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.

SCI Publications

2011


 M.J. Mlodzianoski, J.M. Schreiner, S.P. Callahan, K. Smolková, A. Dlasková, J. Šantorová, P. Ježek, J. Bewersdorf. “Sample drift correction in 3D fluorescence photoactivation localization microscopy,” In Optics Express, Vol. 19, No. 16, pp. 15009--15019. 2011.
DOI: 10.1364/OE.19.015009

2008


 L. Bavoil, S.P. Callahan, and C.T. Silva. “Robust Soft Shadow Mapping with Depth Peeling,” In Journal of Graphics Tools, Vol. 13, No. 1, pp. 19--30. 2008.


S.P. Callahan, J.H. Callahan, C.E. Scheidegger, C.T. Silva. “Direct Volume Rendering: A 3D Plotting Technique for Scientific Data,” In Computing in Science and Engineering, Vol. 10, No. 1, pp. 88--92. 2008.


S.P. Callahan. “Adaptive Visualization of Dynamic Unstructured Meshes,” SCI Technical Report, No. UUSCI-2008-003, Note: Ph.D. Thesis, University of Utah School of Computing, 2008.


S.P. Callahan, C.T. Silva. “Image-Space Acceleration for Direct Volume Rendering of Unstructured Grids using Joint Bilateral Upsampling,” SCI Technical Report, No. UUSCI-2008-002, University of Utah, 2008.


S.P. Callahan, J. Freire, C.E. Scheidegger, C.T. Silva, and H.T. Vo. “Towards a Provenance-Enabling ParaView,” In Proceedings of the Second International Provenance and Annotation Workshop (IPAW 2008), pp. 120--127. 2008.


D. Koop, C.E. Scheidegger, S.P. Callahan, J. Freire, C.T. Silva. “VisComplete: Automating Suggestions for Visualization Systems,” In IEEE Transactions on Visualization and Computer Graphics (Proceedings of IEEE Visualization 2008), Vol. 14, No. 6, pp. 1691--1698. 2008.


L. Lins, D. Koop, E.W. Anderson, S.P. Callahan, E. Santos, C.E. Scheidegger, J. Freire, C.T. Silva. “Examining Statistics of Workflow Evolution Provenance: A First Study,” In Proceedings of the 20th International Conference on Scientific and Statistical Database Management (SSDBM), pp. 573--579. 2008.
DOI: 10.1007/978-3-540-69497-7_40


L. Moreau, B. Ludäscher, I. Altintas, R. Barga, S. Bowers, S.P. Callahan, G. Chin Jr., B. Clifford, S. Cohen, S. Cohen-Boulakia, S. Davidson, E. Deelman, L. Digiampietri, I. Foster, J. Freire, J. Frew, J. Futrelle, T. Gibson, Y. Gil, C. Goble, J. Golbeck, P. Groth, D. A. Holland, S. Jiang, J. Kim, D. Koop, A. Krenek, T. McPhillips, G. Mehta, S. Miles, D. Metzger, S. Munroe, J. Myers, B. Plale, N. Podhorszki, V. Ratnakar, E. Santos, C.E. Scheidegger, K. Schuchardt, M. Seltzer, Y. L. Simmhan, C.T. Silva, P. Slaughter, E. Stephan, R. Stevens, D. Turi, H.T. Vo, M. Wilde, J. Zhao, Y. Zhao. “The First Provenance Challenge,” In Concurrency and Computation: Practice and Experience, Vol. 20, No. 5, pp. 409--418. April, 2008.


C.E. Scheidegger, D. Koop, E. Santos, H.T. Vo, S.P. Callahan, J. Freire, C.T. Silva.. “Tackling the Provenance Challenge One Layer at a Time,” In Concurrency Computat.: Pract. Exper., Vol. 20, No. 5, pp. 473--483. 2008.

2007


 E.W. Anderson, S.P. Callahan, C.E. Scheidegger, J.M. Schriener, C.T. Silva. “Hardware-Assisted Point-Based Volume Rendering of Tetrahedral Meshes,” In Proceedings of SIBGRAPI 2007, pp. 163--170. 2007.


E.W. Anderson, S.P. Callahan, D.A. Koop, E. Santos, C.E. Scheidegger, H.T. Vo, J. Freire, C.T. Silva. “VisTrails: Using Provenance to Streamline Data Exploration,” In Poster Proceedings of the International Workshop on Data Integration in the Life Sciences (DILS) 2007, Note: Poster presentation, 2007.


L. Bavoil, S.P. Callahan, A. Lefohn, J.L.D. Comba, C.T. Silva. “Multi-Fragment Effects on the GPU using the k-Buffer,” In ACM Symposium on Interactive 3D Graphics and Games (i3D), pp. 97--104. 2007.


F.F. Bernardon, S.P Callahan, J.L.D. Comba, C.T. Silva. “An Adaptive Framework for Visualizing Unstructured Grids with Time-Varying Scalar Fields,” In Journal on Parallel Computing, Vol. 33, No. 6, pp. 391--405. 2007.


F.F. Bernardon, L.K. Ha, S.P. Callahan, J.L.D. Comba, C.T. Silva. “Interactive Transfer Function Specification for Direct Volume Rendering of Disparate Volumes,” SCI Institute Technical Report, No. UUSCI-2007-007, University of Utah, 2007.


S.P. Callahan, L. Bavoil, V. Pascucci, C.T. Silva. “Progressive Volume Rendering of Large Unstructured Grids,” In IEEE Transactions on Visualization and Computer Graphics, Vol. 13, No. 1, pp. 1307-1314. 2007.


C.T. Silva, J. Freire, S.P. Callahan. “Provenance for Visualizations: Reproducibility and Beyond,” In IEEE Computing in Science and Engineering, Vol. 9, No. 5, pp. 82--89. 2007.


H.T. Vo, S.P. Callahan, P. Lindstrom, V. Pascucci, C.T. Silva. “Streaming Simplification of Tetrahedral Meshes,” In IEEE Transactions on Visualization and Computer Graphics, Vol. 13, No. 1, pp. 145--155. Jan/Feb, 2007.


H.T. Vo, S.P. Callahan, N. Smith, C.T. Silva, W. Martin, D. Owen, D.M. Weinstein. “iRun: Interactive Rendering of Large Unstructured Grids,” In Proceedings of the 7th Eurographics Symposium on Parallel Graphics and Visualization (EGPGV 2007), pp. 93--100. 2007.

2006


 E.W. Anderson, S.P. Callahan, G.T.Y. Chen, J. Freire, E. Santos, C.E. Scheidegger, C.T. Silva, H.T. Vo. “Visualization in Radiation Oncology: Towards Replacing the Laboratory Notebook,” SCI Institute Technical Report, No. UUSCI-2006-017, University of Utah, 2006.