OSVR is a new open-source virtual reality platform that builds on and extends existing libraries. It provides a common ground for university and commercial research and development, enabling new development at any level to be rapidly tested and deployed in a full application stack. Devices are discovered and enumerated, with self-description data made available to applications for use in sensible auto-configuration. OSVR is agnostic about operating system, graphics language, and rendering framework - enabling rapid porting of applications to new systems.

BACKGROUND: Because of the difficulties involved in learning and using 3D modeling and rendering software, many scientists hire programmers or animators to create models and animations. This both slows the discovery process and provides opportunities for miscommunication. Working with multiple collaborators, a tool was developed (based on a set of design goals) to enable them to directly construct models and animations. RESULTS: SketchBio is presented, a tool that incorporates state-of-the-art bimanual interaction and drop shadows to enable rapid construction of molecular structures and animations. It includes three novel features: crystal-by-example, pose-mode physics, and spring-based layout that accelerate operations common in the formation of molecular models. Design decisions and their consequences are presented, including cases where iterative design was required to produce effective approaches. CONCLUSIONS: The design decisions, novel features, and inclusion of state-of-the-art techniques enabled SketchBio to meet all of its design goals. These features and decisions can be incorporated into existing and new tools to improve their effectiveness.

Conveying data uncertainty in visualizations is crucial for preventing viewers from drawing conclusions based on untrustworthy data points. This paper proposes a methodology for efficiently generating density plots of uncertain multivariate data sets that draws viewers to preattentively identify values of high certainty while not calling attention to uncertain values. We demonstrate how to augment scatter plots and parallel coordinates plots to incorporate statistically modeled uncertainty and show how to integrate them with existing multivariate analysis techniques, including outlier detection and interactive brushing. Computing high quality density plots can be expensive for large data sets, so we also describe a probabilistic plotting technique that summarizes the data without requiring explicit density plot computation. These techniques have been useful for identifying brain tumors in multivariate magnetic resonance spectroscopy data and we describe how to extend them to visualize ensemble data sets.

We present a data-driven method for interactive simulation and visualization of fibrin fibers, a major component of blood clotting. A fibrin fiber is a complex system consisting of a hierarchy with at least three separate levels of detail. Using measurements acquired with an atomic force microscope (AFM) at the smallest scale in this hierarchy, a physically-based model for the larger scales can be constructed and then simulated. Unlike most traditional work dealing with Monte Carlo (MC) or Molecular Dynamics (MD) simulations, our method makes simplifying assumptions about the simulation and enables interactive visualization of simulated fibers in a virtual environment.

We have developed a real-time experiment-control and data-display system for a novel microscope, the 3D-force microscope (3DFM), which is designed for nanometer-scale and nanoNewton-force biophysical experiments. The 3DFM software suite synthesizes the several data sources from the 3DFM into a coherent view and provides control over data collection and specimen manipulation. Herein, we describe the system architecture designed to handle the several feedback loops and data flows present in the microscope and its control system. We describe the visualization techniques used in the 3DFM software suite, where used, and on which types of data. We present feedback from our scientist-users regarding the usefulness of these techniques, and we also present lessons learned from our successive implementations.

This paper describes the adaptation and evaluation of existing nested-surface visualization techniques for the problem of displaying intersecting surfaces. For this work, we collaborated with a neurosurgeon who is comparing multiple tumor segmentations with the goal of increasing the segmentation accuracy and reliability. A second collaborator, a physicist, aims to validate geometric models of specimens against atomic-force microscope images of actual specimens. These collaborators are interested in comparing both surface shape and inter-surface distances. Many commonly employed techniques for visually comparing multiple surfaces (side-by-side, wireframe, colormaps, uniform translucence) do not simultaneously convey inter-surface distance and the shapes of two or more surfaces. This paper describes a simple geometric partitioning of intersecting surfaces that enables the application of existing nested-surface techniques, such as texture-modulated translucent rendering of exteriors, to a broader range of visualization problems. Three user studies investigate the performance of existing techniques and a new shadow-casting glyph technique. The results of the first user study show that texture glyphs on partitioned, intersecting surfaces can convey inter-surface distance better than directly mapping distance to a red-gray-blue color scale on a single surface. The results of the second study show similar results for conveying local surface orientation. The results of the third user study show that adding cast shadows to texture glyphs can increase the understanding of inter-surface distance in static images, but can be overpowered by the shape cues from a simple rocking motion.

