M. Raj, M. Mirzargar, R. Kirby, R. Whitaker, J. Preston. Evaluating Alignment of Shapes by Ensemble Visualization, In IEEE Computer Graphics and Applications, IEEE, 2015.
The visualization of variability in 3D shapes or surfaces, which is a type of ensemble uncertainty visualization for volume data, provides a means of understanding the underlying distribution for a collection or ensemble of surfaces. While ensemble visualization for surfaces is already described in the literature, we conduct an expert-based evaluation in a particular medical imaging application: the construction of atlases or templates from a population of images. In this work, we extend contour boxplots to 3D, allowing us to evaluate it against an enumeration-style visualization of the ensemble members and also other conventional visualizations used by atlas builders, namely examining the atlas image and the corresponding images/data provided as part of the construction process. We present feedback from domain experts on the efficacy of contour boxplots compared to other modalities when used as part of the atlas construction and analysis stages of their work.
D. Reed, M. Berzins, R. Lucas, S. Matsuoka, R. Pennington, V. Sarkar, V. Taylor.
DOE Advanced Scientific Computing Advisory Committee (ASCAC) Report: Exascale Computing Initiative Review, Note: DOE Report, 2015.
DOI: DOI 10.2172/1222712
H. J.V. Rutherford, G. Gerig, S. Gouttard, M. N. Potenza, L. C. Mayes. Investigating maternal brain structure and its relationship to substance use and motivational systems, In Yale Journal of Biology and Medicine, in print, 2015.
Substance use during pregnancy and the postpartum period may have significant implications for both mother and the developing child. However, the neurobiological basis of the impact of substance use on parenting is less well understood. Here we examined the impact of maternal substance use on cortical gray matter (GM) and white matter volumes, and whether this was associated with individual differences in motivational systems of behavioral activation and inhibition. Mothers were included in the substance-using group if any addictive substance was used during pregnancy and/or in the immediate postpartum period (within 3 months of delivery). GM volume was reduced in substance-using mothers compared to non-substance-using mothers, particularly in frontal brain regions. In substance-using mothers, we also found that frontal GM was negatively correlated with levels of behavioral activation (i.e., the motivation to approach rewarding stimuli). This effect was absent in non-substance-using mothers. Taken together, these findings indicate a reduction in GM volume is associated with substance use, and that frontal GM volumetric differences may be related to approach motivation in substance-using mothers.
Note: Scientific Computing and Imaging Institute (SCI), University of Utah, www.sci.utah.edu, 2015.
SCI Institute. Note: SCIRun: A Scientific Computing Problem Solving Environment, Scientific Computing and Imaging Institute (SCI), Download from: http://www.scirun.org, 2015.
CIBC. Note: Seg3D: Volumetric Image Segmentation and Visualization. Scientific Computing and Imaging Institute (SCI), Download from: http://www.seg3d.org, 2015.
SCI Institute. Note: ShapeWorks: An open-source tool for constructing compact statistical point-based models of ensembles of similar shapes that does not rely on specific surface parameterization. Scientific Computing and Imaging Institute (SCI). Download from: http://www.sci.utah.edu/software/shapeworks.html, 2015.
P. Skraba, Bei Wang, G. Chen, P. Rosen. Robustness-Based Simplification of 2D Steady and Unsteady Vector Fields, In IEEE Transactions on Visualization and Computer Graphics (to appear), 2015.
SLASH. Note: SLASH: A hybrid system for high-throughput segmentation of large neuropil datasets, SLASH is funded by the National Institute of Neurological Disorders and Stroke (NINDS) grant 5R01NS075314-03., 2015.
H. Strobelt, B. Alsallakh, J. Botros, B. Peterson, M. Borowsky, H. Pfister,, A. Lex. Vials: Visualizing Alternative Splicing of Genes, In IEEE Transactions on Visualization and Computer Graphics (InfoVis '15), Vol. 22, No. 1, pp. 399-408. 2015.
Alternative splicing is a process by which the same DNA sequence is used to assemble different proteins, called protein isoforms. Alternative splicing works by selectively omitting some of the coding regions (exons) typically associated with a gene. Detection of alternative splicing is difficult and uses a combination of advanced data acquisition methods and statistical inference. Knowledge about the abundance of isoforms is important for understanding both normal processes and diseases and to eventually improve treatment through targeted therapies. The data, however, is complex and current visualizations for isoforms are neither perceptually efficient nor scalable. To remedy this, we developed Vials, a novel visual analysis tool that enables analysts to explore the various datasets that scientists use to make judgments about isoforms: the abundance of reads associated with the coding regions of the gene, evidence for junctions, i.e., edges connecting the coding regions, and predictions of isoform frequencies. Vials is scalable as it allows for the simultaneous analysis of many samples in multiple groups. Our tool thus enables experts to (a) identify patterns of isoform abundance in groups of samples and (b) evaluate the quality of the data. We demonstrate the value of our tool in case studies using publicly available datasets.
