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Virtual globes are becoming ubiquitous in the visualization of planetary bodies and Earth specifically. While many of the current virtual globes have proven to be quite useful for remote geologic investigation, they were never designed for the purpose of serving as virtual geologic instruments. Their shortcomings have become more obvious as earth scientists struggle to visualize recently released digital elevation models of very high spatial resolution (0.5-1m^2/sample) and extent (>2000km^2). We developed Crusta as an alternative virtual globe that allows users to easily visualize their custom imagery and more importantly their custom topography. Crusta represents the globe as a 30-sided polyhedron to avoid distortion of the display, in particular the singularities at the poles characteristic of other projections. This polyhedron defines 30 ''base patches,'' each being a four-sided region that can be subdivided to an arbitrarily fine grid on the surface of the globe to accommodate input data of arbitrary resolution, from global (BlueMarble) to local (tripod LiDAR), all in the same visualization. We designed Crusta to be dynamic with the shading of the terrain surface computed on-the-fly when a user manipulates his point-of-view. In a similarly interactive fashion the globe's surface can be exaggerated vertically. The combination of the two effects greatly improves the perception of shape. A convenient pre-processing tool based on the GDAL library facilitates importing a number of data formats into the Crusta-specific multi-scale hierarchies that enable interactive visualization on a range of platforms from laptops to immersive geowalls and caves. The main scientific user community for Crusta is earth scientists, and their needs have been driving the development.

Integral surfaces are ideal tools to illustrate vector fields and fluid flow structures. However, these surfaces can be visually complex and exhibit difficult geometric properties, owing to strong stretching, shearing and folding of the flow from which they are derived. Many techniques for non-photorealistic rendering have been presented previously. It is, however, unclear how these techniques can be applied to integral surfaces. In this paper, we examine how transparency and texturing techniques can be used with integral surfaces to convey both shape and directional information. We present a rendering pipeline that combines these techniques aimed at faithfully and accurately representing integral surfaces while improving visualization insight. The presented pipeline is implemented directly on the GPU, providing real-time interaction for all rendering modes, and does not require expensive preprocessing of integral surfaces after computation.

We present a volumetric iso-geometric finite element analysis based on Catmull-Clark solids. This concept allows one to use the same representation for the modeling, the physical simulation, and the visualization, which optimizes the design process and narrows the gap between CAD and CAE. In our method the boundary of the solid model is a Catmull-Clark surface with optional corners and creases to support the modeling phase. The crucial point in the simulation phase is the need to perform efficient integration for the elements. We propose a method similar to the standard subdivision surface evaluation technique, such that numerical quadrature can be used. Experiments show that our approach converges faster than methods based on tri-linear and tri-quadratic elements.However, the topological structure of Catmull-Clark elements is as simple as the structure of linear elements. Furthermore, the Catmull-Clark elements we use are C 2 -continuous on the boundary and in the interior except for irregular vertices and edges.

We present an adaptive subdivision scheme for unstructured tetrahedral meshes inspired by the ! 3-subdivision scheme for triangular meshes. Existing tetrahedral subdivision schemes do not support adaptive refinement and have traditionally been driven by the need to generate smooth three-dimensional deformations of solids. These schemes use edge bisections to subdivide tetrahedra, which generates octahedra in addition to tetrahedra. To split octahedra into tetrahedra one routinely chooses a direction for the diagonals for the subdivision step. We propose a new topology-based refinement operator that generates only tetrahedra and supports adaptive refinement. Our tetrahedral subdivision algorithm is motivated by the need to have one representation for the modeling, the simulation and the visualization and so to bridge the gap between CAD and CAE. Our subdivision algorithm design emphasizes on geometric quality of the tetrahedral meshes, local and adaptive refinement operations, and preservation of sharp geometric features on the boundary and in the interior of the physical domain.

Although the geometry and kinematics of the first-order structures accommodating Arabia-Eurasia convergence are relatively well known in Turkey and Iran, major shortening structures remain poorly understood within the central portion of the collision zone, in eastern Anatolia and the Caucasus. New remotely sensed neotectonic mapping, synthesis of regional geologic and stratigraphic data, and balanced cross sections suggest that the Kura fold-thrust belt has accommodated the majority of Arabia-Eurasia convergence since the early Pliocene between the longitudes of ∼45°E and ∼49°E. This belt lies southeast of the N80°W-striking Greater Caucasus Mountains and forms an eastward-narrowing band of elevated topography that roughly parallels the range front for ∼400 km along strike. The belt is separated from the Greater Caucasus to the north by the 10- to 25-km-wide Alazani Basin and comprises a series of predominantly south-verging folds deforming Eocene–Quaternary flysch and molasse. To document structural geometries within the Kura fold-thrust belt, we have used the Real-time Interactive Mapping System (RIMS) software to analyze Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER), visible to near-infrared (VNIR), and digital elevation model (DEM) data. This neotectonic mapping indicates an along-strike, eastward decrease in both structural complexity and the degree to which deformed geomorphic surfaces are dissected. Existing geologic maps indicate a corresponding eastward decrease in the depth of exposure. By integrating the structural geometries determined in our analysis of remote-sensing data with existing geologic data, we have constructed two balanced cross sections, which suggest these systematic along-strike variations result from a west-to-east decrease in total shortening within the Kura fold-thrust belt. We interpret this variable shortening to stem from eastward propagation of the Kura fold-thrust belt. Comparison of our preliminary total shortening estimates with those predicted by current plate motions suggest that the Kura fold-thrust belt has accommodated ∼30%–40% (∼25 km) of total Arabia-Eurasia convergence since 5 Ma, and thus forms a first-order structural system within the central portion of the collision zone.

