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

kaust workshop

A Hands-on Tutorial in Data Generation, Processing, and Delivery for High Performance Computing and High Resolution Imaging
Dates: June 28-29 From 8:30am to 12noon
Location: KAUST Library Computer Classroom

FluoRender 2.15.1 ReleasedWe are pleased to announce the 2.15.2 release of FluoRender. It mainly fixed several issues from the previous versions. Please see the release notes for more details. You can download FluoRender at

Uintah 1.6 ReleasedThe Uintah software suite is a set of libraries and applications for simulating and analyzing complex chemical and physical reactions. These reactions are modeled by solving partial differential equations on structured adaptive grids using hundreds to thousands of processors (though smaller simulations may also be run on a scientist's desktop computer). Key software applications have been developed for exploring the fine details of metal containers (encompassing energetic materials) embedded in large hydrocarbon fires. Uintah's underlying technologies have led to novel techniques for understanding large pool eddy fires as well as new methods for simulating fluid-structure interactions. The software is general purpose in nature and the breadth of simulation domains continues to grow beyond the original focus of the C-SAFE initiative.

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FluoRender 2.15.1 ReleasedWe are happy to announce the 2.15.1 release of FluoRender. For details, check the release notes and download FluoRender at

fluorender newsWe are happy to announce the 2.15 release of FluoRender. For details, check the release notes and download FluoRender at

deformetricaDeveloped in collaboration with INRIA, and available for download at, Deformetrica is a software for the statistical analysis of 2D and 3D shape data. It essentially computes deformations of the 2D or 3D ambient space, which, in turn, warp any object embedded in this space, whether this object is a curve, a surface, a structured or unstructured set of points, or any combination of them.

Deformetrica comes with two applications: 1. Registration, which computes the best possible deformation between two sets of objects, and 2. Atlas construction, which computes an average object configuration from a collection of object sets, and the deformations from this average to each sample in the collection.

FEBio2 newsIt’s with great pleasure that we announce the release of version 2.0 of FEBio (Finite Elements for Biomechanics). This new version can be downloaded here.  FEBio is an open-source finite element package, specifically designed for solving problems in the field of computational biomechanics. This new version includes some major changes and contains a number of new and exciting features. Some of the noteworthy changes and additions are listed below.

itkSNAP3 newsThe itk-SNAP project, a collaboration between UPenn's Paul Yushkevich and SCI's Guido Gerig, has released a major new version 3.0. SNAP is a software application used to segment structures in 3D medical images. It provides semi-automatic segmentation using active contour methods, as well as manual delineation and image navigation. In addition to these core functions, SNAP provides a number of supporting utilities. Version 3.0 is the first major release of itk-SNAP that is funded by the NIH grant R01 EB014346, "Continued development and maintenance of the itk-SNAP 3D image segmentation software." This version includes an almost complete rewrite of the software, along with new features focused on multi-modality image support.

For more information and downloads please visit the itk-SNAP project website.
visus-david newsThe first gigapixel, multi-view rendering of The Digital Michelangelo Project's David can now be downloaded and viewed on your iPhone, iPad, or iPod touch. The ViSUS Gigapixel David app allows you to explore the digital laser-scan of the statue David in extreme detail. With a simple pinch or spread of the fingers, users may zoom in and out to explore such details as the drill marks and scratches left by the artist Michelangelo. 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 original data is made of 8 million polygons, each about 2.0 mm in size, smaller than the thickness of 2 dimes.

fluorender newsWe are happy to announce the 2.12 release of FluoRender. For details, check the release notes and download FluoRender at

Release Notes

FluoRender 2.12

fluorender-cropCongratulations to Yong Wan and Charles Hansen, et al on their winning submission to this year's FASEB BioArt Competition

A. Kelsey Lewis1, Yong Wan1, Mary Colasanto1, Mark van Langeveld1, Ronen Schweitzer, Charles D. Hansen1, and Gabrielle Kardon

1University of Utah, Salt Lake City, UT, 2Shriners Hospital, Portland, OR, §Society for Developmental Biology