Feature-aligned shape texturing
The essence of a 3D shape can often be well captured by its salient feature curves. In this paper, we explore the use of salient curves in synthesizing intuitive, shape-revealing textures on surfaces. Our texture synthesis is guided by two principles: matching the direction of the texture patterns to those of the salient curves, and aligning the prominent feature lines in the texture to the salient curves exactly. We have observed that textures synthesized by these principles not only fit naturally to the surface geometry, but also visually reveal, even reinforce, the shape's essential characteristics. We call these feature-aligned shape texturing. Our technique is fully automatic, and introduces two novel technical components in vector-field-guided texture synthesis: an algorithm that orients the salient curves on a surface for constrained vector field generation, and a feature-to-feature texture optimization.

title: A mass-spring model for surface mesh deformation based on shape matching
abstract: In this paper, we propose a mass-spring model based on shape matching for real-time deformable modeling in virtual reality systems. By defining a rigid core for surface mesh model and adding a new generalized spring for each mass, our surface mesh model can preserve its original geometric features such as volume and shape. Then, we use shape matching approaches to update the rigid core of the model dynamically so as to simulate global deformations. At last, we adopt an inverse dynamics technique to deal with the resulting deformations. We correct the non-real "super-elastic" effect for linear elastic models so that the visual reality is improved.

title: A simple and stable feature-preserving smoothing method for contours-based reconstructed meshes
abstract: In this paper, we develop a new feature preserving smoothing method for the irregular and coarse meshes reconstructed from 2D contours. To make the feature detecting robust, a new detecting algorithm using the continuity among adjacent contours is proposed. Then the original mesh is subdivided adaptively according to the detected geometric features and smoothed with isotropic method. With the help of that, our algorithm obtains not only the feature-preserving result of anisotropic methods but also the simple and stable process of isotropic ones. After smoothing, the resolution of mesh can be resumed by moving the vertices in the original mesh to the positions of their corresponding vertices in the smoothed adaptive mesh. For smoothing of contours-based reconstructed meshes, experimental results show that our method can smooth the meshes satisfactorily and preserve their geometric features much better than other implemented methods.

title: An adaptive octree textures painting algorithm
abstract: Traditional Texturing using a set of two dimensional image maps is an established and widespread practice. However, it is difficult to parameterize a model in texture space, particularly with representations such as implicit surfaces, subdivision surfaces, and very dense or detailed polygonal meshes. Based on an adaptive octree textures definition, this paper proposes a direct reverse-projecting pixel-level painting approach which has less storage requirements to general octree textures maps. In addition, it depends on texture lookup in the GPU, which particularly lookup faster than the non-GPU program.

title: 2D shape deformation based on rigid square matching
abstract: In this paper, we propose a fast and stable method for 2D shape deformation based on rigid square matching. Our method utilizes uniform quadrangular control meshes for 2D shapes and tries to maintain the rigidity of each square in the control mesh during user manipulation. A rigid shape matching method is performed to find an optimal pure rotational transformation for each square in the control mesh. An iterative solver is proposed to compute the final deformation result for the entire control mesh by minimizing the difference between the deformed vertices and their counterparts in the neighboring rigid square. The deformation result on the 2D shape is as rigid as possible and the details of the shape are preserved well. As extensions, we present a shape-aware splitting method to improve the deformation effect for coarse meshes and a simple sketch-based clustering method for skeletal deformation. Experiments with various 2D shapes show that our method is efficient and easy to use, and can provide physically plausible result for shapes of objects in real world. Therefore, our shape deformation method is especially suitable for applications in cartoon character animation.