We present a reverse engineering method for constructing a surface approximation scheme whose input is a set of unorganized noisy points in space and whose output is a set of quadric patches. The local surface properties, necessary for the subsequent segmentation, are estimated directly from the data using a simple and efficient data structure - the neighborhood graph. Our segmentation scheme, based on principal curvatures, constructs initial point sub-sets, which may be enlarged or further subdivided based on associated approximation error estimates obtained through approximation of the initial segments by quadric surfaces. Our method is highly efficient and producesa high-quality piecewise quadric surface approximation of engineering objects, which we demonstrate for several simple and complex example data sets.

We describe visualization software, Visualizer, that was developed specifically for interactive, visual exploration in immersive virtual reality (VR) environments. Visualizer uses carefully optimized algorithms and data structures to support the high frame rates required for immersion and the real-time feedback required for interactivity. As an application developed for VR from the ground up, Visualizer realizes benefits that usually cannot be achieved by software initially developed for the desktop and later ported to VR. However, Visualizer can also be used on desktop systems (unix/linux-based operating systems including Mac OS X) with a similar level of real-time interactivity, bridging the ''software gap'' between desktop and VR that has been an obstacle for the adoption of VR methods in the Geosciences. While many of the capabilities of Visualizer are already available in other software packages used in a desktop environment, the features that distinguish Visualizer are: (1) Visualizer can be used in any VR environment including the desktop, GeoWall, or CAVE, (2) in non-desktop environments the user interacts with the data set directly using a wand or other input devices instead of working indirectly via dialog boxes or text input, (3) on the desktop, Visualizer provides real-time interaction with very large data sets that cannot easily be viewed or manipulated in other software packages. Three case studies are presented that illustrate the direct scientific benefits realized by analyzing data or simulation results with Visualizer in a VR environment. We also address some of the main obstacles to widespread use of VR environments in scientific research with a user study that shows Visualizer is easy to learn and to use in a VR environment and can be as effective on desktop systems as native desktop applications.

We introduce a system that adds a foveal inset to large-scale projection displays. The effective resolution of the foveal inset projection is higher than the original display resolution, allowing the user to see more details and finer features in large data sets. The foveal inset is generated by projecting a high-resolution image onto a mirror mounted on a panCtilt unit that is controlled by the user with a laser pointer. Our implementation is based on Chromium and supports many OpenGL applications without modifications.We present experimental results using high-resolution image data from medical imaging and aerial photography.

The geological seiences are challenged to manage and interpret increasing volumes of data as observations and simulations increase in size and complexity. For example, simulations of earthquake-related processes typically generate complex, time-varying data sets in two or more dimensions. To facilitate interpretation and analysis of these data sets, evaluate the underlying models, and to drive future calculations, we have developed methods of interactive visualization with a special focus on using immersive virtual reality (VR) environments to interact with models of Earth’s surface and interior. Virtual mapping tools allow virtual “field studies” in inaccessible regions. Interactive tools allow us to manipulate shapes in order to construct models of geological features for geodynamic models, while feature extraction tools support quantitative measurement of structures that emerge from numerical simulation or field observations, thereby enabling us to improve our interpretation of the dynamical processes that drive earthquakes. VR has traditionally been used primarily as a presentation tool, albeit with active navigation through data. Reaping the full intellectual benefits of immersive VR as a tool for scientific analysis requires building on the method’s strengths, that is, using both 3D perception and interaction with observed or simulated data. This approach also takes advantage of the specialized skills of geological scientists who are trained to interpret, the often limited, geological and geophysical data available from field observations.

