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

soundartCongratulations to Erik Brunvand and Nina McCurdy whose paper, Making Noise: Using Sound-­Art to Explore Technological Fluency, will receive one of three best paper awards at SIGCSE 2017.

Abstract: We describe our experience designing and delivering a general education technological fluency course that frames the discussion of computer science and engineering technology (electronics and programming) in the context of sound-art: art that uses sound as its medium. This course is aimed at undergraduate students from a wide variety of backgrounds and is designed to fit into the "Intellectual Explorations" area of a general undergraduate program. The goal is to introduce computer engineering and computational principles to non-CS students through an exploration of sound-art, experimental and electronic music, noise-making circuits, hardware hacking, and circuit bending.

vis miccaiWith fall conferences in full swing, the SCI Institute and our alumni had an amazing showing.

Alex Bigelow and SCI alumnus Roni Choudhury, who, along with Jeff Baumes from Kitware received the Visualization in Practice Best Paper Award at the IEEE Visualization Conference for their paper: Resonant Laboratory and Candela: Spreading your Visualization Ideas to the Masses. Chris Johnson was a participant in the panel: Pathways for Theoretical Advances in Visualization, moderated by Min Chen, which won the best panel award at the IEEE Visualization Conference. The other panelists included Georges Grinstein, Jessie Kennedy, Tamara Munzner, and Melanie Tory. Finally, congratulations to SCI Alumnus Julien Tierny, who with Hamish Carr received the Scientific Visualization Best Paper Award at the IEEE Visualization Conference for their paper: Jacobi Fiber Surfaces for Bivariate Reeb Space Computation.

Yong Wan recieved best poster at BioVis for his display of the functionality and application of FluoRender.

Caleb Rottman, who was a finalist for the MICCAI 2016 Young Scientist Award for his paper: Diffeomorphic Density Registration in Thoracic Computed Tomography. Caleb Rottman, Ben Larson, Pouya Sabouri, Amit Sawant, Sarang Joshi. Also at MICCAI, recent SCI Alumnus Miaomiao Zhang (Ph.D. 2015), was another of the finalists for the Young Scientist Award for her paper: Low-Dimensional Statistics of Anatomical Variability Via Compact Representation of Image Deformations. Miaomiao Zhang, William Sandy Wells, Polina Golland.

making sense of dataMaking Sense of Data, by Miriah Meyer and Danyel Fisher now available for pre-order from Amazon.

From Amazon: You have a mound of data sitting in front of you and a suite of computation tools at your disposal. And yet, you're stumped as to how to turn that data into insight. Which part of that data actually matters, and where is this insight hidden?

If you're a data scientist who struggles to navigate the murky space between data and insight, this book will help you think about and reshape data for visual data exploration. It's ideal for relatively new data scientists, who may be computer-knowledgeable and data-knowledgeable, but do not yet know how to create effective, explorable representations of data.

pacificvis16Congratulations Bei and Valerio and SCI alumni: Paul Rosen, Guoning Chen and Harsh Bhatia who were awarded Best Paper at IEEE PacificVis 2016.

Critical Point Cancellation in 3D Vector Fields: Robustness and Discussion Primoz Skraba (Jozef Stefan Institute), Paul Rosen (University of South Florida), Bei Wang (University of Utah), Guoning Chen (University of Houston), Harsh Bhatia (Lawrence Livermore National Laboratory), Valerio Pascucci (University of Utah)
Congratulations to James King, Thomas Gilray, Robert M. Kirby and Matthew Might, whose paper: Dynamic Sparse-Matrix Allocation on GPUs, won the International SuperComputing PRACE-ISC Award 2016
ivapp 16Congratulations to Hao Nguyen for winning both best paper and best PhD progect at the International Conference on Information Visualization Theory and Applications (IVAPP).

Best Paper: H. Nguyen, P. Rosen, Improved identification of data correlations through correlation coordinate plots, Intl. Conf. on Information Visualization Theory and Applications (IVAPP), 2016.

Best PhD Project: H. Nguyen, P. Rosen, Data Scalable Approach for Identifying Correlation in Large and Muti-Dimensional Data, Intl. Conf. on Information Visualization Theory and Applications Doctoral Consortium (IVAPP), 2016.
spatio-temporal-book newsS. Durrleman, P.T. Fletcher, G. Gerig, M. Niethammer, X. Pennec (Eds.)

Third International Workshop, STIA 2014, Held in Conjunction with MICCAI 2014, Boston, MA, USA, September 18, 2014, Revised Selected Papers

Series: Image Processing, Computer Vision, Pattern Recognition, and Graphics, Vol. 8682, Springer LNCS

TopoStatMethComplexData news Edited by J. Bennett, F. Vivodtzev, V. Pascucci

  • Latest peer-reviewed results in a growing research area
  • Many applications in science and engineering
  • Important contributions to the fields of mathematics and computer science

This book contains papers presented at the Workshop on the Analysis of Large-scale, High-Dimensional, and Multi-Variate Data Using Topology and Statistics, held in Le Barp, France, June 2013. It features the work of some of the most prominent and recognized leaders in the field who examine challenges as well as detail solutions to the analysis of extreme scale data.

miaomiao miccaiCongratulations to PhD student Miaomiao Zhang, who won the MICCAI 2014 Young Scientist Award (a.k.a., best paper award) for her paper:

M. Zhang, P. T. Fletcher, Bayesian Principal Geodesic Analysis in Diffeomorphic Image Registration, MICCAI 2014.

MICCAI is the premiere venue in medical image analysis with ~1000 attendees.
Journal of Cardiovascular ElectrophysiologyCongratulations to Josh Blauer, Darrell Swenson, and Rob MacLeod, et. al. whose paper:

J.J.E. Blauer, D. Swenson, K. Higuchi, G. Plank, R. Ranjan, N. Marrouche, and R.S. MacLeod. Sensitivity and Specificity of Substrate Mapping: An In Silico Framework for the Evaluation of Electroanatomical Substrate Mapping Strategies,” In Journal of Cardiovascular Electrophysiology, In Journal of Cardiovascular Electrophysiology, Vol. 25, No. 7, pp. 774--780. May, 2014.

is featured on the cover of the July 2014 issue of the Journal of Cardiovascular Electrophysiology.
Deformation Causes Vascular Alignment During AngiogenesisJeff Weiss speaks with Deputy Editor of the AJP Heart and Circulatory Physiology Journal Dr. Merry Lindsey about the recent MRL publication:

Clayton J. Underwood, Lowell T. Edgar, James B. Hoying, Jeffrey A. Weiss "Cell-generated traction forces and the resulting matrix deformation modulate microvascular alignment and growth during angiogenesis" Am J Physiol Heart Circ Physiol, published July 15, 2014. DOI: 10.1152/ajpheart.00995.2013.

Listen to the podcast here.