Showing papers by "David H. Laidlaw published in 2008"

The Immunological Genome Project: networks of gene expression in immune cells

Abstract: nology is an ideal field for the application of systems approaches, with its detailed descriptions of cell types (over 200 immune cell types are defined in the scope of the Immunological Genome Project (ImmGen)), wealth of reagents and easy access to cells. Thanks to the broad and robust approaches allowed by gene-expression microarrays and related techniques, the transcriptome is probably the only ‘-ome’ that can be reliably tackled in its entirety. Generating a complete perspective of gene expression in the immune system

Chronic cigarette smoking and the microstructural integrity of white matter in healthy adults: a diffusion tensor imaging study.

Abstract: Results from recent studies suggest that chronic cigarette smoking is associated with increased white matter volume in the brain as determined by in vivo neuroimaging. We used diffusion tensor imaging to examine the microstructural integrity of the white matter in 10 chronic smokers and 10 nonsmokers. All individuals were healthy, without histories of medical or psychiatric illness. Fractional anisotropy (FA) and trace were measured in the genu, body, and splenium of the corpus callosum. FA provides a measure of directional versus nondirectional water diffusion, whereas trace provides a measure of nondirectional water diffusion. Lower FA and higher trace values are considered to reflect less brain integrity. Voxel-based morphometry was used to define volumes in each of these regions of the corpus callosum. Chronic smokers exhibited significantly higher FA in the body and whole corpus callosum and a strong trend for higher FA in the splenium compared with nonsmokers. FA did not differ between groups in the genu, and neither trace nor white matter volumes differed between groups in any of the regions of interest. When subdivided by Fagerstrom score (low vs. high), the low Fagerstrom group exhibited significantly higher FA in the body of the corpus callosum compared with the high Fagerstrom group and the nonsmokers. These results suggest that, among healthy adults, lower exposure to cigarette smoking is associated with increased microstructural integrity of the white matter compared with either no exposure or higher exposure. Additional studies are needed to further explore differences in white matter integrity between smokers and nonsmokers.

Identifying White-Matter Fiber Bundles in DTI Data Using an Automated Proximity-Based Fiber-Clustering Method

Abstract: We present a method for clustering diffusion tensor imaging (DTI) integral curves into anatomically plausible bundles. An expert rater evaluated the anatomical accuracy of the bundles. We also evaluated the method by applying an experimental cross-subject labeling method to the clustering results. We first employ a sampling and culling strategy for generating DTI integral curves and then constrain the curves so that they terminate in gray matter. We then employ a clustering method based on a proximity measure calculated between every pair of curves. We interactively selected a proximity threshold to achieve visually optimal clustering in models from four DTI datasets. An expert rater then assigned a confidence rating about bundle presence and accuracy for each of 12 target fiber bundles of varying calibers and type in each dataset. We then created a fiber bundle template to cluster and label the fiber bundles automatically in new datasets. According to expert evaluation, the automated proximity-based clustering and labeling algorithm consistently yields anatomically plausible fiber bundles on large and coherent clusters. This work has the potential to provide an automatic and robust way to find and study neural fiber bundles within DTI.

Scientific Sketching for Collaborative VR Visualization Design

Abstract: We present four studies investigating tools and methodologies for artist-scientist-technologist collaboration in designing multivariate virtual reality (VR) visualizations. Design study 1 identifies the promise of 3D interfaces for rapid VR design and also establishes limitations of the particular tools tested with respect to precision and support for animation. Design study 2 explores animating artist-created visualization designs with scientific 3D fluid flow data. While results captured an accurate sense of flow that was advantageous as compared to the results of study 1, the potential for visual exploration using the design tools tested was limited. Design study 3 reveals the importance of a new 3D interface that overcomes the precision limitation found in study 1 while remaining accessible to artist collaborators. Drawing upon previous results, design study 4 engages collaborative teams in a design process that begins with traditional paper sketching and moves to animated interactive VR prototypes "sketched" by designers in VR using interactive 3D tools. Conclusions from these four studies identify important characteristics of effective artist-accessible VR visualization design tools and lead to a proposed formalized methodology for successful collaborative design that we expect to be useful in guiding future collaborations. We call this proposed methodology scientific sketching.

Using Visual Design Experts in Critique-Based Evaluation of 2D Vector Visualization Methods

Abstract: We describe an experiment in which art and illustration experts evaluated six 2D vector visualization methods. We found that these expert critiques mirrored previously recorded experimental results; these findings support that using artists, visual designers, and illustrators to critique scientific visualizations can be faster and more productive than quantitative user studies. Our participants successfully evaluated how well the given methods would let users complete a given set of tasks. Our results show a statistically significant correlation with a previous objective study: designers' subjective predictions of user performance by these methods match the users measured performance. The experts improved the evaluation by providing insights into the reasons for the effectiveness of each visualization method and suggesting specific improvements.

Visualization Criticism

Abstract: Criticism is a vital part of the practice of design, architecture, and art. It's extremely difficult to establish rules for making good art or designing a new object. Criticizing a work means applying the standards to identify weaknesses and suggest improvements. Critiquing can be a useful tool for teaching, developing better techniques, and deeper thinking about visualization.