title: Quality encoding for tetrahedral mesh optimization
abstract: We define quality differential coordinates (QDC) for per-vertex encoding of the quality of a tetrahedral mesh. QDC measures the deviation of a mesh vertex from a position which maximizes the combined quality of the set of tetrahedra incident at that vertex. Our formulation allows the incorporation of different choices of element quality metrics into QDC construction to penalize badly shaped and inverted tetrahedra. We develop an algorithm for tetrahedral mesh optimization through energy minimization driven by QDC. The variational problem is solved efficiently and robustly using gradient flow based on a stable semi-implicit integration scheme. To ensure quality boundary of the resulting tetrahedral mesh, we propose a harmonic-guided optimization scheme which leads to consistent handling of both the interior and boundary tetrahedra.

title: Test-Driven Component Integration with UML 2.0 Testing and Monitoring Profile
abstract: Test-driven development (TDD) is a software development methodology for achieving high reliability. However, the practice of TDD at the integration level is rare. In this paper, we propose a test-driven component integration approach with the support of UML 2.0 Testing and Monitoring Profile (U2TMP) that is also proposed in this paper. In our approach, automated integration-level test cases are specified using U2TMP before writing the glue-code that integrates components. U2TMP enhances UML 2.0 diagrams for specifying how test scenarios should be set up and how the integrated components are expected to interact under these scenarios. Test cases written in U2TMP can be automatically transformed into test artifacts that setup the test environment, generate test stimuli, and monitor the component interactions at runtime. These test cases serve as a guideline for writing the glue-code and a regression test- bed. With this approach, the software developers may produce glue-code of high reliability.

title: 2.5D Visualisation of Overlapping Biological Networks
abstract: Biological data is often structured in the form of complex interconnected networks such as protein interaction and metabolic networks. In this paper, we investigate a new problem of visualising such overlapping biological networks. Two networks overlap if they share some nodes and edges. We present an approach for constructing visualisations of two overlapping networks, based on a restricted three dimensional representation. More specifically, we use three parallel two dimensional planes placed in three dimensions to represent overlapping networks: one for each network (the top and the bottom planes) and one for the overlapping part (in the middle plane). Our method aims to achieve both drawing aesthetics (or conventions) for each individual network, and highlighting the intersection part by them. Using three biological datasets, we evaluate our visualisation design with the aim to test whether overlapping networks can support the visual analysis of heterogeneous and yet interconnected networks.

title: Visual Representations

title: PathBank: Web-Based Querying and Visualziation of an Integrated Biological Pathway Database
abstract: PathBank is a Web-based query and visualization system for biological pathways using an integrated pathway database. To address the needs for biologists to visualize and analyze biological pathways, PathBank is designed to be user-friendly, flexible and extensible. It is, to the best of our knowledge, the first Web-based system that allows biological pathways to be visualized in three dimensions. PathBank demonstrates the ability to automatically generate and layout biological pathways in response to Web-based database query about proteins, genes, gene ontology and small molecules. Using a novel OWL-to-relational database schema generation approach, it can automatically integrate biological data from different sources that support the BioPAX exchange format (e.g. KEGG, Bio- Cyc). The systems Web interface allows both simple keyword and complex query-based searches in the database. The pathway visualization component provides fast and interactive data access by using asynchronous data retrieval. Due to its modular implementation, it can be easily extended with new visualization algorithms

title: GraphScape: integrated multivariate network visualization
abstract: In this paper, we introduce a new method, GraphScape, to visualize multivariate networks, i.e., graphs with multivariate data associated with their nodes. GraphScape adopts a landscape metaphor with network structure displayed on a 2D plane and the surface height in the third dimension represents node attribute. More than one attribute can be visualized simultaneously by using multiple surfaces. In addition, GraphScape can be easily combined with existing methods to further increase the total number of attributes visualized. One of the major goals of GraphScape is to reveal multivariate graph clustering, which is based on both network structure and node attributes. This is achieved by a new layout algorithm and an innovative way of constructing attribute surface, which also allows visual clustering at different scales through interaction. A simplified attribute surface model is also proposed to reduce computation requirement when visualizing large networks. GraphScape is applied to networks of three different size (20, 100, and 1500) to demonstrate its effectiveness.