We present a simple and robust method for image and volume data segmentation based on manifold distance metrics. This is done by treating the image as a function that maps the 2D (image) or 3D (volume) to a 2D or 3D manifold in a higher dimensional feature space. We explore a range of possible feature spaces, including value, gradient, and probabilistic measures, and examine the consequences of including these measures in the feature space. The time and space computational complexity of our segmentation algorithm is O(N), which allows interactive, user-centric segmentation even for large data sets. We show that this method, given appropriate choice of feature vector, produces results both qualitatively and quantitatively similar to Level Sets, Random Walkers, and others. We validate the robustness of this segmentation scheme with comparisons to standard ground-truth models and sensitivity analysis of the algorithm.

Abstract The graphical depiction of uncertainty information is emerging as a problem of great importance. Scientific data sets are not considered complete without indications of error, accuracy, or levels of confidence. The visual portrayal of this information is a challenging task. This work takes inspiration from graphical data analysis to create visual representations that show not only the data value, but also important characteristics of the data including uncertainty. The canonical box plot is reexamined and a new hybrid summary plot is presented that incorporates a collection of descriptive statistics to highlight salient features of the data. Additionally, we present an extension of the summary plot to two dimensional distributions. Finally, a use‐case of these new plots is presented, demonstrating their ability to present high‐level overviews as well as detailed insight into the salient features of the underlying data distribution.

Abstract This work introduces a technique for interactive walk‐throughs of non‐photorealistically rendered (NPR) scenes using three‐dimensional (3D) line primitives to define architectural features of the model, as well as indicate textural qualities. Line primitives are not typically used in this manner in favour of texture mapping techniques which can encapsulate a great deal of information in a single texture map, and take advantage of GPU optimizations for accelerated rendering. However, texture mapped images may not maintain the visual quality or aesthetic appeal that is possible when using 3D lines to simulate NPR scenes such as hand‐drawn illustrations or architectural renderings. In addition, line textures can be modified interactively, for instance changing the sketchy quality of the lines. The technique introduced here extracts feature edges from a model, and using these edges, generates a reduced set of line textures which indicate material properties while maintaining interactive frame rates. A clipping algorithm is presented to enable 3D lines to reside only in the interior of the 3D model without exposing the underlying triangulated mesh. The resulting system produces interactive illustrations with high visual quality that are free from animation artifacts.

We study the single class SVM (SCSVM) classifier performance on the positive data points while considering the impact of SCSVM on negative protein pair data points. We compare the result with the AA classifier (amino acids maximum entropy classifier) [9] to see if a better performance can be achieved for the same data configuration. The conclusion is that although positive classifier is slightly better than the negative one, the SCSVM classifier performance does not outperform the AA classifier for current data configuration. The "vote" strategy does not change the SCSVM's ROC behavior but increase the confidence of the true positive. Our explanation is that in SCSVM, only one class of training data is available. It is very hard to determine how tight the decision boundary should be to best characterize the known class. Due to the same reason, SCSVM tends to over-fit and under-fit easily. Furthermore, the SCSVM's performance depends on testing data's distribution.

Much progress has been made toward interactive ray tracing, but most research has focused specifically on ray casting. A common approach is to use "packets" of rays to amortize cost across sets of rays. Whether "packets" can be used to speed up the cost of reflection and refraction rays is unclear. The issue is complicated since such rays do not share common origins and often have less directional coherence than viewing and shadow rays. Since the primary advantage of ray tracing over rasterization is the computation of global effects, such as accurate reflection and refraction, this lack of knowledge should be corrected. We are also interested in exploring whether distribution ray tracing, due to its stochastic properties, further erodes the effectiveness of techniques used to accelerate ray casting. This paper addresses the question of whether packet-based ray tracing algorithms can be effectively used for more than visibility computation. We show that by choosing an appropriate data structure and a suitable packet assembly algorithm we can extend the idea of "packets" from ray casting to Whitted-style and distribution ray tracing, while maintaining efficiency.

