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.

Software News

epinomeEarly detection and rapid response to infectious-disease outbreaks rely on effective decision making based on information from disparate sources. To improve decision-making in outbreak detection and response, it's important to understand how public health practitioners seek relevant information. Epinome, a user-centric visual-analytics system, supports research on decision-making in public health, particularly evaluation of information search strategies. Epinome facilitates investigation of scripted high-fidelity large-scale simulated disease outbreaks. Its dynamic environment seamlessly evolves and adapts as the user's tasks and focus change. This video shows how the Epinome system facilitates interactive simulations of disease outbreaks.

Read Full Article (pdf)

Y. Livnat, T.-M. Rhyne, M. Samore. "Epinome: A Visual-Analytics Workbench for Epidemiology Data," In IEEE Computer Graphics and Applications, Vol. 32, No. 2, pp. 89--95. 2012. ISSN: 0272-1716 DOI: 10.1109/MCG.2012.31
fluorenderA stunning FluoRender image visualizing embryogenesis is featured in a set on's "Cell Picture Show." See "Limbs" on slide #8:

By A. Kelsey Lewis, Gabrielle Kardon, Yong Wan (University of Utah) and Ronen Schweitzer (Oregon Health and Science University)

Caption: In mice, muscles (red), tendons (green), and nerves (blue) of the limbs are largely established by ~14.5 after fertilization. In humans, this occurs after ~9 weeks of embryogenesis. Image: Here the limb of a Scleraxis-GFPmouse embryo is imaged by confocal microscopy (Nikon A1R). Scleraxis is a basic helix-turn-helix transcription factor expressed in tendon cells. Antibodies to mysosin (red) and neurofilaments (blue) label muscle and nerves, respectively. 3D rendering by FluoRender.
febioThe MRL Software development team is excited to announce the arrival of version 1.4 of FEBio (Finite Elements for Biomechanics).

Download FEBio 1.4

geneologyResearch groups from the Department of Human Genetics and the Scientific Computing and Imaging Institute (SCI) have recently attracted widespread commercial and academic interest in their software inventions related to genetic data processing and the display of ancestral data.
fluorender-releaseWe are happy to announce the 2.8 release of FluoRender. For details, check the release notes and download FluoRender at



davidSCI announces the first gigapixel, multi-view rendering of The Digital Michelangelo Project's David.The David model consists of 933 million triangles from a laser-scan of the original statue created by Professor Marc Levoy and members of The Digital Michelangelo Project at Stanford university. The model was aligned by Benedict Brown and Szymon Rusinkiewicz using the non-rigid alignment method described in their 2007 SIGGRAPH paper.

fluorender-2-7We are happy to announce the 2.7 release of FluoRender. There are some exciting improvements in this version, including a rewritten rendering core, which improves the overall quality and performance of FluoRender. FluoRender can render more fine details, especially in the low signal intensity regions. It renders both volumes and mesh data faster, especially at higher zoom. And parameter adjusting feels smoother. For details, check the release notes and download FluoRender at

visus-newsViSUS software has received a great deal of news recently due to it's ability to quickly generate small preview images from very large images.

fluorender-nikonSCI collaborator Hideo Otsuna, won 2nd place in Nikon's Small World photomicrography competition 2010 for his image of a 5-day old zebrafish rendered with FluoRender. Nikon Small World is regarded as the leading forum for showcasing the beauty and complexity of life as seen through the light microscope. For over 30 years, Nikon has rewarded the world's best photomicrographers who make critically important scientific contributions to life sciences, bio-research and materials science. The prize for Hideo as the winner of the 2nd place is $2000 toward the purchase of Nikon equipment.

fluorender-2-6The FluoRender development team is pleased to announce the release of FluoRender 2.6. The new version has a number of new features. For details and downloads see the FluoRender Documentation page.
vistrails-1-5The VisTrails development team is pleased to announce the release of VisTrails 1.5. The new version contains quite a list of improvements and bug fixes. For details, see the release notes.

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