We present a practical approach to generate stochastic anisotropic samples with Poisson-disk characteristic over a two-dimensional domain. In contrast to isotropic samples, we understand anisotropic samples as nonoverlapping ellipses whose size and density match a given anisotropic metric. Anisotropic noise samples are useful for many visualization and graphics applications. The spot samples can be used as input for texture generation, for example, line integral convolution (LIC), but can also be used directly for visualization. The definition of the spot samples using a metric tensor makes them especially suitable for the visualization of tensor fields that can be translated into a metric. Our work combines ideas from sampling theory and mesh generation to approximate generalized blue noise properties. To generate these samples with the desired properties, we first construct a set of nonoverlapping ellipses whose distribution closely matches the underlying metric. This set of samples is used as input for a generalized anisotropic Lloyd relaxation to distribute noise samples more evenly. Instead of computing the Voronoi tessellation explicitly, we introduce a discrete approach that combines the Voronoi cell and centroid computation in one step. Our method supports automatic packing of the elliptical samples, resulting in textures similar to those generated by anisotropic reaction-diffusion methods. We use Fourier analysis tools for quality measurement of uniformly distributed samples. The resulting samples have nice sampling properties, for example, they satisfy a blue noise property where low frequencies in the power spectrum are reduced to a minimum..

We present a method for extracting boundary surfaces from segmented cross-section image data. We use a constrained Potts model to interpolate an arbitrary number of region boundaries between segmented images. This produces a segmented volume from which we extract a triangulated boundary surface using well-known marching tetrahedra methods. This surface contains staircase-like artifacts and an abundance of unnecessary triangles. We describe an approach that addresses these problems with a voxel-accurate simplification algorithm that reduces surface complexity by an order of magnitude. Our boundary interpolation and simplification methods are novel contributions to the study of surface extraction from segmented cross-sections. We have applied our method to construct polycrystal grain boundary surfaces from micrographs of a sample of the metal tantalum.

Objective To evaluate the safety and endometrial protection of low-dose transdermal estradiol (E2)/norethisterone acetate (NETA) patches (Estalis 25/125) in terms of post-treatment incidence of endometrial hyperplasia/cancer after 1 year of treatment in postmenopausal women with intact uteri. Methods Patients were randomized to receive either transdermal E2/NETA (delivering daily doses of E2 25 μg and NETA 125 μg; applied every 3–4 days) or oral E2/NETA (E2 1 mg and NETA 0.5 mg; given daily) in this open-label study. The primary variable was the incidence of endometrial hyperplasia/cancer based on endometrial biopsies; secondary variables included vaginal bleeding/spotting patterns, patch adhesion, safety and tolerability. Results Six hundred and seventy-seven patients were randomized (507 in the transdermal group and 169 in the oral group; one did not receive study drug) and >80% completed the study. There were no cases of endometrial hyperplasia or cancer in either group and the upper limit of the one-sided 95% confidence interval in the transdermal group was 0.85%. Over time, both treatments were associated with a decreasing frequency of spotting/bleeding days. The overall incidence of adverse events (AEs) was comparable in both groups, and the majority was mild-to-moderate in intensity. Breast tenderness was the most frequently reported AE (transdermal 19.9% versus oral 28.4%). AEs related to the gastrointestinal system were more frequent with oral E2/NETA, and episodes of spotting and bleeding were more frequent with transdermal E2/NETA. Local skin tolerability of the transdermal matrix system was good. Conclusions Transdermal E2/NETA (25 and 125 μg) provided adequate endometrial protection in postmenopausal women when evaluated according to CPMP/CHMP criteria, achieved a high rate of amenorrhea, and was well tolerated.

For view-dependent visualization, adaptively refined volumetric meshes are used to adapt resolution to given error constraints. A mesh hierarchy based on the 3√2-subdivision scheme produces structured grids with the highest adaptivity. Downsampling filters reduce aliasing effects and lead to higher quality data representation (in terms of lower approximation error) at coarser levels of resolution. We present a method for applying wavelet based downsampling filters to adaptively refined meshes. We use a linear B-spline wavelet lifting scheme to derive narrow filter masks. Using these narrow masks, the wavelet filters are applicable to adaptively refined meshes without imposing any restrictions on the adaptivity of the meshes, such that all wavelet filtering operations can be performed without further subdivision steps. We define rules for vertex dependencies in wavelet-based adaptive refinement and resolve them in an unambiguous manner. We use the wavelet filters for view-dependent visualization in order to demonstrate the functionality and the benefits of our approach. When using wavelet filters, the approximation quality is higher at each resolution level. Thus, less polyhedra need to be traversed by a visualization method to meet certain error bounds/quality measures.

Asynchrony and non-determinism in Charm++ programs present a significant challenge in analyzing their event traces. We present a new framework to organize event traces of parallel programs written in Charm++. Our reorganization allows one to more easily explore and analyze such traces by providing context through logical structure. We describe several heuristics to compensate for missing dependencies between events that currently cannot be easily recorded. We introduce a new task ordering that recovers logical structure from the non-deterministic execution order. Using the logical structure, we define several metrics to help guide developers to performance problems. We demonstrate our approach through two proxy applications written in Charm++. Finally, we discuss the applicability of this framework to other task-based runtimes and provide guidelines for tracing to support this form of analysis.