Tech-note: Dynamic Dragging for Input of 3D Trajectories

Abstract: We present Dynamic Dragging, a virtual reality (VR) technique for input of smooth 3D trajectories with varying curvature. Users "drag" a virtual pen behind a hand-held tracked stylus to sweep out curving 3D paths in the air. Previous explorations of dragging-style input have established its utility for producing controlled, smooth inputs relative to freehand alternatives. However, a limitation of previous techniques is the reliance on a fixed-length drag line, biasing input toward trajectories of a particular curvature range. Dynamic Dragging explores the design space of techniques utilizing an adaptive drag line that adjusts length dynamically based on the local properties of the input, such as curvature and drawing speed. Finding the right mapping from these local properties to drag line length proves to be critical and challenging. Three potential mappings have been explored, and results of informal evaluations are reported. Initial findings indicate that Dynamic Dragging makes input of many styles of 3D curves easier than traditional drag-style input, allowing drag techniques to approach the flexibility for varied input of more sophisticated and much harder to learn techniques, such as two-handed tape drawing.

Exploratory visualization of animal kinematics using instantaneous helical axes

Abstract: We present novel visual and interactive techniques for exploratory visualization of animal kinematics using instantaneous helical axes (IHAs). The helical axis has been used in orthopedics, biomechanics, and structural mechanics as a construct for describing rigid body motion. Within biomechanics, recent imaging advances have made possible accurate high-speed measurements of individual bone positions and orientations during experiments. From this high-speed data, instantaneous helical axes of motion may be calculated. We address questions of effective interactive, exploratory visualization of this high-speed 3D motion data. A 3D glyph that encodes all parameters of the IHA in visual form is presented. Interactive controls are used to examine the change in the IHA over time and relate the IHA to anatomical features of interest selected by a user. The techniques developed are applied to a stereoscopic, interactive visualization of the mechanics of pig mastication and assessed by a team of evolutionary biologists who found interactive IHA-based analysis a useful addition to more traditional motion analysis techniques.

A case study in using gestures and bimanual interaction to extend a high-DOF input device

Abstract: Interactive 3D visualizations typically require complex, high-dimensional input. As a result, generating simple, efficient input mappings from device controllers to desired interactions is often a non-trivial design problem. While natural solutions include increasing the number of input controllers and overloading devices via key mappings, these methods add a level of complexity to the interaction that may ultimately detract from the utility of the visualization. In this work, we explore two alternatives to these approaches. First, we present a cooperative bimanual technique for overloading a six degree-offreedom (DOF) Space Navigator (3D Connexion, Inc.) via context sensitivity. We then present a manually triggered, gesture-based technique for extending the Space Navigator’s control. While neither context-driven nor gesture-based interactions are entirely novel, combining these approaches within a complex visualization application creates challenging, driving design problems. Here, we present a case study of the design and application of these techniques within a real 3D scientific visualization application. Analysis of the design principles explored in this work has far-reaching implications. In the case of scientific visualizations, creating effective, inconspicuous interaction schemes will allow science to remain the preeminent focus of the application, and, in turn, facilitate research and lead to greater productivity. It should also be noted that while these techniques were designed to aid in scientific research, they also address the more general problem of overloading input controllers in a clear, seamless manner.

An Analytical Model of Diffusion and Exchange of Water in White Matter from Diffusion-MRI and its Application in Measuring Axon Radii

Abstract: ( P ∂ ) ( ) 0 , | ( 0 0 ) 1 ( r r r r Ps r r r r s s P D t ∇ = ∂ , Initial Condition: − =δ ( ) 1 ( = + ∂ ∂ = = a s a s MP P D ρ ρ ρ • Define: Transport rate through interface 1 D Ma h = , M is the permeability coefficient The solution to the diffusion problem posed above, given rotational symmetry about the direction of the field gradient, is

Exploring dimensionality reduction of animal flight kinematics in an interactive virtual reality setting

Abstract: We discovered that displaying experimentally captured kinematics data in an interactive three-dimensional setting provided an intuitive biological interpretation of biomechanical patterns. In particular, feedback from users who compared this environment with traditional two-dimensional graph methods showed that the advantage of seeing inherently 3D data in a virtual environment allowed them to better concentrate on data analyses. Subsequently, they were able to notice new motion patterns as well as differences and similarities in flight behavior at varying flight speeds.

A Slicing-Based Coherence Measure for Clusters of DTI Integral Curves

Abstract: We present a slicing-based coherence measure for clusters of DTI integral curves. For a given cluster, we probe samples from the cluster by slicing it with a plane at regularly spaced locations parametrized by curve arc lengths. Then we compute a stability measure based on the spatial relations between the projections of the curve points in individual slices and their change across the slices. We demonstrate its use in refining agglomerative hierarchical clustering results of DTI curves that correspond to neural pathways. Expert evaluation shows that refinement based on our measure can lead to improvement of clustering that is not possible directly by using standard methods.