Piecewise Affine Registration of Biological Images for Volume Reconstruction

This manuscript tackles the reconstruction of 3D volumes via mono-modal registration of series of 2D biological images (histological sections, autoradiographs, cryosections, etc.). The process of acquiring these images typically induces composite transformations that we model as a number of rigid or affine local transformations embedded in an elastic one. We propose a registration approach closely derived from this model. Given a pair of input images, we first compute a dense similarity field between them with a block matching algorithm. We use as a similarity measure an extension of the classical correlation coefficient that improves the consistency of the field. A hierarchical clustering algorithm then automatically partitions the field into a number of classes from which we extract independent pairs of sub-images. Our clustering algorithm relies on the Earth mover’s distribution metric and is additionally guided by robust least-square estimation of the transformations associated with each cluster. Finally, the pairs of sub-images are, independently, affinely registered and a hybrid affine/non-linear interpolation scheme is used to compose the output registered image. We investigate the behavior of our approach on several batches of histological data and discuss its sensitivity to parameters and noise

Contour matching using ant colony optimization and curve evolution

Shape retrieval is a very important topic in computer vision. Image retrieval consists of selecting images that fulfil specific criteria from a collection of images. This thesis concentrates on contour-based image retrieval, in which we only explore the information located on the shape contour. There are many different kinds of shape retrieval methods. Most of the research in this field has till now concentrated on matching methods and how to achieve a meaningful correspondence. The matching process consist of finding correspondence between the points located on the designed contours. However, the huge number of incorporated points in the correspondence makes the matching process more complex. Furthermore, this scheme does not support computation of the correspondence intuitively without considering noise effect and distortions. Hence, heuristics methods are convoked to find acceptable solution. Moreover, some researches focus on improving polygonal modelling methods of a contour in such a way that the resulted contour is a good approximation of the original contour, which can be used to reduce the number of incorporated points in the matching. In this thesis, a novel approach for Ant Colony Optimization (ACO) contour matching that can be used to find an acceptable matching between contour shapes is developed. A polygonal evolution method proposed previously is selected to simplify the extracted contour. The main reason behind selecting this method is due to the use of a stopping criterion which must be predetermined. The match process is formulated as a Quadratic Assignment Problem (QAP) and resolved by using ACO. An approximated similarity is computed using original shape context descriptor and the Euclidean metric. The experimental results justify that the proposed approach is invariant to noise and distortions, and it is more robust to noise and distortion compared to the previously introduced Dominant Point (DP) Approach. This work serves as the fundamental study for assessing the Bender Test to diagnose dyslexic and non-dyslexic symptom in children

Matching sets of features for efficient retrieval and recognition

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2006.Includes bibliographical references (p. 145-153).In numerous domains it is useful to represent a single example by the collection of local features or parts that comprise it. In computer vision in particular, local image features are a powerful way to describe images of objects and scenes. Their stability under variable image conditions is critical for success in a wide range of recognition and retrieval applications. However, many conventional similarity measures and machine learning algorithms assume vector inputs. Comparing and learning from images represented by sets of local features is therefore challenging, since each set may vary in cardinality and its elements lack a meaningful ordering. In this thesis I present computationally efficient techniques to handle comparisons, learning, and indexing with examples represented by sets of features. The primary goal of this research is to design and demonstrate algorithms that can effectively accommodate this useful representation in a way that scales with both the representation size as well as the number of images available for indexing or learning. I introduce the pyramid match algorithm, which efficiently forms an implicit partial matching between two sets of feature vectors.(cont.) The matching has a linear time complexity, naturally forms a Mercer kernel, and is robust to clutter or outlier features, a critical advantage for handling images with variable backgrounds, occlusions, and viewpoint changes. I provide bounds on the expected error relative to the optimal partial matching. For very large databases, even extremely efficient pairwise comparisons may not offer adequately responsive query times. I show how to perform sub-linear time retrievals under the matching measure with randomized hashing techniques, even when input sets have varying numbers of features. My results are focused on several important vision tasks, including applications to content-based image retrieval, discriminative classification for object recognition, kernel regression, and unsupervised learning of categories. I show how the dramatic increase in performance enables accurate and flexible image comparisons to be made on large-scale data sets, and removes the need to artificially limit the number of local descriptions used per image when learning visual categories.by Kristen Lorraine Grauman.Ph.D