We present a method for segmenting 2D microscopy images of freshwater green microalgae. Our approach is based on a specialized level set method, leading to efficient and highly accurate algae segmentation. The level set formulation of our problem allows us to generate an algae's boundary curve as the result of an evolving level curve, based on computed background and algae regions in a given image. By characterizing the distributions of image intensity values in local regions, we are able to automatically classify image regions into background and algae regions. We present results obtained with our method. These results are very promising as they document that we can achieve highly accurate algae segmentations when comparing ours against manually segmented images (segmented by an expert biologist) and with results derived by other approaches covered in the literature.

Reconstruction of hand-held laser scanner data is used in industry primarily for reverse engineering. Traditionally, scanning and reconstruction are separate steps. The operator of the laser scanner has no feedback from the reconstruction results. On-line reconstruction of the CAD geometry allows for such an immediate feedback.

This paper presents a new method for segmentation of molecular surfaces. Topological analysis of a scalar function defined on the surface and its associated gradient field reveals the relationship between the features of interest and critical points of the scalar function. The segmentation is obtained by associating segments with local minima/maxima. Controlled simplification of the function merges segments resulting in a hierarchical segmentation of the molecular surface. This segmentation is used to identify rigid components of protein molecules and to study the role of cavities and protrusions in protein-protein interactions.

We introduce 3D warp brush, a new method for interactive shape modeling in an immersive virtual reality environment. 3D warp brushes are implicitly defined tools that operate on triangle meshes. We combine the efficiency of explicit mesh representations with intuitive implicit modeling operators. The area of influence of a 3D warp brush can be of arbitrary shape since it has an associated distance field. We define different warp functions including drag, explode, and whittle. A unique feature of our framework is the ability to convert meshes into 3D warp brushes at run time. Thus, we can easily expand our set of brushes based on a small set of base brushes, such as spheres or ellipsoids. Our underlying split-edge mesh data structure supports adaptive refinement and efficient rendering with onthe-fly triangle strip generation. 3D warp brushes only operate on mesh vertices, hence, underlying mesh processing is transparent to the modeling operations. The use of a Responsive Workbench and two-handed interaction allows the user to exploit the full potential of the modeling system by intuitive and easy modification of a base surface into a desired shape. We present several models, which have been created and modified using 3D warp brushes, to demonstrate the usefulness of our framework. r 2006 Elsevier Ltd. All rights reserved.

This paper describes an efficient combinatorial method for simplification of topological features in a 3D scalar function. The Morse-Smale complex, which provides a succinct representation of a function's associated gradient flow field, is used to identify topological features and their significance. The simplification process, guided by the Morse-Smale complex, proceeds by repeatedly applying two atomic operations that each remove a pair of critical points from the complex. Efficient storage of the complex results in execution of these atomic operations at interactive rates. Visualization of the simplified complex shows that the simplification preserves significant topological features while removing small features and noise.

Natural-neighbor interpolation methods, such as Sibson's method, are well-known schemes for multivariate data fitting and reconstruction. Despite its many desirable properties, Sibson's method is computationally expensive and difficult to implement, especially when applied to higher-dimensional data. The main reason for both problems is the method's implementation based on a Voronoi diagram of all data points. We describe a discrete approach to evaluating Sibson's interpolant on a regular grid, based solely on finding nearest neighbors and rendering and blending $d$-dimensional spheres. Our approach does not require us to construct an explicit Voronoi diagram, is easily implemented using commodity three-dimensional~graphics hardware, leads to a significant speed increase compared to traditional approaches, and generalizes easily to higher dimensions. For large scattered data sets, we achieve two-dimensional(2D) interpolation at interactive rates and three-dimensional interpolation(3D) with computation times of a few seconds.

Recent progress in retinal image acquisition techniques, including optical coherence tomography (OCT) and scanning laser ophthalmoscopy (SLO), combined with improved performance of adaptive optics (AO) instrumentation, has resulted in improvement in the quality of in vivo images of cellular structures in the human retina. Here, we present a short review of progress on developing AO-OCT instruments. Despite significant progress in imaging speed and resolution, eye movements present during acquisition of a retinal image with OCT introduce motion artifacts into the image, complicating analysis and registration. This effect is especially pronounced in high-resolution datasets acquired with AO-OCT instruments. Several retinal tracking systems have been introduced to correct retinal motion during data acquisition. We present a method for correcting motion artifacts in AO-OCT volume data after acquisition using simultaneously captured adaptive optics-scanning laser ophthalmoscope (AO-SLO) images. We extract transverse eye motion data from the AO-SLO images, assign a motion adjustment vector to each AO-OCT A-scan, and re-sample from the scattered data back onto a regular grid. The corrected volume data improve the accuracy of quantitative analyses of microscopic structures.

