abstract: Fluctuations with a power spectral density depending on frequency as $1/f^\alpha$ ($0<\alpha<2$) are found in a wide class of systems. The number of systems exhibiting $1/f$ noise means it has far-reaching practical implications; it also suggests a possibly universal explanation, or at least a set of shared properties. Given this diversity, there are numerous models of $1/f$ noise. In this dissertation, I summarize my research into models based on linking the characteristic times of fluctuations of a quantity to its multiplicity of states. With this condition satisfied, I show that a quantity will undergo $1/f$ fluctuations and exhibit associated properties, such as slow dynamics, divergence of time scales, and ergodicity breaking. I propose that multiplicity-dependent characteristic times come about when a system shares a constant, maximized amount of entropy with a finite bath. This may be the case when systems are imperfectly coupled to their thermal environment and the exchange of conserved quantities is mediated through their local environment. To demonstrate the effects of multiplicity-dependent characteristic times, I present numerical simulations of two models. The first consists of non-interacting spins in $0$-field coupled to an explicit finite bath. This model has the advantage of being degenerate, so that its multiplicity alone determines the dynamics. Fluctuations of the alignment of this model will be compared to voltage fluctuations across a mesoscopic metal-insulator-metal junction. The second model consists of classical, interacting Heisenberg spins with a dynamic constraint that slows fluctuations according to the multiplicity of the system's alignment. Fluctuations in one component of the alignment will be compared to the flux noise in superconducting quantum interference devices (SQUIDs). Finally, I will compare both of these models to each other and some of the most popular models of $1/f$ noise, including those based on a superposition of exponential relaxation processes and those based on power law renewal processes. / Dissertation/Thesis / Doctoral Dissertation Physics 2018

We explore the applicability of local polynomial approximation of signals for noise suppression. In the context of data regression, Savitzky and Golay showed that least-squares approximation of data with a polynomial of fixed order, together with a constant window length, is identical to convolution with a finite impulse response filter, whose characteristics depend entirely on two parameters, namely, the order and window length. Schafer’s recent article in IEEE Signal Processing Magazine provides a detailed account of one-dimensional Savitzky-Golay (SG) filters. Drawing motivation from this idea, we present an elaborate study of two-dimensional SG filters and employ them for image denoising by optimizing the filter response to minimize the mean-squared error (MSE) between the original image and the filtered output. The key contribution of this thesis is a method for optimal selection of order and window length of SG filters for denoising images. First, we apply the denoising technique for images contaminated by additive Gaussian noise. Owing to the absence of ground truth in practice, direct minimization of the MSE is infeasible. However, the classical work of C. Stein provides a statistical method to overcome the hurdle. Based on Stein’s lemma, an estimate of the MSE, namely Stein’s unbiased risk estimator (SURE), is derived, and the two critical parameters of the filter are optimized to minimize the cost. The performance of the technique improves when a regularization term, which penalizes fast variations in the estimate, is added to the optimization cost. In the next three chapters, we focus on non-Gaussian noise models. In Chapter 3, image degradation in the presence of a compound noise model, where images are corrupted by mixed Poisson-Gaussian noise, is addressed. Inspired by Hudson’s identity, an estimate of MSE, namely Poisson unbiased risk estimator (PURE), which is analogous to SURE, is developed. Combining both lemmas, Poisson-Gaussian unbiased risk estimator (PGURE) minimization is performed to obtain the optimal filter parameters. We also show that SG filtering provides better lowpass approximation for a multiresolution denoising framework. In Chapter 4, we employ SG filters for reducing multiplicative noise in images. The standard SG filter frequency response can be controlled along horizontal or vertical directions. This limits its ability to capture oriented features and texture that lie at other angles. Here, we introduce the idea of steering the SG filter kernel and perform mean-squared error minimization based on the new concept of multiplicative noise unbiased risk estimation (MURE). Finally, we propose a method to robustify SG filters, robustness to deviation from Gaussian noise statistics. SG filters work on the principle of least-squares error minimization, and are hence compatible with maximum-likelihood (ML) estimation in the context of Gaussian statistics. However, for heavily-tailed noise such as the Laplacian, where ML estimation requires mean-absolute error minimization in lieu of MSE minimization, standard SG filter performance deteriorates. `1 minimization is a challenge since there is no closed-form solution. We solve the problem by inducing the `1-norm criterion using the iteratively reweighted least-squares (IRLS) method. At every iteration, we solve an l`2 problem, which is equivalent to optimizing a weighted SG filter, but, as iterations progress, the solution converges to that corresponding to `1 minimization. The results thus obtained are superior to those obtained using the standard SG filter.

Color theory was first formalized in the seventeenth century by Isaac Newton just a couple of decades after the first microscope was built. But it was not until the twentieth century that technological advances led to the integration of color theory, optical spectroscopy and light microscopy through spectral image processing. However, while the focus of image processing often concerns modeling of how images are perceived by humans, the goal of image processing in natural sciences and medicine is the objective analysis. This thesis is focused on color theory that promotes quantitative analysis rather than modeling how images are perceived by humans. Color and fluorescent dyes are routinely added to biological specimens visualizing features of interest. By applying spectral image processing to histopathology, subjectivity in diagnosis can be minimized, leading to a more objective basis for a course of treatment planning. Also, mathematical models for spectral image processing can be used in biotechnology research increasing accuracy and throughput, and decreasing bias. This thesis presents a model for spectral image formation that applies to both fluorescence and transmission light microscopy. The inverse model provides estimates of the relative concentration of each individual component in the observed mixture of dyes. Parameter estimation for the model is based on decoupling light intensity and spectral information. This novel spectral decomposition method consists of three steps: (1) photon and semiconductor noise modeling providing smoothing parameters, (2) image data transformation to a chromaticity plane removing  intensity variation while maintaining chromaticity differences, and (3) a piecewise linear decomposition combining advantages of spectral angle mapping and linear decomposition yielding relative dye concentrations. The methods described herein were used for evaluation of molecular biology techniques as well as for quantification and interpretation of image-based measurements. Examples of successful applications comprise quantification of colocalization, autofluorescence removal, classification of multicolor rolling circle products, and color decomposition of histological images.