Topology has been an important tool for analyzing scalar data and flow fields in visualization. In this work, we analyze the topology of multivariate image and volume data sets with discontinuities in order to create an efficient, raster-based representation we call IStar. Specifically, the topology information is used to create a dual structure that contains nodes and connectivity information for every segmentable region in the original data set. This graph structure, along with a sampled representation of the segmented data set, is embedded into a standard raster image which can then be substantially downsampled and compressed. During rendering, the raster image is upsampled and the dual graph is used to reconstruct the original function. Unlike traditional raster approaches, our representation can preserve sharp discontinuities at any level of magnification, much like scalable vector graphics. However, because our representation is raster-based, it is well suited to the real-time rendering pipeline. We demonstrate this by reconstructing our data sets on graphics hardware at real-time rates.

This article presents Glift, an abstraction and generic template library for defining complex, random-access graphics processor (GPU) data structures. Like modern CPU data structure libraries, Glift enables GPU programmers to separate algorithms from data structure definitions; thereby greatly simplifying algorithmic development and enabling reusable and interchangeable data structures. We characterize a large body of previously published GPU data structures in terms of our abstraction and present several new GPU data structures. The structures, a stack, quadtree, and octree, are explained using simple Glift concepts and implemented using reusable Glift components. We also describe two applications of these structures not previously demonstrated on GPUs: adaptive shadow maps and octree three-dimensional paint. Last, we show that our example Glift data structures perform comparably to handwritten implementations while requiring only a fraction of the programming effort.

Rendering directly from packed or compressed volume data formats using graphics hardware has advantages in terms of memory consumption and bandwidth, but results in lower-quality images due to the prohibitive cost of performing interpolation and gradient-based shading on the reconstructed data. The problem with the existing method lies in its close coupling of decompression and interpolation. We demonstrate that deferred filtering overcomes this problem by using a two-pass decompression and rendering strategy. With this method interpolation and gradient calculations are very efficient, allowing high quality rendering directly from packed or compressed volume data. We evaluate the cost of creating interpolated, gradient-shaded renderings using traditional on-the-fly decompression and deferred filtering, and show that deferred filtering can provide up to twenty times speed-up for high quality rendering.

Visualization users are increasingly in need of techniques for assessing quantitative uncertainty and error in the images produced. Statistical segmentation algorithms compute these quantitative results, yet volume rendering tools typically produce only qualitative imagery via transfer function-based classification. This paper presents a visualization technique that allows users to interactively explore the uncertainty, risk, and probabilistic decision of surface boundaries. Our approach makes it possible to directly visualize the combined "fuzzy" classification results from multiple segmentations by combining these data into a unified probabilistic data space. We represent this unified space, the combination of scalar volumes from numerous segmentations, using a novel graph-based dimensionality reduction scheme. The scheme both dramatically reduces the dataset size and is suitable for efficient, high quality, quantitative visualization. Lastly, we show that the statistical risk arising from overlapping segmentations is a robust measure for visualizing features and assigning optical properties.

Deformable isosurfaces, implemented with level-set methods, have demonstrated a great potential in visualization and computer graphics for applications such as segmentation, surface processing, and physically-based modeling. Their usefulness has been limited, however, by their high computational cost and reliance on significant parameter tuning. This paper presents a solution to these challenges by describing graphics processor (GPU) based algorithms for solving and visualizing level-set solutions at interactive rates. The proposed solution is based on a new, streaming implementation of the narrow-band algorithm. The new algorithm packs the level-set isosurface data into 2D texture memory via a multidimensional virtual memory system. As the level set moves, this texture-based representation is dynamically updated via a novel GPU-to-CPU message passing scheme. By integrating the level-set solver with a real-time volume renderer, a user can visualize and intuitively steer the level-set surface as it evolves. We demonstrate the capabilities of this technology for interactive volume segmentation and visualization.