We present a method for the hierarchical approximation of functions in one, two, or three variables based on the finite element method (Ritz approximation). Starting with a set of data sites with associated function, we first determine a smooth (scattered-data) interpolant. Next, we construct an initial triangulation by triangulating the region bounded by the minimal subset of data sites defining the convex hull of all sites. We insert only original data sites, thus reducing storage requirements. For each triangulation we solve a minimization problem: computing the best linear spline approximation of the interpolant of all data, based on a functional involving function values and first derivatives. The error of a best linear spline approximation is computed in a Sobolev-like norm, leading to element-specific error values. We use these interval-/triangle-/tetrahedron-specific values to identify the element to subdivide next. The subdivision of an element with largest error value requires the re-computation of all spline coefficients due to the global nature of the problem. We improve efficiency by (i) subdividing multiple elements simultaneously and (ii) by using a sparse-matrix representation and system solver.

We describe ProteinShop, a new visualization tool that streamlines and simplifies the process of determining optimal protein folds. ProteinShop may be used at different stages of a protein structure prediction process. First, it can create protein configurations containing secondary structures specified by the user. Second, it can interactively manipulate protein fragments to achieve desired folds by adjusting the dihedral angles of selected coil regions using an Inverse Kinematics method. Last, it serves as a visual framework to monitor and steer a protein structure prediction process that may be running on a remote machine. ProteinShop was used to create initial configurations for a protein structure prediction method developed by a team that competed in CASP5. ProteinShop's use accelerated the process of generating initial configurations, reducing the time required from days to hours. This paper describes the structure of ProteinShop and discusses its main features.

Multiresolution methods are a common technique used for dealing with large-scale data and representing it at multiple levels of detail. We present a multiresolution hierarchy construction based on n√2 subdivision, which has all the advantages of a regular data organization scheme while reducing the drawback of coarse granularity. The n√2-subdivision scheme only doubles the number of vertices in each subdivision step regardless of dimension n. We describe the construction of 2D, 3D, and 4D hierarchies representing surfaces, volume data, and time-varying volume data, respectively. The 4D approach supports spatial and temporal scalability. For high-quality data approximation on each level of detail, we use downsampling filters based on n-variate B-spline wavelets. We present a B-spline wavelet lifting scheme for n√2-subdivision steps to obtain small or narrow filters. Narrow filters support adaptive refinement and out-of-core data exploration techniques.

We present a new method for topological segmentation in steady three-dimensional vector fields. Depending on desired properties, the algorithm replaces the original vector field by a derived segmented data set, which is utilized to produce separating surfaces in the vector field. We define the concept of a segmented data set, develop methods that produce the segmented data by sampling the vector field with streamlines, and describe algorithms that generate the separating surfaces. This method is applied to generate local separatrices in the field, defined by a movable boundary region placed in the field. The resulting partitions can be visualized using standard techniques for a visualization of a vector field at a higher level of abstraction.

Motivation: The power of multi-sequence comparison for biological discovery is well established. The need for new capabilities to visualize and compare cross-species alignment data is intensified by the growing number of genomic sequence datasets being generated for an ever-increasing number of organisms. To be efficient these visualization algorithms must support the ability to accommodate consistently a wide range of evolutionary distances in a comparison framework based upon phylogenetic relationships. Results: We have developed Phylo-VISTA, an interactive tool for analyzing multiple alignments by visualizing a similarity measure for multiple DNA sequences. The complexity of visual presentation is effectively organized using a framework based upon interspecies phylogenetic relationships. The phylogenetic organization supports rapid, user-guided interspecies comparison. To aid in navigation through large sequence datasets, Phylo-VISTA leverages concepts from VISTA that provide a user with the ability to select and view data at varying resolutions. The combination of multiresolution data visualization and analysis, combined with the phylogenetic framework for interspecies comparison, produces a highly flexible and powerful tool for visual data analysis of multiple sequence alignments. Availability: Phylo-VISTA is available at http://www-gsd.lbl.gov/phylovista. It requires an Internet browser with Java Plug-in 1.4.2 and it is integrated into the global alignment program LAGAN at http://lagan.stanford.edu

This paper presents an algorithm for material interface reconstruction for data sets where fractional material information is given as a percentage for each element of the underlying grid. The reconstruction problem is transformed to a problem that analyzes a dual grid, where each vertex in the dual grid has an associated barycentric coordinate tuple that represents the fraction of each material present. Material boundaries are constructed by analyzing the barycentric coordinate tuples of a tetrahedron in material space and calculating intersections with Voronoi cells that represent the regions where one material dominates. These intersections are used to calculate intersections in the Euclidean coordinates of the tetrahedron. By triangulating these intersection points one creates the material boundary. The algorithm can treat data sets containing any number of materials. The algorithm can also create non-manifold boundary surfaces if necessary. By clipping the generated material boundaries against the original cells, one can examine the error in the algorithm. Error analysis shows that the algorithm preserves volume fractions within an error range of 0.5% per material.

