Exploring 3D DTI fiber tracts with linked 2D representations.

We present a visual exploration paradigm that facilitates navigation through complex fiber tracts by combining traditional 3D model viewing with lower dimensional representations. To this end, we create standard streamtube models along with two two-dimensional representations, an embedding in the plane and a hierarchical clustering tree, for a given set of fiber tracts. We then link these three representations using both interaction and color obtained by embedding fiber tracts into a perceptually uniform color space. We describe an anecdotal evaluation with neuroscientists to assess the usefulness of our method in exploring anatomical and functional structures in the brain. Expert feedback indicates that, while a standalone clinical use of the proposed method would require anatomical landmarks in the lower dimensional representations, the approach would be particularly useful in accelerating tract bundle selection. Results also suggest that combining traditional 3D model viewing with lower dimensional representations can ease navigation through the complex fiber tract models, improving exploration of the connectivity in the brain.

Coloring 3D line fields using Boy's real projective plane immersion.

We introduce a new method for coloring 3D line fields and show results from its application in visualizing orientation in DTI brain data sets. The method uses Boy's surface, an immersion of RP2 in 3D. This coloring method is smooth and one-to-one except on a set of measure zero, the double curve of Boy's surface.

Data2Vis: Automatic Generation of Data Visualizations Using Sequence-to-Sequence Recurrent Neural Networks.

Rapidly creating effective visualizations using expressive grammars is challenging for users who have limited time and limited skills in statistics and data visualization. Even high-level, dedicated visualization tools often require users to manually select among data attributes, decide which transformations to apply, and specify mappings between visual encoding variables and raw or transformed attributes. In this paper we introduce Data2Vis, an end-to-end trainable neural translation model for automatically generating visualizations from given datasets. We formulate visualization generation as a language translation problem, where data specifications are mapped to visualization specifications in a declarative language (Vega-Lite). To this end, we train a multilayered attention-based encoder-decoder network with long short-term memory (LSTM) units on a corpus of visualization specifications. Qualitative results show that our model learns the vocabulary and syntax for a valid visualization specification, appropriate transformations (count, bins, mean), and how to use common data selection patterns that occur within data visualizations. We introduce two metrics for evaluating the task of automated visualization generation (language syntax validity, visualization grammar syntax validity) and demonstrate the efficacy of bidirectional models with attention mechanisms for this task. Data2Vis generates visualizations that are comparable to manually created visualizations in a fraction of the time, with potential to learn more complex visualization strategies at scale.

Task-Based Effectiveness of Basic Visualizations.

Visualizations of tabular data are widely used; understanding their effectiveness in different task and data contexts is fundamental to scaling their impact. However, little is known about how basic tabular data visualizations perform across varying data analysis tasks. In this paper, we report results from a crowdsourced experiment to evaluate the effectiveness of five small scale (5-34 data points) two-dimensional visualization types-Table, Line Chart, Bar Chart, Scatterplot, and Pie Chart-across ten common data analysis tasks using two datasets. We find the effectiveness of these visualization types significantly varies across task, suggesting that visualization design would benefit from considering context-dependent effectiveness. Based on our findings, we derive recommendations on which visualizations to choose based on different tasks. We finally train a decision tree on the data we collected to drive a recommender, showcasing how to effectively engineer experimental user data into practical visualization systems.

Clustrophile 2: Guided Visual Clustering Analysis.

Data clustering is a common unsupervised learning method frequently used in exploratory data analysis. However, identifying relevant structures in unlabeled, high-dimensional data is nontrivial, requiring iterative experimentation with clustering parameters as well as data features and instances. The number of possible clusterings for a typical dataset is vast, and navigating in this vast space is also challenging. The absence of ground-truth labels makes it impossible to define an optimal solution, thus requiring user judgment to establish what can be considered a satisfiable clustering result. Data scientists need adequate interactive tools to effectively explore and navigate the large clustering space so as to improve the effectiveness of exploratory clustering analysis. We introduce Clustrophile 2, a new interactive tool for guided clustering analysis. Clustrophile 2 guides users in clustering-based exploratory analysis, adapts user feedback to improve user guidance, facilitates the interpretation of clusters, and helps quickly reason about differences between clusterings. To this end, Clustrophile 2 contributes a novel feature, the Clustering Tour, to help users choose clustering parameters and assess the quality of different clustering results in relation to current analysis goals and user expectations. We evaluate Clustrophile 2 through a user study with 12 data scientists, who used our tool to explore and interpret sub-cohorts in a dataset of Parkinson's disease patients. Results suggest that Clustrophile 2 improves the speed and effectiveness of exploratory clustering analysis for both experts and non-experts.

Sampling for Scalable Visual Analytics.

Sampling is becoming an essential tool for scalable interactive visual analysis. After outlining prior work by the database community on sampling for visualization of aggregation queries, this article considers how these results might be improved and extended to a broader setting. The goal is to better understand how users interact with sampling to enable wider adoption of sampling for scalable visual analytics.

CAVE and fishtank virtual-reality displays: a qualitative and quantitative comparison.

We present the results from a qualitative and quantitative user study comparing fishtank virtual-reality (VR) and CAVE displays. The results of the qualitative study show that users preferred the fishtank VR display to the CAVE system for our scientific visualization application because of perceived higher resolution, brightness and crispness of imagery, and comfort of use. The results of the quantitative study show that users performed an abstract visual search task significantly more quickly and more accurately on the fishtank VR display system than in the CAVE. The same study also showed that visual context had no significant effect on task performance for either of the platforms. We suggest that fishtank VR displays are more effective than CAVEs for applications in which the task occurs outside the user's reference frame, the user views and manipulates the virtual world from the outside in, and the size of the virtual object that the user interacts with is smaller than the user's body and fits into the fishtank VR display. The results of both studies support this proposition.

