Abstract: Molecular surfaces often exhibit a complicated interior structure that is not fully visible from exterior viewpoints due to occlusion. In many cases this interior cavity is the most important feature of the surface. Applying standard blended transparency can reveal some of the hidden structure, but often results in confusion due to impaired surface-shape perception. We present ambient occlusion opacity mapping (AOOM), a novel visualization technique developed to improve understanding of the interior of molecular structures. Ambient occlusion is a shading method used in computer graphics that approximates complex shadows from an ambient light source by rendering objects darker when surrounded by other objects. Although ambient occlusion has previously been applied in molecular visualization to better understand surface shape, we instead use ambient occlusion information to determine a variable opacity at each point on the molecular surface. In this manner, AOOM enables rendering interior structures more opaque than outer structures, displaying the inner surface of interest more effectively than with constant-opacity blending. Furthermore, AOOM works for cases not handled by previous cavity-extraction techniques. This work has been driven by collaborators studying enzyme-ligand interactions, in which the active site of the enzyme is typically formed as a cavity in the molecular surface. In this paper we describe the AOOM technique and extensions, using visualization of the active site of enzymes as the driving problem.
Abstract: What are desirable and undesirable features of virtual environment (VE) software architectures? What should be present (and absent) from such systems if they are to be optimally useful? How should they be structured? In order to help answer these questions, we present experience from application designers, toolkit designers, and VE system architects along with examples of useful features from existing systems. Topics are organized under the major headings of 3D space management, supporting display hardware, interaction, event management, time management, computation, portability, and the observation that less can be better. Lessons learned are presented as discussion of the issues, field experiences, nuggets of knowledge, and case studies.
Abstract: Contact formation dynamics and electronic perturbations arising from the interaction of a metallic probe and a single molecule (1,3 cyclohexadiene) bound on the Si (100) surface are examined using a series of plane wave, density functional theory calculations. The approach of the probe induces a relaxation of the molecule that ultimately leads to the formation of an interface state due to a specific interaction between the probe apex atom and the Cî—»C bond of the molecule. The calculated interface state is located 0.2 eV above the Fermi energy, in agreement with low temperature scanning tunneling spectroscopy local density of states data (0.35 eV), and is responsible for the contrast observed in low bias empty-state STM images.
Abstract: The aim of the study is to test a new volume-rendering method, volumetric depth peeling (VDP), for use in virtual pyeloscopy.
MATERIALS AND METHODS: VDP was applied to axial contrast-enhanced source computed tomographic (CT) images and coronal reformatted maximum intensity projections of three contrast-filled gloves containing objects of varying density. Similar renderings were performed on CT urograms performed to evaluate hematuria (n = 20). Renderings were assessed for anatomic appearance of ureters and specific calyces in comparison with source images.
RESULTS: Objects of soft-tissue and calcific density ranging in size from 4 to 20 mm were identified by using VDP within the glove phantoms. Normal and deformed renal calyces were well visualized by using VDP; however, two stones were not identified. The minimal ureteral width that could be visualized was 3 mm.
CONCLUSION: VDP may be a useful technique for virtual pyeloscopy providing that a robust and user-friendly computer interface can be developed.
Abstract: As humans we commonly (and seemingly effortlessly) use our hands to learn about the world around us as we use sensory information gained through touch to build our understandings of complex objects and events. Relatively recent advances in technology have made the addition of “touch” to computer-generated virtual environments possible. While potentially a breakthrough technology for instructional simulation environments, there is little research to guide instructional designers. There is a burgeoning research base on haptics but touch remains an understudied and perhaps underutilized sensory modality in the creation of computer-mediated instructional programs.
Abstract: The Social Computing Room (SCR) is a novel collaborative visualization environment for viewing and interacting with large amounts of visual data. The SCR consists of a square room with 12 projectors (3 per wall) used to display a single 360-degree desktop environment that provides a large physical real estate for arranging visual information. The SCR was designed to be cost-effective, collaborative, configurable, widely applicable, and approachable for naive users. Because the SCR displays a single desktop, a wide range of applications is easily supported, making it possible for a variety of disciplines to take advantage of the room. We provide a technical overview of the room and highlight its application to scientific visualization, arts and humanities projects, research group meetings, and virtual worlds, among other uses.
Abstract: Inconsistencies in the preparation of histology slides make it difficult to perform quantitative analysis on their results. In this paper we provide two mechanisms for overcoming many of the known inconsistencies in the staining process, thereby bringing slides that were processed or stored under very different conditions into a common, normalized space to enable improved quantitative analysis.
Abstract: Volumetric depth peeling (VDP) is an extension to volume rendering that enables display of otherwise occluded features in volume data sets. VDP decouples occlusion calculation from the volume rendering transfer function, enabling independent optimization of settings for rendering and occlusion. The algorithm is flexible enough to handle multiple regions occluding the object of interest, as well as object self-occlusion, and requires no pre-segmentation of the data set. VDP was developed as an improvement for virtual arthroscopy for the diagnosis of shoulder-joint trauma, and has been generalized for use in other simple and complex joints, and to enable non-invasive urology studies. In virtual arthroscopy, the surfaces in the joints often occlude each other, allowing limited viewpoints from which to evaluate these surfaces. In urology studies, the physician would like to position the virtual camera outside the kidney collecting system and see inside it. By rendering invisible all voxels between the observer's point of view and objects of interest, VDP enables viewing from unconstrained positions. In essence, VDP can be viewed as a technique for automatically defining an optimal data- and task-dependent clipping surface. Radiologists using VDP display have been able to perform evaluations of pathologies more easily and more rapidly than with clinical arthroscopy, standard volume rendering, or standard MRI/CT slice viewing.
Abstract: The goal of this work is to enable more rapid and accurate diagnosis of pathology from three-dimensional (3D) medical images by augmenting standard volume rendering techniques to display otherwise-occluded features within the volume. When displaying such data sets with volume rendering, appropriate selection of the transfer function is critical for determining which features of the data will be displayed. In many cases, however, no transfer function is able to produce the most useful views for diagnosis of pathology.
Flexible Occlusion Rendering (FOR) is an addition to standard ray cast volume rendering that modulates accumulated color and opacity along each ray upon detecting features indicating the separation between objects of the same intensity range. For contrast-enhanced MRI and CT data, these separation features are intensity peaks. To detect these peaks, a dual-threshold method is used to reduce sensitivity to noise. To further reduce noise and enable control over the spatial scale of the features detected, a smoothed version of the original data set is used for feature detection, while rendering the original data at high resolution. Separating the occlusion feature detection from the volume rendering transfer function enables robust occlusion determination and seamless transition from occluded views to non-occluded views of surfaces during virtual flythroughs.
FOR has been applied to virtual arthroscopy of joints from MRI data. For example, survey views of entire shoulder socket surfaces have been rendered to enable rapid evaluation by automatically removing the occluding material of the humeral head. Such views are not possible with standard volume rendering. FOR has also been successfully applied to virtual ureteroscopy of the renal collecting system from CT data, and knee fracture visualization from CT data.
