JIGSAW-GEO (1.0): locally orthogonal staggered unstructured grid generation for general circulation modelling on the sphere

An algorithm for the generation of non-uniform, locally-orthogonal staggered unstructured spheroidal grids is described. This technique is designed to generate very high-quality staggered Voronoi/Delaunay meshes appropriate for general circulation modelling on the sphere, including applications to atmospheric simulation, ocean-modelling and numerical weather prediction. Using a recently developed Frontal-Delaunay refinement technique, a method for the construction of high-quality unstructured spheroidal Delaunay triangulations is introduced. A locally-orthogonal polygonal grid, derived from the associated Voronoi diagram, is computed as the staggered dual. It is shown that use of the Frontal-Delaunay refinement technique allows for the generation of very high-quality unstructured triangulations, satisfying a-priori bounds on element size and shape. Grid-quality is further improved through the application of hill-climbing type optimisation techniques. Overall, the algorithm is shown to produce grids with very high element quality and smooth grading characteristics, while imposing relatively low computational expense. A selection of uniform and non-uniform spheroidal grids appropriate for high-resolution, multi-scale general circulation modelling are presented. These grids are shown to satisfy the geometric constraints associated with contemporary unstructured C-grid type finite-volume models, including the Model for Prediction Across Scales (MPAS-O). The use of user-defined mesh-spacing functions to generate smoothly graded, non-uniform grids for multi-resolution type studies is discussed in detail.Comment: Final revisions, as per: Engwirda, D.: JIGSAW-GEO (1.0): locally orthogonal staggered unstructured grid generation for general circulation modelling on the sphere, Geosci. Model Dev., 10, 2117-2140, https://doi.org/10.5194/gmd-10-2117-2017, 201

Nuclei/Cell Detection in Microscopic Skeletal Muscle Fiber Images and Histopathological Brain Tumor Images Using Sparse Optimizations

Nuclei/Cell detection is usually a prerequisite procedure in many computer-aided biomedical image analysis tasks. In this thesis we propose two automatic nuclei/cell detection frameworks. One is for nuclei detection in skeletal muscle fiber images and the other is for brain tumor histopathological images. For skeletal muscle fiber images, the major challenges include: i) shape and size variations of the nuclei, ii) overlapping nuclear clumps, and iii) a series of z-stack images with out-of-focus regions. We propose a novel automatic detection algorithm consisting of the following components: 1) The original z-stack images are first converted into one all-in-focus image. 2) A sufficient number of hypothetical ellipses are then generated for each nuclei contour. 3) Next, a set of representative training samples and discriminative features are selected by a two-stage sparse model. 4) A classifier is trained using the refined training data. 5) Final nuclei detection is obtained by mean-shift clustering based on inner distance. The proposed method was tested on a set of images containing over 1500 nuclei. The results outperform the current state-of-the-art approaches. For brain tumor histopathological images, the major challenges are to handle significant variations in cell appearance and to split touching cells. The proposed novel automatic cell detection consists of: 1) Sparse reconstruction for splitting touching cells. 2) Adaptive dictionary learning for handling cell appearance variations. The proposed method was extensively tested on a data set with over 2000 cells. The result outperforms other state-of-the-art algorithms with F1 score = 0.96

Saliency-guided integration of multiple scans

we present a novel method..

Registration and categorization of camera captured documents

Camera captured document image analysis concerns with processing of documents captured with hand-held sensors, smart phones, or other capturing devices using advanced image processing, computer vision, pattern recognition, and machine learning techniques. As there is no constrained capturing in the real world, the captured documents suffer from illumination variation, viewpoint variation, highly variable scale/resolution, background clutter, occlusion, and non-rigid deformations e.g., folds and crumples. Document registration is a problem where the image of a template document whose layout is known is registered with a test document image. Literature in camera captured document mosaicing addressed the registration of captured documents with the assumption of considerable amount of single chunk overlapping content. These methods cannot be directly applied to registration of forms, bills, and other commercial documents where the fixed content is distributed into tiny portions across the document. On the other hand, most of the existing document image registration methods work with scanned documents under affine transformation. Literature in document image retrieval addressed categorization of documents based on text, figures, etc. However, the scalability of existing document categorization methodologies based on logo identification is very limited. This dissertation focuses on two problems (i) registration of captured documents where the overlapping content is distributed into tiny portions across the documents and (ii) categorization of captured documents into predefined logo classes that scale to large datasets using local invariant features. A novel methodology is proposed for the registration of user defined Regions Of Interest (ROI) using corresponding local features from their neighborhood. The methodology enhances prior approaches in point pattern based registration, like RANdom SAmple Consensus (RANSAC) and Thin Plate Spline-Robust Point Matching (TPS-RPM), to enable registration of cell phone and camera captured documents under non-rigid transformations. Three novel aspects are embedded into the methodology: (i) histogram based uniformly transformed correspondence estimation, (ii) clustering of points located near the ROI to select only close by regions for matching, and (iii) validation of the registration in RANSAC and TPS-RPM algorithms. Experimental results on a dataset of 480 images captured using iPhone 3GS and Logitech webcam Pro 9000 have shown an average registration accuracy of 92.75% using Scale Invariant Feature Transform (SIFT). Robust local features for logo identification are determined empirically by comparisons among SIFT, Speeded-Up Robust Features (SURF), Hessian-Affine, Harris-Affine, and Maximally Stable Extremal Regions (MSER). Two different matching methods are presented for categorization: matching all features extracted from the query document as a single set and a segment-wise matching of query document features using segmentation achieved by grouping area under intersecting dense local affine covariant regions. The later approach not only gives an approximate location of predicted logo classes in the query document but also helps to increase the prediction accuracies. In order to facilitate scalability to large data sets, inverted indexing of logo class features has been incorporated in both approaches. Experimental results on a dataset of real camera captured documents have shown a peak 13.25% increase in the F–measure accuracy using the later approach as compared to the former

Speaker segmentation and clustering

This survey focuses on two challenging speech processing topics, namely: speaker segmentation and speaker clustering. Speaker segmentation aims at finding speaker change points in an audio stream, whereas speaker clustering aims at grouping speech segments based on speaker characteristics. Model-based, metric-based, and hybrid speaker segmentation algorithms are reviewed. Concerning speaker clustering, deterministic and probabilistic algorithms are examined. A comparative assessment of the reviewed algorithms is undertaken, the algorithm advantages and disadvantages are indicated, insight to the algorithms is offered, and deductions as well as recommendations are given. Rich transcription and movie analysis are candidate applications that benefit from combined speaker segmentation and clustering. © 2007 Elsevier B.V. All rights reserved