augmenter la masse et donc de réduire le bruit brownien; inversement, une couche fine permet de réduire la taille des entrefers entre les électrodes, d’obtenir une variation de capacité plus importante, et donc de réduire la contribution du bruit électronique. Plusieurs composants MEMS multicouches ont déjà été réalisés et rapportés dans la littérature, mais aucun n’a cherché à augmenter la densité capacitive tout en réduisant le bruit thermomécanique. Pourtant, la disparition du compromis lié au procédé monocouche permet d’atteindre les hautes performances nécessaires aux applications émergeantes, en conservant la surface d’un capteur grand public.Cette thèse présente des accéléromètres multicouches à détection dans le plan et hors plan. Le procédé de fabrication combine une couche épaisse, dédiée à la réalisation de grandes masses d’épreuve, et une couche fine, permettant d’obtenir de fortes densités capacitives. Ces deux avantages, combinés à une détection par variation de surface, permettent d’obtenir une résolution de l’ordre du µg/rtHz, une grande gamme dynamique, tout en conservant une taille réduite. Le dimensionnement des capteurs a cherché à maximiser la gamme dynamique et minimiser le bruit en partant d’une taille fixée. D’abord analytique, il a été validé par des simulations par éléments finis.Le procédé de fabrication VLSI a été appliqué à des plaques 200mm. Plusieurs points critiques ont été rencontrés, notamment la surgravure des fonds de tranchée (notching). Combinée à la disparité de vitesse de gravure, elle a entrainé la destruction de beaucoup de capteurs hors plan. Ce problème a été résolu en amincissant la couche épaisse, entrainant une légère perte de performances.Les capteurs ont été caractérisés sur plaque (capacité statique, fréquence de résonance), puis au niveau puce (sensibilité, niveau de bruit, gamme dynamique). Ces dernières mesures ont nécessité le développement d’une électronique dédiée, à partir de composants discrets.Les accéléromètres dans le plan présentent une capacité statique et une fréquence de résonance très proches de la théorie. Ils atteignent une résolution de 8µg/rtHz pour une gamme dynamique de l’ordre de 160g. Cette dynamique de 145dB est fournie par un composant de seulement 0.24mm² ; elle est 100 fois plus élevée que la dynamique d’un composant grand public de même taille. De plus, la bande passante est importante et le capteur est lu en boucle ouverte.Les accéléromètres hors-plan présentent une forte fréquence de résonance, au-delà de 8kHz. La masse sismique plus fine, combinée à des ressorts plus larges, explique ce décalage par rapport au dimensionnement initial. Malgré la réduction de sensibilité induite, les capteurs présentent une résolution de 50 à 80µg/rtHz. L’encombrement est faible (jusqu’à 0.22mm²) et la gamme dynamique a été évaluée à plus de 200g. Dans le futur, des corrections de design et des améliorations dans le procédé de fabrication permettront d’utiliser l’épaisseur initialement prévue, afin d’harmoniser les performances avec celles de l’accéléromètre dans le plan et d’obtenir un accéléromètre 3-axes hautes performances.Ce type de capteurs pourrait jouer un grand rôle dans les applications émergentes en fournissant une bonne stabilité, un faible bruit et une grande gamme dynamique, tout en conservant l’empreinte d’un capteur grand-public.Ce nouveau procédé de fabrication montre donc déjà un gros potentiel à travers les premiers composants réalisés, mais ouvre également de nouvelles possibilités en termes de design. Dans le futur, il pourrait servir de plateforme technologique pour les capteurs inertiels, notamment les gyromètres, mais aussi pour les actionneurs, comme les micro-miroirs. / In the vast majority of commercial MEMS inertial sensors, both seismic mass and sensing elements are patterned in the same silicon layer. This sets stringent design trade-offs, in particular for a capacitive sensor: a large silicon thickness increases seismic mass and decreases the Brownian noise floor. A low silicon thickness on the other hand, allows smaller gaps between electrodes, higher capacitance variation and lower electrical noise floor. For this reason, several examples of multi-layer MEMS devices were presented in the past. Yet, increasing capacitance density while reducing mechanical noise floor has not been achieved so far. Breaking the single-layer trade-off could enable new emerging applications that require high-performance sensors within a consumer size.In this work, multi-layer, in-plane and out-of-plane accelerometer are presented. Thanks to the multi-layer process the devices can feature a thick layer for large inertial mass, as well as a thin layer for high capacitive density. These aspects, together with surface-variation detection, allow to obtain µg/√Hz resolution and large full-scale while keeping compact size.The sensors are designed through analytical modeling and finite elements method simulations in order to reach the highest dynamic range with the lowest noise at given footprint.Few critical aspects were encountered during the fabrication of the sensors, especially for out-of-plane accelerometers. The notching of the thick-layer etching coupled to the strong lag effect caused most of the z-axis sensors to fail. This forced a reduction of the process thickness and relative loss of performance for this type of sensors.The characterization of the sensors is performed both at wafer-level (static capacitance, resonance frequency) and at die level (scale factor, noise-floor, full-scale). The die-level measurements are carried out with a dedicated electronic circuit implemented with discrete components, developed during this work.In-plane accelerometers showed static capacitance and resonance frequency in line with theory. They achieved resolution smaller than 8 µg/rtHz and full scale in the order of 160g. These aspects together lead to a dynamic range of more than 145dB (BW=1Hz) for a device with a footprint of only 0.24 mm². This it more than 100 times larger than the DR of consumer device of similar size. These results are achieved while keeping a large bandwidth and working with an open-loop readout.Out-of-plane sensors showed resonance frequency higher than expected due to fabrication tolerances. The devices had both smaller mass and thicker springs explaining the observed mechanical behavior. Despite the loss of scale factor due to the larger resonance frequency, these sensors achieved resolution ranging from 50-80 µg/rtHz. Again, such performance was obtained while keeping large resonance frequency (>8 kHz), small footprint (down to 0.22 mm²) and a potential full-scale of more than 200g. In the future, design corrections and process improvement could lead to device with thicker inertial layer, aligning the performance of out-of-plane sensors to those of in-plane ones and leading to a high-performance 3-axis accelerometer.This type of sensor could address the demand of emerging applications for high-stability, low-noise and large DR accelerometers within consumer footprint.Finally, the proposed technology offers a fabrication platform for inertial MEMS sensors and actuators. New design possibilities and great potentialities have been demonstrated with the first fabricated accelerometers. In the future this new concept could be applied to several other types of MEMS, like gyroscope or micro-mirrors.