Model and Appearance Based Analysis of Neuronal Morphology from Different Microscopy Imaging Modalities

The neuronal morphology analysis is key for understanding how a brain works. This process requires the neuron imaging system with single-cell resolution; however, there is no feasible system for the human brain. Fortunately, the knowledge can be inferred from the model organism, Drosophila melanogaster, to the human system. This dissertation explores the morphology analysis of Drosophila larvae at single-cell resolution in static images and image sequences, as well as multiple microscopy imaging modalities. Our contributions are on both computational methods for morphology quantification and analysis of the influence of the anatomical aspect. We develop novel model-and-appearance-based methods for morphology quantification and illustrate their significance in three neuroscience studies. Modeling of the structure and dynamics of neuronal circuits creates understanding about how connectivity patterns are formed within a motor circuit and determining whether the connectivity map of neurons can be deduced by estimations of neuronal morphology. To address this problem, we study both boundary-based and centerline-based approaches for neuron reconstruction in static volumes. Neuronal mechanisms are related to the morphology dynamics; so the patterns of neuronal morphology changes are analyzed along with other aspects. In this case, the relationship between neuronal activity and morphology dynamics is explored to analyze locomotion procedures. Our tracking method models the morphology dynamics in the calcium image sequence designed for detecting neuronal activity. It follows the local-to-global design to handle calcium imaging issues and neuronal movement characteristics. Lastly, modeling the link between structural and functional development depicts the correlation between neuron growth and protein interactions. This requires the morphology analysis of different imaging modalities. It can be solved using the part-wise volume segmentation with artificial templates, the standardized representation of neurons. Our method follows the global-to-local approach to solve both part-wise segmentation and registration across modalities. Our methods address common issues in automated morphology analysis from extracting morphological features to tracking neurons, as well as mapping neurons across imaging modalities. The quantitative analysis delivered by our techniques enables a number of new applications and visualizations for advancing the investigation of phenomena in the nervous system

Phenotype Operators for Improved Performance of Heuristic Encoding Within Genetic Algorithms

Many approaches to applying Genetic Algorithms (GAs) to Nondeterministic Polynomial time Complete (NPC) problems involve population members encoded directly from the problem solution space. While this technique enables trivial mapping of the population members to solutions, it can cause complex problems for GA operators as they attempt to direct the evolution of the population toward more promising areas of the solution space. These operators, using inspiration from genetics and evolution in the biological world, combine and manipulate the current population to produce a new population that, it is hoped, will eventually converge toward better solutions to the original problem. However, many problems, especially graph-space problems, cannot be so easily manipulated when GA members consist of direct encodings. In such cases, GA operators must perform awkward transformations to convert the progeny into viable solutions. Here is where heuristic encoding comes into play, in that any combination of genes will produce a viable solution. However, this additional level of abstraction does cause other problems and tends to weaken the guiding effects of traditional GA operators. Thus, I have designed custom GA operators that mitigate these problems by using the solutions produced by the heuristic encoded members to better guide the manipulation when producing the next generation. This dissertation shows that heuristic encoding is an effective technique for the representation of solutions to graph-space problems. It also shows that, when using heuristic encoding, GAs with traditional operators perform well compared to more direct encoding techniques. Finally it shows the combination of heuristic encoding and GA operators designed to work with them increases GA performance and can be competitive with other techniques. I believe that these techniques will also work well for other types of problems for which GAs are commonly applied

Cellular Automata

Modelling and simulation are disciplines of major importance for science and engineering. There is no science without models, and simulation has nowadays become a very useful tool, sometimes unavoidable, for development of both science and engineering. The main attractive feature of cellular automata is that, in spite of their conceptual simplicity which allows an easiness of implementation for computer simulation, as a detailed and complete mathematical analysis in principle, they are able to exhibit a wide variety of amazingly complex behaviour. This feature of cellular automata has attracted the researchers' attention from a wide variety of divergent fields of the exact disciplines of science and engineering, but also of the social sciences, and sometimes beyond. The collective complex behaviour of numerous systems, which emerge from the interaction of a multitude of simple individuals, is being conveniently modelled and simulated with cellular automata for very different purposes. In this book, a number of innovative applications of cellular automata models in the fields of Quantum Computing, Materials Science, Cryptography and Coding, and Robotics and Image Processing are presented

The Victorian Naturalist

v.112 (1995

Using contour information and segmentation for object registration, modeling and retrieval

This thesis considers different aspects of the utilization of contour information and syntactic and semantic image segmentation for object registration, modeling and retrieval in the context of content-based indexing and retrieval in large collections of images. Target applications include retrieval in collections of closed silhouettes, holistic w ord recognition in handwritten historical manuscripts and shape registration. Also, the thesis explores the feasibility of contour-based syntactic features for improving the correspondence of the output of bottom-up segmentation to semantic objects present in the scene and discusses the feasibility of different strategies for image analysis utilizing contour information, e.g. segmentation driven by visual features versus segmentation driven by shape models or semi-automatic in selected application scenarios. There are three contributions in this thesis. The first contribution considers structure analysis based on the shape and spatial configuration of image regions (socalled syntactic visual features) and their utilization for automatic image segmentation. The second contribution is the study of novel shape features, matching algorithms and similarity measures. Various applications of the proposed solutions are presented throughout the thesis providing the basis for the third contribution which is a discussion of the feasibility of different recognition strategies utilizing contour information. In each case, the performance and generality of the proposed approach has been analyzed based on extensive rigorous experimentation using as large as possible test collections

Robust iris recognition under unconstrained settings

Tese de mestrado integrado. Bioengenharia. Faculdade de Engenharia. Universidade do Porto. 201