The Multimodal Brain Tumor Image Segmentation Benchmark (BRATS).

In this paper we report the set-up and results of the Multimodal Brain Tumor Image Segmentation Benchmark (BRATS) organized in conjunction with the MICCAI 2012 and 2013 conferences. Twenty state-of-the-art tumor segmentation algorithms were applied to a set of 65 multi-contrast MR scans of low- and high-grade glioma patients-manually annotated by up to four raters-and to 65 comparable scans generated using tumor image simulation software. Quantitative evaluations revealed considerable disagreement between the human raters in segmenting various tumor sub-regions (Dice scores in the range 74%-85%), illustrating the difficulty of this task. We found that different algorithms worked best for different sub-regions (reaching performance comparable to human inter-rater variability), but that no single algorithm ranked in the top for all sub-regions simultaneously. Fusing several good algorithms using a hierarchical majority vote yielded segmentations that consistently ranked above all individual algorithms, indicating remaining opportunities for further methodological improvements. The BRATS image data and manual annotations continue to be publicly available through an online evaluation system as an ongoing benchmarking resource.

Estimating joint contact areas and ligament lengths from bone kinematics and surfaces.

We present a novel method for modeling contact areas and ligament lengths in articulations. Our approach uses volume images generated by computed tomography and allows the in vivo and noninvasive study of articulations. In our method, bones are modeled both implicitly (scalar distance fields) and parametrically (manifold surfaces). Using this double representation, we compute interbone distances and estimate joint contact areas. Using the same types of representation, we model ligament paths; in our model, the ligaments are approximated by the shortest paths in a three-dimensional space with bone obstacles. We demonstrate the method by applying our contact area and ligament model to the distal radioulnar joints of a volunteer diagnosed with malunited distal radius fracture in one forearm. Our approach highlights focal changes in the articulation at the distal radioulnar joint (location and area of bone contact) and potential soft-tissue constraints (increased "length" of the distal ligaments and ligament-bone impingement in the injured forearm). Results suggest that the method could be useful in the study of normal and injured anatomy and kinematics of complex joints.

Learning Perceptual Kernels for Visualization Design.

Visualization design can benefit from careful consideration of perception, as different assignments of visual encoding variables such as color, shape and size affect how viewers interpret data. In this work, we introduce perceptual kernels: distance matrices derived from aggregate perceptual judgments. Perceptual kernels represent perceptual differences between and within visual variables in a reusable form that is directly applicable to visualization evaluation and automated design. We report results from crowd-sourced experiments to estimate kernels for color, shape, size and combinations thereof. We analyze kernels estimated using five different judgment types--including Likert ratings among pairs, ordinal triplet comparisons, and manual spatial arrangement--and compare them to existing perceptual models. We derive recommendations for collecting perceptual similarities, and then demonstrate how the resulting kernels can be applied to automate visualization design decisions.

Visual embedding: a model for visualization.

The authors propose visual embedding as a model for automatically generating and evaluating visualizations. A visual embedding is a function from data points to a space of visual primitives that measurably preserves structures in the data (domain) within the mapped perceptual space (range). The authors demonstrate its use with three examples: coloring of neural tracts, scatterplots with icons, and evaluation of alternative diffusion tensor glyphs. They discuss several techniques for generating visual-embedding functions, including probabilistic graphical models for embedding in discrete visual spaces. They also describe two complementary approaches--crowdsourcing and visual product spaces--for building visual spaces with associated perceptual--distance measures. In addition, they recommend several research directions for further developing the visual-embedding model.

Exploring brain connectivity with two-dimensional neural maps.

We introduce two-dimensional neural maps for exploring connectivity in the brain. For this, we create standard streamtube models from diffusion-weighted brain imaging data sets along with neural paths hierarchically projected into the plane. These planar neural maps combine desirable properties of low-dimensional representations, such as visual clarity and ease of tract-of-interest selection, with the anatomical familiarity of 3D brain models and planar sectional views. We distribute this type of visualization both in a traditional stand-alone interactive application and as a novel, lightweight web-accessible system. The web interface integrates precomputed neural-path representations into a geographical digital-maps framework with associated labels, metrics, statistics, and linkouts. Anecdotal and quantitative comparisons of the present method with a recently proposed 2D point representation suggest that our representation is more intuitive and easier to use and learn. Similarly, users are faster and more accurate in selecting bundles using the 2D path representation than the 2D point representation. Finally, expert feedback on the web interface suggests that it can be useful for collaboration as well as quick exploration of data.

Tract-based probability densities of diffusivity measures in DT-MRI.

We evaluate probability density functions of diffusivity measures in DTI fiber tracts as biomarkers. For this, we estimate univariate and bivariate densities, such as joint probability densities of the tract arc length and FA, MD, RD, and AD, in the transcallosal fibers in the brain. We demonstrate the utility of estimated densities in hypothesis testing of differences between a group of patients with VCI and a control group. We also use the estimated densities in classifying individual subjects in these two groups. Results show that these estimates and derived quantities, such as entropy, can detect group differences with high statistical power as well as help obtain low classification errors.

A slicing-based coherence measure for clusters of DTI integral curves.

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.