This thesis describes the theoretical, experimental, and practical aspects of a noise-limited method for scene-change detection in images. The research is divided into three sections: noise analysis and modelling, dual illumination scene-change modelling, and integration of noise into the scene-change model. The sources of noise within commercially available digital cameras are described, with a new model for image noise derived for charge-coupled device (CCD) cameras. The model is validated experimentally through the development of techniques that allow the individual noise components to be measured from the analysis of output images alone. A generic model for complementary metal-oxide-semiconductor (CMOS) cameras is also derived. Methods for the analysis of spatial (inter-pixel) and temporal (intra-pixel) noise are developed. These are used subsequently to investigate the effects of environmental temperature on camera noise. Based on the cameras tested, the results show that the CCD camera noise response to variation in environmental temperature is complex whereas the CMOS camera response simply increases monotonically. A new concept for scene-change detection is proposed based upon a dual illumination concept where both direct and ambient illumination sources are present in an environment, such as that which occurs in natural outdoor scenes with direct sunlight and ambient skylight. The transition of pixel colour from the combined direct and ambient illuminants to the ambient illuminant only is modelled. A method for shadow-free scene-change is then developed that predicts a pixel's colour when the area in the scene is subjected to ambient illumination only, allowing pixel change to be distinguished as either being due to a cast shadow or due to a genuine change in the scene. Experiments on images captured in controlled lighting demonstrate 91% of scene-change and 83% of cast shadows are correctly determined from analysis of pixel colour change alone. A statistical method for detecting shadow-free scene-change is developed. This is achieved by bounding the dual illumination model by the confidence interval associated with the pixel's noise. Three benefits arise from the integration of noise into the scene-change detection method: - The necessity for pre-filtering images for noise is removed; - All empirical thresholds are removed; and - Performance is improved. The noise-limited scene-change detection algorithm correctly classifies 93% of scene-change and 87% of cast shadows from pixel colour change alone. When simple post-analysis size-filtering is applied both these figures increase to 95%.

La modélisation pharmacocinétique en tomographie par émission par positrons (TEP) permet d’estimer les paramètres physiologiques liés à l’accumulation dynamique d’un radiotraceur. Les paramètres estimés sont biaisés par le bruit dans les images TEP dynamiques durant l’ajustement des courbes d’activité des tissus, plus communément appelées TAC de l’anglais Time Activity Curve. La qualité des images TEP dynamiques est limitée par la statistique de comptage et influencée par les paramètres de reconstruction choisis en termes de résolution spatiale et temporelle. Il n’existe pas de recommandations claires pour les paramètres de reconstruction à utiliser pour les images dynamiques TEP. L’objectif de ce projet de maitrise est d’évaluer le biais dans l’estimation des paramètres pharmacocinétiques afin de trouver les paramètres de reconstruction TEP les plus optimaux en termes de résolution spatiale et de niveau de bruit. Plus précisément, ce projet cherche à déterminer quel modèle d’AIF offre les meilleurs ajustements, mais aussi quel modèle de poids permet la meilleure estimation des paramètres pharmacocinétiques pour le modèle à deux compartiments. Ce faisant, il serait possible de mieux planifier la reconstruction d’images TEP dynamique et potentiellement améliorer leur résolution spatiale. Afin de tester les biais dans les paramètres pharmacocinétiques sous différents niveaux de bruit, un objet de référence numérique (DRO) avec les informations trouvées dans la littérature sera construit. Ensuite, des simulations numériques seront effectuées avec ce DRO afin de trouver les paramètres de reconstruction et le niveau de bruit le plus optimal. Un biais réduit des paramètres pharmacocinétiques et une meilleure résolution spatiale des images TEP dynamique permettrait de détecter des cancers ou tumeurs à des stades moins avancés de la maladie, permettant potentiellement un traitement plus efficace et avec moins de séquelles et d’effets secondaires pour les patients. En outre, cela permettrait aussi de visualiser l’hétérogénéité des tumeurs. / Pharmacokinetic models in positron emission tomography (PET) allow for the estimation of physiological parameters linked to the dynamic accumulation of a radiotracer. Estimated parameters are biased by noise in dynamic PET images during the fitting of Time Activity Curves (TAC). Image quality in dynamic PET is limited by counting statistics and influenced by the chosen reconstruction parameters in terms of spatial and temporal resolution. Clear recommendations and guidelines for the reconstruction parameters that should be used do not exist at the moment for dynamic PET. The goal of this masters project is to evaluate the bias in the pharmacokinetic parameters estimation to find the optimal PET reconstruction parameters in terms of spatial resolution and noise levels. More precisely, this project aims to determine which AIF model produces the best fits, but also which weight noise model allows for the best parameters estimation with the two compartment model. It would then be possible to plan the PET image reconstruction more finely and potentially improve spatial resolution. To test the pharmacokinetic parameters’ biases under different noise levels, a Digital Reference Object (DRO) with information and specifications found from the litterature will be built. Then, numerical simulations will be done with that DRO to find the optimal noise level and value for the pharmacokinetic parameter. A reduced bias in these parameters and an improved spatial resolution would allow the detection of tumors or lesions at earlier stages, which could potentially allow for a more potent treatment with less short and long term side effects. It would also allow the visualization and quantification of lesion heterogeneity.