ImageSurfer is a tool designed to explore correlations between two 3D scalar fields. Our scientific goal was to determine where a protein is located, and how much its concentration varies along the membrane of a neuronal dendrite. The 3D scalar field data sets fall into two categories: dendritic plasma membranes (defining the structure) and immunofluorescent staining (defining protein concentration along the structure). ImageSurfer enables scientists to analyze relationships between multiple data sets obtained with confocal microscopy by providing 3D surface view, height field, and graphing tools. Each tool reduces the complexity of the problem by extracting a restricted subset of data: finding a region of interest in 3D; getting a sense of relative concentrations in 2D, and getting exact concentration values in 1D. The current design is presented, along with the rationale for each design decision. The tool is already proving useful for data exploration, analysis, and presentation.

We present a design methodology for a nanoscale self-assembling fabrication process that uses the specificity of DNA hybridization to guide the formation of electrical circuitry. Custom design software allows us to specify the function of a structure in a way similar to that used by VLSI circuit designers. In an analogous manner to generating masks for a photolithographic process, our software generates an assembly procedure including DNA sequence allocation. We have found that the number of unique DNA sequences needed to assemble a structure scales with its surface area. Using a simple face-serial assembly order we can specify an unambiguous assembly sequence for a structure of any size with only 15 unique DNA sequences.

The Virtual-Reality Peripheral Network (VRPN) system provides a device-independent and network-transparent interface to virtual-reality peripherals. VRPN's application of factoring by function and of layering in the context of devices produces an interface that is novel and powerful. VRPN also integrates a wide range of known advanced techniques into a publicly-available system. These techniques benefit both direct VRPN users and those who implement other applications that make use of VR peripherals.

We present a framework for fast and accurate collision detection for haptic interaction with polygonal models. Given a model, we pre-compute a hybrid hierarchical representation, consisting of uniform grids and trees of tight-fitting oriented bounding box trees (OBB-Trees). At run time, we use hybrid hierarchical representations and exploit frame-to-frame coherence for fast proximity queries. We describe a new overlap test, which is specialized for intersection of a line segment with an oriented bounding box for haptic simulation and takes 6-36 operations excluding transformation costs. The algorithms have been implemented as part of H-COLLIDE and interfaced with a PHANToM arm and its haptic toolkit, GHOST, and applied to a number of models. As compared to the commercial implementation, we are able to achieve up to 20 times speedup in our experiments and sustain update rates over 1000 Hz on a 400 MHz Pentium II.

Since 1991, our team of computer scientists, chemists and physicists have worked together to develop an advanced, virtual-environment interface to scanned-probe microscopes. The interface has provided insights and useful capabilities well beyond those of the traditional interface. This paper lists the particular visualization and control techniques that have enabled actual scientific discovery, including specific examples of insight gained using each technique. This information can help scientists determine which features are likely to be useful in their particular application, and which would be just sugar coating. It can also guide computer scientists to suggest the appropriate type of interface to help solve a particular problem. We have found benefit in advanced rendering with natural viewpoint control (but not always), from semi-automatic control techniques, from force feedback during manipulation, and from storing/replaying data for an entire experiment. These benefits come when the system is well-integrated into the existing tool and allows export of the data to standard visualization packages.

Integrating force feedback with a complete real-time virtual environment system presents problems which are more difficult than those encountered in building simpler forcefeedback systems. In particular, lengthy computations for graphics or simulation require a decoupling of the haptic servo loop from the main application loop if high-quality forces are to be produced. We present some approaches to these problems and describe our force-feedback software library which implements these techniques and provides other benefits including haptic-textured surfaces, device independence, distributed operation and easy enhancement.

The NanoManipulator system has been expanded from a virtual-reality interface for a specific scanning tunneling microscope to include control of atomic force microscopes. The current state of the system is reviewed, and new tools extending the user's feel and control in manipulation and fabrication in the mesoscopic regime are detailed. Manipulations that could not be performed using the techniques available from commercial SPM systems are demonstrated, and the direction of ongoing research is outlined.

We present an atomic-scale teleoperation system that uses a head-mounted display and force-feedback manipulator arm for a user interface and a Scanning Tunneling Microscope (STM) as a sensor and effector.The system approximates presence at the atomic scale, placing the scientist on the surface, in control, w h i l e the experiment is happening.A scientist using the Nanomanipulator can view incoming STM data, feel the surface, and modify the surface (using voltage pulses) in real time.The Nanomanipulator has been used to study the effects of bias pulse duration on the creation of gold mounds.We intend to use the system to make controlled modifications to silicon surfaces.