In this paper we present the findings and recommendations that emerged from a one-day workshop held at Lawrence Berkeley National Laboratory (LBNL) on June 5, 2002, in conjunction with the National Energy Research Scientific Computing (NERSC) User Group (NUG) Meeting. The motivation for this workshop was to solicit direct input from the application science community on the subject of visualization. The workshop speakers and participants included computational scientists from a cross-section of disciplines that use the NERSC facility, as well as visualization researchers from across the country. We asked the workshop contributors how they currently visualize their results, and how they would like to do visualization in the future. We were especially interested in each individual's view of how visualization tools and services could be improved in order to better meet the needs of future computational science projects. The outcome of this workshop is a set of findings and recommendations that are presented in more detail later in this paper, and are briefly summarized here. Scientific visualization is a crucial technological capability that plays an important role in understanding data created by computational science projects as well as experiments. In order to be effective, visualization technology should be easy to use for a non-expert. The term “easy to use” encompasses a number of different categories, including a short learning curve, tight integration with computational frameworks, availability on the desktop as well as the fixed visualization facility, tools that are tailored for each specific application domain, and low cost. Current visualization tools fall short in several key areas of capability. Few visualization tools are capable of processing large datasets, such as those commonly generated at NERSC. Better support for parallel visualization tools may prove useful in leveraging large parallel machines as visualization resources. Multivariate visualization - multiple grids, many species, and many dimensions - is needed in order to quickly gain insight into large datasets. Related “drill-down” capabilities, such as the ability to quickly move from macro to micro views (used in “data mining”), would be extremely helpful in understanding data but are missing from most visualization tools. Many application scientists perceive a conundrum when it comes to visualization support. Support for visualization within each individual program level is often inadequate or nonexistent due to funding constraints, yet support for visualization at the institutional level is also often inadequate or nonexistent. Better solutions are needed for remote visualization. Current approaches are further constrained by network bandwidth and access to resources. The proliferation of visualization tools and data formats poses challenges. Researchers must often master many different tools in order to achieve the desired results. Data format conversion is often required when moving between tools. Common data formats and frameworks for visualization tools are needed to reduce duplication of effort and better promote sharing of resources and results. Better communication is needed between the visualization and computational science communities. The computational scientists are often unaware of current trends and practices in the visualization community. By being more aware of the needs of the computational science community, the visualization research programs can be crafted so as to be more responsive to their needs. As a result of the workshop, we have developed a set of recommendations that can be summarized as follows: • Establish a coherent program that focuses on remote visualization. A remote visualization program should provide tools and infrastructure that can be used by multiple “virtual teams”. • Establish mechanisms whereby generally-applicable visualization technology is developed and deployed in a centralized fashion. • Develop a research program in interactive visualization with running codes that stresses the integrated design and development of coupled simulation-visualization methods. • Establish a research program in the areas of multi-field visualization and multi-dimensional data visualization. • Establish a research program in the area of automated data exploration for next generation petascale datasets.

Grid-based computing facilitates access to different resources. But management in a grid-based environment isn't centralized. To use grid resources effectively, researchers need a central access point to manage the resources, provide a visual means to explore the data, and record these explorations for further investigation and dissemination. This article describes such a system that's being developed jointly by the University of California, Davis, and the Lawrence Berkeley National Laboratory (LBNL). The centralized system acts as a portal into grid-enabled visualization systems. Scientists using the portal can focus on the important task of extracting insights from their data through visualization instead of having to worry about process management. Because scientists at LBNL and their collaborators require access to the portal from around the world, the portal's interface is entirely Web-based. Authenticated users only need a standards-compliant Web browser to explore their data from anywhere in the world. The portal provides a Web-based interface not just for exploring but also for encapsulating visualization data. Encapsulating the process lets users reproduce the visualization results for validation or extend those results by continuing data exploration. We discuss the integration of our grid-enabled visualization server, the visualization Web application that performs the visualization session management, and the Web-based interface.

We present a novel technique for visualizing tensors in three dimensional (3D) space. Of particular interest is the visualization of stress tensors resulting from 3D numerical simulations in computational geomechanics. To this end we present three different approaches to visualizing tensors in 3D space, namely hedgehogs, hyperstreamlines and hyperstreamsurfaces. We also present a number of examples related to stress distributions in 3D solids subjected to single and load couples. In addition, we present stress visualizations resulting from single-pile and pile-group computations. The main objective of this work is to investigate various techniques for visualizing general Cartesian tensors of rank 2 and it's application to geomechanics problems.