Wasserstein β-Diversity Metrics over Graphs: Derivation, Efficient Computation and Applications

Microbial ecology has been transformed by metagenomics, the study of the genetic in-formation in entire communities of organisms. In the following we develop metagenomic tools arising from the classic Wasserstein metric as applied to questions regarding the diversity between microbial communities. We provide a novel proof of the characteriza-tion of the successful UniFrac metric as the Wasserstein metric over a graph-theoretic tree, and use the proof to develop an extremely e°cient computational algorithm. The analytic framework we develop is then leveraged to provide formulations for the distri-bution of this Wasserstein based metric. We implement these ideas and demonstrate their utility on realworld datasets. We next turn to applying the Wasserstein metric as a reference-free diversity metric by utilizing de Bruijn graphs, mathematical structures at the heart of genome assembly techniques. We show how these techniques are related to established phylogenetically-aware diversity metrics. We then implement our results using newly developed approximation techniques for the computation of the Wasserstein metric and demonstrate this novel metric's utility in comparison to established metrics

A generalisable framework for saliency-based line segment detection

Here we present a novel, information-theoretic salient line segment detector. Existing line detectors typically only use the image gradient to search for potential lines. Consequently, many lines are found, particularly in repetitive scenes. In contrast, our approach detects lines that define regions of significant divergence between pixel intensity or colour statistics. This results in a novel detector that naturally avoids the repetitive parts of a scene while detecting the strong, discriminative lines present. We furthermore use our approach as a saliency filter on existing line detectors to more efficiently detect salient line segments. The approach is highly generalisable, depending only on image statistics rather than image gradient; and this is demonstrated by an extension to depth imagery. Our work is evaluated against a number of other line detectors and a quantitative evaluation demonstrates a significant improvement over existing line detectors for a range of image transformation

A generalisable framework for saliency-based line segment detection

Here we present a novel, information-theoretic salient line segment detector. Existing line detectors typically only use the image gradient to search for potential lines. Consequently, many lines are found, particularly in repetitive scenes. In contrast, our approach detects lines that define regions of significant divergence between pixel intensity or colour statistics. This results in a novel detector that naturally avoids the repetitive parts of a scene while detecting the strong, discriminative lines present. We furthermore use our approach as a saliency filter on existing line detectors to more efficiently detect salient line segments. The approach is highly generalisable, depending only on image statistics rather than image gradient; and this is demonstrated by an extension to depth imagery. Our work is evaluated against a number of other line detectors and a quantitative evaluation demonstrates a significant improvement over existing line detectors for a range of image transformation

An Unsupervised Cluster: Learning Water Customer Behavior Using Variation of Information on a Reconstructed Phase Space

The unsupervised clustering algorithm described in this dissertation addresses the need to divide a population of water utility customers into groups based on their similarities and differences, using only the measured flow data collected by water meters. After clustering, the groups represent customers with similar consumption behavior patterns and provide insight into ‘normal’ and ‘unusual’ customer behavior patterns. This research focuses upon individually metered water utility customers and includes both residential and commercial customer accounts serviced by utilities within North America. The contributions of this dissertation not only represent a novel academic work, but also solve a practical problem for the utility industry. This dissertation introduces a method of agglomerative clustering using information theoretic distance measures on Gaussian mixture models within a reconstructed phase space. The clustering method accommodates a utility’s limited human, financial, computational, and environmental resources. The proposed weighted variation of information distance measure for comparing Gaussian mixture models places emphasis upon those behaviors whose statistical distributions are more compact over those behaviors with large variation and contributes a novel addition to existing comparison options