Volume rendering is a flexible technique for visualizing dense 3D volumetric datasets. A central element of volume rendering is the conversion between data values and observable quantities such as color and opacity. This process is usually realized through the use of transfer functions that are precomputed and stored in lookup tables. For multidimensional transfer functions applied to multivariate data, these lookup tables become prohibitively large. We propose the direct evaluation of a particular type of transfer functions based on a sum of Gaussians. Because of their simple form (in terms of number of parameters), these functions and their analytic integrals along line segments can be evaluated efficiently on current graphics hardware, obviating the need for precomputed lookup tables. We have adopted these transfer functions because they are well suited for classification based on a unique combination of multiple data values that localize features in the transfer function domain. We apply this technique to the visualization of several multivariate datasets (CT, cryosection) that are difficult to classify and render accurately at interactive rates using traditional approaches.

Deformable isosurfaces, implemented with level-set methods, have demonstrated a great potential in visualization for applications such as segmentation, surface processing, and surface reconstruction. Their usefulness has been limited, however, by their high computational cost and reliance on significant parameter tuning. This paper presents a solution to these challenges by describing graphics processor (GPU) based on algorithms for solving and visualizing level-set solutions at interactive rates. Our efficient GPU-based solution relies on packing the level-set isosurface data into a dynamic, sparse texture format. As the level set moves, this sparse data structure is updated via a novel GPU to CPU message passing scheme. When the level-set solver is integrated with a real-time volume renderer operating on the same packed format, a user can visualize and steer the deformable level-set surface as it evolves. In addition, the resulting isosurface can serve as a region-of-interest specifier for the volume renderer. This paper demonstrates the capabilities of this technology for interactive volume visualization and segmentation.

Direct volume rendering is a commonly used technique in visualization applications. Many of these applications require sophisticated shading models to capture subtle lighting effects and characteristics of volumetric data and materials. For many volumes, homogeneous regions pose problems for typical gradient-based surface shading. Many common objects and natural phenomena exhibit visual quality that cannot be captured using simple lighting models or cannot be solved at interactive rates using more sophisticated methods. We present a simple yet effective interactive shading model which captures volumetric light attenuation effects that incorporates volumetric shadows, an approximation to phase functions, an approximation to forward scattering, and chromatic attenuation that provides the subtle appearance of translucency. We also present a technique for volume displacement or perturbation that allows realistic interactive modeling of high frequency detail for both real and synthetic volumetric data.

Direct volume rendering is a commonly used technique in visualization applications. Many of these applications require sophisticated shading models to capture subtle lighting effects and characteristics of volumetric data and materials. Many common objects and natural phenomena exhibit visual quality that cannot be captured using simple lighting models or cannot be solved at interactive rates using more sophisticated methods. We present a simple yet effective interactive shading model which captures volumetric light attenuation effects to produce volumetric shadows and the subtle appearance of translucency. We also present a technique for volume displacement or perturbation that allows realistic interactive modeling of high frequency detail for real and synthetic volumetric data.

Most direct volume renderings produced today employ 1D transfer functions which assign color and opacity to the volume based solely on the single scalar quantity which comprises the data set. Though they have not received widespread attention, multi-dimensional transfer functions are a very effective way to extract materials and their boundaries for both scalar and multivariate data. However, identifying good transfer functions is difficult enough in 1D, let alone 2D or 3D. This paper demonstrates an important class of 3D transfer functions for scalar data, and describes the application of multi-dimensional transfer functions to multivariate data. We present a set of direct manipulation widgets that make specifying such transfer functions intuitive and convenient. We also describe how to use modern graphics hardware to both interactively render with multidimensional transfer functions and to provide interactive shadows for volumes. The transfer functions, widgets and hardware combine to form a powerful system for interactive volume exploration.

Most direct volume renderings produced today employ one-dimensional transfer functions, which assign color and opacity to the volume based solely on the single scalar quantity which comprises the dataset. Though they have not received widespread attention, multi-dimensional transfer functions are a very effective way to extract specific material boundaries and convey subtle surface properties. However, identifying good transfer functions is difficult enough in one dimension, let alone two or three dimensions. This paper demonstrates an important class of three-dimensional transfer functions for scalar data (based on data value, gradient magnitude, and a second directional derivative), and describes a set of direct manipulation widgets which make specifying such transfer functions intuitive and convenient. We also describe how to use modem graphics hardware to interactively render with multi-dimensional transfer functions. The transfer functions, widgets, and hardware combine to form a powerful system for interactive volume exploration.