© 2013 IEEE. Recent progress in retinal image acquisition techniques, including optical coherence tomography (OCT) and scanning laser ophthalmoscopy (SLO), combined with improved performance of adaptive optics (AO) instrumentation, has resulted in improvement in the quality of in vivo images of cellular structures in the human retina. Here, we present a short review of progress on developing AO-OCT instruments. Despite significant progress in imaging speed and resolution, eye movements present during acquisition of a retinal image with OCT introduce motion artifacts into the image, complicating analysis and registration. This effect is especially pronounced in high-resolution datasets acquired with AO-OCT instruments. Several retinal tracking systems have been introduced to correct retinal motion during data acquisition. We present a method for correcting motion artifacts in AO-OCT volume data after acquisition using simultaneously captured adaptive optics-scanning laser ophthalmoscope (AO-SLO) images. We extract transverse eye motion data from theAO-SLO images, assign a motion adjustment vector to each AO-OCTA-scan, and re-sample from the scattered data back onto a regular grid. The corrected volume data improve the accuracy of quantitative analyses of microscopic structures.

Merge trees represent the topology of scalar functions. To assess the topological similarity of functions, one can compare their merge trees. To do so, one needs a notion of a distance between merge trees, which we define. We provide examples of using our merge tree distance and compare this new measure to other ways used to characterize topological similarity (bottleneck distance for persistence diagrams) and numerical difference (L ∞ -norm of the difference between functions).

This chapter introduces a novel method for vortex detection in flow fields based on the corotation of line segments and glyph rendering. The corotation measure is defined as a point-symmetric scalar function on a sphere, suitable for direct representation in the form of a three-dimensional glyph. Appropriate placement of these glyphs in the domain of a flow field makes it possible to depict vortical features present in the flow. We demonstrate how topological analysis of this novel glyph-based representation of vortex features can reveal vortex characteristics that lie beyond the capabilities of visualization techniques that consider vortex direction and magnitude information only.

Processing images of underwater environments of Antarctic lakes is challenging due to poor lighting conditions, low saturation and noise. This paper presents a novel pipeline for dense point cloud scene reconstruction from underwater stereo images and video obtained with low-cost consumer recording hardware. Features in stereo frames are selected and matched at high density. Putative matches are triangulated to produce point clouds in 3D space. Temporal feature tracking is performed to produce and merge point clouds. We demonstrate that this framework produces dense and accurate reconstructions for several tests.

We describe the algorithms and data structures used for optimizing linear spline approximations of bivariate functions. Our method creates a random initial triangulation of a given data set and then employs a simulated annealing algorithm to improve this initial approximation. In every iteration step, the current approximation is changed in a random but local way, and the distance measure between it and the data is re-calculated. Depending on the difference between the old and new distance measures, an iteration step is either accepted or rejected. We discuss the basic operations and data structures of our optimization technique. We present a variant of the half-edge data structure and associated algorithms.

Author(s): Pinskiy, Dimitriy V.; Meyer, Joerg; Hamann, Bernd; Joy, Ken; Brugger, Eric S.; Duchaineau, Mark A. | Abstract: We present an octree-based approach supporting multiresolution visualization of large three-dimenstional scientific data sets. Given an irregular gridded data set, we initially impose an octree data structure of relatively low resolution, i.e., consisting of a relatively small number of cells. The construction of this initial octree structure is controlled by the original data resolution and cell-specific error value. It is thus possible to use the octree to visualize either the field function value or the local error value. The octreee data structure can be refined further in areas that are specified by a user of a visualization system: A user would identify a region in space, i.e., an octree cell, where the field is of greater interest or where octree cells carry relatively large error values. This usage of our data sturcture ensures that we use the highest resolution to render only regions of interest in a large-scale scientific data set.

Author(s): LaMar, Eric C.; Hamann, Bernd; Joy, Ken | Editor(s): Wiley, John | Abstract: Animation and visualization of rectilinear data require interpolation schemes for smooth image generation. Piecewise trilinear interpolation, the de facto standard for interpolating rectilinear data, usually leads to significant visual artifacts in the resulting imagery. These artifacts reduce the confidence in the resulting visualization, and may even lead to false interpretations of the data. This paper is concerned with the generation of smooth isosurface image sequences, obtained by casting rays through the image plane and computing their intersections with an isosurface. We describe a novel solution to this problem: We replace trilinear interpolation by tricubic interpolation, smoothing out the artifacts in the images; and we simplify the ray-isosurface intersection calculations by rotating and resampling the original rectilinear data in a second rectilinear grid -- a grid with one family of grid planes parallel to the image plane. Our solution significantly reduces artifacts in individual images and leads to smooth animations.

Presents a method for the construction of multiple levels of tetrahedral meshes approximating a trivariate scalar-valued function at different levels of detail. Starting with an initial, high-resolution triangulation of a 3D region, we construct coarser representation levels by collapsing edges of the mesh. Each triangulation defines a linear spline function, where the function values associated with the vertices are the spline coefficients. Error bounds are stored for individual tetrahedra and are updated as the mesh is simplified. Two algorithms are presented that simplify the mesh within prescribed error bounds. Each algorithm treats simplification on the mesh boundary. The result is a hierarchical data description that is suited for the efficient visualization of large data sets at varying levels of detail.

