Designed especially for neurobiologists, FluoRender is an interactive tool for multi-channel fluorescence microscopy data visualization and analysis.
Deep brain stimulation
BrainStimulator is a set of networks that are used in SCIRun to perform simulations of brain stimulation such as transcranial direct current stimulation (tDCS) and magnetic transcranial stimulation (TMS).
Developing software tools for science has always been a central vision of the SCI Institute.

Publications News

topological-methods-3 newsCongratulations to Valerio Pascucci and Peer-Timo Bremer whose co-edited book "Topological Methods in Data Analysis and Visualization III" has just been published.
PacVis2014-bestpaper newsCongratulations to Bei Wang, Paul Rosen, Guoning Chen and their collaborator from Slovenia, Primoz Skraba whose paper:

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P. Skraba, Bei Wang, G. Chen, P. Rosen. “2D Vector Field Simplification Based on Robustness,” In Proceedings of the 2014 IEEE Pacific Visualization Symposium, PacificVis, Note: Awarded Best Paper!, 2014.

won "Best Paper" at PacificVis 2014. Their paper presents a new approach to simplification of vector flow fields necessary to reveal essential features within a vector flow field. Traditional methods based on the topological skeleton successively remove pairs of critical points connected by separatrices, using distance or area-based relevance measures. These geometric metrics do not consider the flow magnitude, an important physical property of the flow. The new simplification scheme proposed is based on the recently introduced notion of topological robustness. Robustness enables the pruning of sets of critical points according to a quantitative measure of their stability, that is, the minimum amount of vector field perturbation required to remove them. This leads to a hierarchical simplification scheme that encodes flow magnitude in its perturbation metric.
MBIA-bestpaper2013 newsCongratulations to Bo Wang, Marcel Prastawa, Avishek Saha, Suyash Awate, Andrei Irimia, Micah Chambers, Paul Vespa, John Van Horn, Valerio Pascucci, and Guido Gerig whose paper:

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B. Wang, M. Prastawa, A. Saha, S.P. Awate, A. Irimia, M.C. Chambers, P.M. Vespa, J.D. Van Horn, V. Pascucci, G. Gerig. “Modeling 4D changes in pathological anatomy using domain adaptation: analysis of TBI imaging using a tumor database,” In Proceedings of the 2013 MICCAI-MBIA Workshop, Lecture Notes in Computer Science (LNCS), Vol. 8159, Note: Awarded Best Paper!, pp. 31--39. 2013.
DOI: 10.1007/978-3-319-02126-3_4

maljovec bp-runnerup-PSA2013 newsCongratulations to Dan Maljovec, et. at, whose paper was chosen first runner-up for Best Student Paper at the 2013 International Topical Meeting on Probabilistic Safety Assessment and Analysis (PSA). See:

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D. Maljovec, B. Wang, D. Mandelli, P.-T. Bremer, V. Pascucci. “Adaptive Sampling Algorithms for Probabilistic Risk Assessment of Nuclear Simulations,” In Proceedings of the 2013 International Topical Meeting on Probabilistic Safety Assessment and Analysis (PSA 2013), Note: First runner-up for Best Student Paper Award, pp. (accepted). 2013.
sibgrapi2013-bestpaper newsCongratulations to Wathsala Widanagamaachchi, Paul Rosen, and Valerio Pascucci whose paper:

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W. Widanagamaachchi, P. Rosen, V. Pascucci. "A Flexible Framework for Fusing Image Collections into Panoramas," In Proceedings of the 2013 SIBGRAPI Conference on Graphics, Patterns, and Images, Note: Awarded Best Paper., pp. (to appear). 2013.

won "Best Paper" at the 2013 SIBGRAPI Conference on Graphics, Patterns, and Images. Their paper presents a new approach for the construction of panoramas called "Ray Graphs". This framework allows users to create arbitrarily shaped panoramas. In addition, this framework also allows modification of panoramas to remove undesirable objects.
Schott TVCG2013 newsCongratulations to Harsh Bhatia, Valerio Pascucci, and Peer-Timo Bremer, et. al. whose paper:

