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

skalakCongratulations to Nicholas Drury, Ben Ellis, Jeff Weiss, Pat McMahon and Richard Debski who's paper: N.J. Drury, B.J. Ellis, J.A. Weiss, P.J. McMahon, R.E. Debski. The impact of glenoid labrum thickness and modulus on labrum and glenohumeral capsule function,” In Journal of Biomechanical Engineering, Vol. 132, No. 12, Note: Awarded 2010 Skalak Best Paper!, pp. 121003--121010. 2010.
DOI: 10.1115/1.4002622

has been awarded "2010 Skalak Best Paper" by the Journal of Biomechanical Engineering Honors committee. This honor is awarded to the best paper of the year as determined by reviewer rankings.
acm-scaCongratulations to Linh Ha, Jens Krüger, Joao Comba, Sarang Joshi, and Claudio Silva who's paper:

Linh K. Ha, Jens Krüger, Joao Comba, Sarang Joshi, Cláudio T. Silva. "Optimal Multi-Image Processing Streaming Framework on Parallel Heterogeneous Systems", Eurographics Symposium on Parallel Graphics and Visualization, 2011.

received the Best Paper Award at the ACM Eurographics Symposium on Parallel Graphics and Visualization 2011.

neuroimageThe journal NeuroImage recently released it's list of the top ten most cited articles over the last 5 years. On it was a paper co-authored by Dr. Gerig entitled "User-guided 3D active contour segmentation of anatomical structures: Significantly improved efficiency and reliability". It has been cited 170 times! (Scopus statistics) The paper describes the use of a free software tool called itk-SNAP for efficient segmentation of 3D volumetric image data via 3D snakes. See: NeuroImage Top Cited Articles.

Yushkevich, P.A.; Piven, J.; Hazlett, H.C.; Smith, R.G.; Ho, S.; Gee, J.C.; Gerig, G. "User-guided 3D active contour segmentation of anatomical structures: Significantly improved efficiency and reliability" NeuroImage, Volume 31, Issue 3, Pages 1116-1128, 2006.
miccai-09Congratulations to Samuel Gerber, Tolga Tasdizen, P. Thomas Fletcher, Sarang Joshi, Ross Whitaker whose paper received the MICCAI 2010 Best of the Journal Issue Award, which selects the best paper among the top conference papers appearing in a special issue of the Journal of Medical Image Analysis (citation below). The MICCAI conferences hosts several hundred papers with an acceptance rate of below 30%, so it is quite an honor.

S. Gerber, T. Tasdizen, P.T. Fletcher, S. Joshi, R.T. Whitaker, and the Alzheimers Disease Neuroimaging Initiative (ADNI). “Manifold modeling for brain population analysis,” In Medical Image Analysis, Special Issue on the 12th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) 2009, Vol. 14, No. 5, Note: Awarded MICCAI 2010, Best of the Journal Issue Award, pp. 643--653. 2010.
ISSN: 1361-8415
teragrid-10Congratulations to Justin Luitjens, Qingyu Meng, and Martin Berzins whose paper received the Best Paper Award in the Science Track at the 2010 Teragrid Conference in Pittsburgh, August 2-5th 2010:

M. Berzins, J. Luitjens, Q. Meng, T. Harman, C.A. Wight, J.R. Peterson. “Uintah - A Scalable Framework for Hazard Analysis,” In Proceedings of the Teragrid 2010 Conference, pp. (accepted). 2010.

manifoldCongratulations to Samuel Gerber, Tolga Tasdizen, P. Thomas Fletcher, Sarang Joshi, Ross Whitaker whose paper received the MICCAI 2010 Best of the Journal Issue Award, which selects the best paper among the top conference papers appearing in a special issue of the Journal of Medical Image Analysis (citation below). The MICCAI conferences hosts several hundred papers with an acceptance rate of below 30%, so it is quite an honor.

eurographics-2010Congratulations to Claudio Silva, Erik Anderson, Emanuele Santos, and Juliana Freire who received the "Best Paper" award at EUROGRAPHICS 2010 for:  

C. Silva, E. Anderson, E. Santos, J. Freire. "Using VisTrails and Provenance for Teaching Scientific Visualization," In EUROGRAPHICS 2010 Educator Program, 2010.
brownlee-pacific-visCongratulations to SCI graduate student Carson Brownlee who was awarded "Best Paper" at IEEE Pacific Visualization 2010 for:

C. Brownlee, V. Pegoraro, S. Shankar, P. McCormick, C. Hansen "Physically-Based Interactive Schlieren Flow Visualization", Proceedings of Pacific Vis 2010.
lowell-cmbbe10SCI/MRL Lab graduate student Lowell Edgar received 1st prize in the Student Presentation Competition for his research presentation at the Computer Methods in Biomechanics and Biomedical Engineering conference this last week in Valencia, Spain.  The award includes 500 Euros.

riemannianThe international journal Signal Processing has announced its award for the 2010 Signal Processing most cited paper goes to Riemannian Geometry for the Statistical Analysis of Diffusion Tensor Data” by Drs. Tom Fletcher and Sarang Joshi. This distinction is based solely on the highest number of cites, excluding self-citations, received by the end of 2009 for all articles published in the journal between the years 2007–2009 as reported by SCOPUS reports (www.scopus.com).


P.T. Fletcher, S. Joshi. Riemannian Geometry for the Statistical Analysis of Diffusion Tensor Data, In Signal Processing, Vol. 87, No. 2, pp. 250--262. February, 2007.
fourth-paradigmFour SCI faculty members, Chuck Hansen, Chris Johnson, Valerio Pascucci, and Claudio Silva contributed a chapter on visualization for data-intensive science in the recently released book The Fourth Paradigm: Data-Intensive Scientific Discovery.