B. Summa, A. A. Gooch, G. Scorzelli, V. Pascucci.
Paint and Click: Unified Interactions for Image Boundaries, In Computer Graphics Forum, Vol. 34, No. 2, Wiley-Blackwell, pp. 385--393. May, 2015.
Image boundaries are a fundamental component of many interactive digital photography techniques, enabling applications such as segmentation, panoramas, and seamless image composition. Interactions for image boundaries often rely on two complementary but separate approaches: editing via painting or clicking constraints. In this work, we provide a novel, unified approach for interactive editing of pairwise image boundaries that combines the ease of painting with the direct control of constraints. Rather than a sequential coupling, this new formulation allows full use of both interactions simultaneously, giving users unprecedented flexibility for fast boundary editing. To enable this new approach, we provide technical advancements. In particular, we detail a reformulation of image boundaries as a problem of finding cycles, expanding and correcting limitations of the previous work. Our new formulation provides boundary solutions for painted regions with performance on par with state-of-the-art specialized, paint-only techniques. In addition, we provide instantaneous exploration of the boundary solution space with user constraints. Finally, we provide examples of common graphics applications impacted by our new approach.
M. R. Swanson, J. J. Wolff, J. T. Elison, H. Gu, H. C. Hazlett, K. Botteron, M. Styner, S. Paterson, G. Gerig, J. Constantino, S. Dager, A. Estes, C. Vachet, J. Piven.
Splenium development and early spoken language in human infants, In Developmental Science, Wiley Online Library, 2015.
The association between developmental trajectories of language-related white matter fiber pathways from 6 to 24 months of age and individual differences in language production at 24 months of age was investigated. The splenium of the corpus callosum, a fiber pathway projecting through the posterior hub of the default mode network to occipital visual areas, was examined as well as pathways implicated in language function in the mature brain, including the arcuate fasciculi, uncinate fasciculi, and inferior longitudinal fasciculi. The hypothesis that the development of neural circuitry supporting domain-general orienting skills would relate to later language performance was tested in a large sample of typically developing infants. The present study included 77 infants with diffusion weighted MRI scans at 6, 12 and 24 months and language assessment at 24 months. The rate of change in splenium development varied significantly as a function of language production, such that children with greater change in fractional anisotropy (FA) from 6 to 24 months produced more words at 24 months. Contrary to findings from older children and adults, significant associations between language production and FA in the arcuate, uncinate, or left inferior longitudinal fasciculi were not observed. The current study highlights the importance of tracing brain development trajectories from infancy to fully elucidate emerging brain–behavior associations while also emphasizing the role of the splenium as a key node in the structural network that supports the acquisition of spoken language.
Note: VisTrails: A scientific workflow management system. Scientific Computing and Imaging Institute (SCI), Download from: http://www.vistrails.org, 2015.
R. Whitaker, W. Thompson, J. Berger, B. Fischhof, M. Goodchild, M. Hegarty, C. Jermaine, K. S. McKinley, A. Pang, J. Wendelberger. Workshop on Quantification, Communication, and Interpretation of Uncertainty in Simulation and Data Science, Note: Computing Community Consortium, 2015.
Modern science, technology, and politics are all permeated by data that comes from people, measurements, or computational processes. While this data is often incomplete, corrupt, or lacking in sufficient accuracy and precision, explicit consideration of uncertainty is rarely part of the computational and decision making pipeline. The CCC Workshop on Quantification, Communication, and Interpretation of Uncertainty in Simulation and Data Science explored this problem, identifying significant shortcomings in the ways we currently process, present, and interpret uncertain data. Specific recommendations on a research agenda for the future were made in four areas: uncertainty quantification in large-scale computational simulations, uncertainty quantification in data science, software support for uncertainty computation, and better integration of uncertainty quantification and communication to stakeholders.
J. J. Wolff, G. Gerig, J. D. Lewis, T. Soda, M. A. Styner, C. Vachet, K. N. Botteron, J. T. Elison, S. R. Dager, A. M. Estes, H. C. Hazlett, R. T. Schultz, L. Zwaigenbaum, J. Piven.
Altered corpus callosum morphology associated with autism over the first 2 years of life, In Brain, 2015.
M. Zhang, P. T. Fletcher. Finite-Dimensional Lie Algebras for Fast Diffeomorphic Image Registration, In Information Processing in Medical Imaging (IPMI), 2015.