H. Bhatia, G. Norgard, V. Pascucci, P.-T. Bremer. The Helmholtz-Hodge Decomposition - A Survey,” In IEEE Transactions on Visualization and Computer Graphics (TVCG), Vol. 19, No. 8, pp. 1386--1404, Note: Selected as Spotlight paper for August 2013 issue, 2013.

is spotlighted in the August Issue of IEEE Transactions on Visualization and Computer Graphics (TVCG). Their paper surveys the use of the Helmholtz-Hodge Decomposition in modeling flow phenomena in various fields of science and addresses the problem of the fragmented nature of research in this area. The goal of this paper is to promote further research in the field by creating a common repository of HHD techniques and assemble a large collection of example applications in a broad range of areas. See: TVCG August 2013.

EGPGV-bestpaper2013 newsCongratulations to Sujin Philip, Brian Summa, Julien Tierny, Peer-Timo Bremer, and Valerio Pascucci whose paper:

S. Philip, B. Summa, J. Tierny, P.-T. Bremer, V. Pascucci. Scalable Seams for Gigapixel Panoramas,” In Proceedings of the 2013 Eurographics Symposium on Parallel Graphics and Visualization, Note: Awarded Best Paper!, pp. (to appear). 2013.

won "Best Paper" at the 2013 Eurographics Symposium on Parallel Graphics and Visualization. Their paper presents a fast and efficient method for blending seams between images in very large panoramas composed of mosaics of smaller images. While current methods may take many hours (or even days) to blend the images composing a gigapixel panorama, the new method takes just a few minutes.
ISBI BestPaper2013 newsCongratulations to Nikhil Singh, Jacob Hinkle, Sarang Joshi and Tom Fletcher whose paper was awarded "Best Student Paper" at the ISBI 2013 Conference.

N.P. Singh, J. Hinkle, S. Joshi, P.T. Fletcher. A Vector Momenta Formulation of Diffeomorphisms for Improved Geodesic Regression and Atlas Construction,” In IEEE Proceedings of ISBI 2013, Note: Received Best Student Paper Award, 2013.

 
Dr. Guido GerigAJPBestPaper news co-authored a paper that made the list of the American Journal of Psychiatry's "Best of 2012" for their paper “Differences in White Matter Fiber Tract Development Present from 6 to 24 Months in Infants with Autism”

In the AJP's 2012 Year in Review, the editors discuss the significance of this paper:

ldav2012-bestpaperCongratulations to Shusen Liu, Joshua Levine, Peer-Timo Bremer, and Valerio Pascucci whose paper:

"Gaussian Mixture Model Based Volume Visualization," Proceedings of the IEEE Symposium on Large-Scale Data Analysis and Visualization (LDAV) 2012, Note: Awarded Best Paper, 2012.

has been awarded "Best Paper" at the IEEE Symposium on Large-Scale Data Analysis and Visualization (LDAV) 2012. Winning papers are chosen by the LDAV committee based on which submission is deemed the strongest to the conference according to the reviewing criteria.

Congratulations also go out to Liang Zhou, and Charles Hansen who received a Best Poster Honorable Mention for their poster entitled "A System for More Intuitive Multivariate Volume Exploration and Visualization."
eurovis-11Congratulations to Erik Anderson, Kristi Potter and Claudio Silva whose paper won 2nd Best Paper at Eurographics/IEEE Symposium on Visualization 2011.

E.W. Anderson, K.C. Potter, L.E. Matzen, J.F. Shepherd, G.A. Preston, C.T. Silva. "A User Study of Visualization Effectiveness Using EEG and Cognitive Load," In Eurographics/IEEE Symposium on Visualization 2011, Vol. 30, No. 3, Edited by H. Hauser, H. Pfister, and J.J. van Wijk, 2011.