We present a method for the construction of hierarchies of single-valued functions in one, two, and three variables. The input to our method is a coarse decomposition of the compact domain of a function in the form of an interval (univariate case), triangles (bivariate case), or tetrahedra (trivariate case). We compute the best linear spline approximations, understood in an integral least squares sense, for functions defined over such triangulations and refine triangulations using repeated bisection. This requires the identification of the interval (triangle, tetrahedron) with largest error and splitting it into two intervals (triangles, tetrahedra). Each bisection step requires the re-computation of all spline coefficients due to the global nature of the best approximation problem. Nevertheless, this can be done efficiently by bisecting multiple intervals (triangles, tetrahedra) in one step and by reducing the bandwidths of the matrices resulting from the normal equations.

Summary: We describe a general multiplatform exploratory tool called TreeQ-Vista, designed for presenting functional annotations in a phylogenetic context. Traits, such as phenotypic and genomic properties, are interactively queried from a user-provided relational database with a user-friendly interface which provides a set of tools for users with or without SQL knowledge. The query results are projected onto a phylogenetic tree and can be displayed in multiple color groups. A rich set of browsing, grouping and query tools are provided to facilitate trait exploration, comparison and analysis. Availability: The program, detailed tutorial and examples are available online (http:/genome.lbl.gov/vista/TreeQVista). Contact: vista@lbl.gov

Many applications deal with the rendering of trimmed surfaces and the generation of grids for trimmed surfaces. Usually, a structured or unstructured grid must be constructed in the parameter space of the trimmed surface. Trimmed surfaces not only cause problems in the context of grid generation but also when exchanging data between different CAD systems. This paper describes a new approach for decomposing the valid part of the parameter space of a trimmed surface into a set of four-sided surfaces. The boundaries of these four-sided surfaces are line segments, segments of the trimming curves themselves, and segments of bisecting curves that are defined by a generalized Voronoi diagram implied by the trimming curves in parameter space. We use a triangular background mesh for the computation of the bisecting curves of the generalized Voronoi diagram.

Given a three dimensional (3D) array of function values F/sub i,j,k/ on a rectilinear grid, the marching cubes (MC) method is the most common technique used for computing a surface triangulation T approximating a contour (isosurface) F(x, y, z)=T. We describe the construction of a C/sup 0/ continuous surface consisting of rational quadratic surface patches interpolating the triangles in T. We determine the Bezier control points of a single rational quadratic surface patch based on the coordinates of the vertices of the underlying triangle and the gradients and Hessians associated with the vertices.

Characterizing the interplay between the vortices and forces acting on a wind turbine's blades in a qualitative and quantitative way holds the potential for significantly improving large wind turbine design. This paper introduces an integrated pipeline for highly effective wind and force field analysis and visualization. We extract vortices induced by a turbine's rotation in a wind field, and characterize vortices in conjunction with numerically simulated forces on the blade surfaces as these vortices strike another turbine's blades downstream. The scientifically relevant issue to be studied is the relationship between the extracted, approximate locations on the blades where vortices strike the blades and the forces that exist in those locations. This integrated approach is used to detect and analyze turbulent flow that causes local impact on the wind turbine blade structure. The results that we present are based on analyzing the wind and force field data sets generated by numerical simulations, and allow domain scientists to relate vortex-blade interactions with power output loss in turbines and turbine life expectancy. Our methods have the potential to improve turbine design to save costs related to turbine operation and maintenance.

Knowledge discovery from large and complex scientific data is a challenging task. With the ability to measure and simulate more processes at increasingly finer spatial and temporal scales, the growing number of data dimensions and data objects presents tremendous challenges for effective data analysis and data exploration methods and tools. The combination and close integration of methods from scientific visualization, information visualization, automated data analysis, and other enabling technologies—such as efficient data management—supports knowledge discovery from multi-dimensional scientific data. This paper surveys two distinct applications in developmental biology and accelerator physics, illustrating the effectiveness of the described approach.

Part 1: Cross-Domain Conference and Workshop on Multidisciplinary Research and Practice for Information Systems (CD-ARES 2013); International audience; Large displays are helpful tools for knowledge discovery applications. The increased screen real estate allows for more data to be shown at once. In some cases using virtual reality visualizations helps in creating more useful visualizations. In such settings, traditional input devices are not well-suited. They also do not scale well to multiple users, effectively limiting collaborative knowledge discovery scenarios. Smart phones and tablet computers are becoming increasingly ubiquitous and powerful, even having multi-core CPUs and dedicated Graphic Processing Units (GPUs). Given their built-in sensors they can serve as replacements for currently-used input devices, and provide novel functionality not achieved with traditional devices. Furthermore, their ubiquity ensures that they scale well to multi-user environments, where users can use their own devices. We present an application-independent way to integrate smart phones and tablets into knowledge discovery applications as input devices with additional functionality. This approach is based on Marking Menus, but extends the basic idea by employing the special capabilities of current consumer-level smart phones and tablets.