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.


rob aimbeCongratulations to Rob MacLeod for being elected a Fellow of the American Institute for Medical and Biological Engineering (AIMBE). After very careful consideration, including the most rigorous and selective review process in AIMBE's history, Rob was among an impressive group who were elected to the 2017 Class of the College of Fellows.

christmas teapots 9Congratulations to Laura Lediaev, who won the Utah Rendering Competition for the third year in a row. Laura's entry, titled Christmas Teapots, was the overall winner and receiver of the audience choice award. The rendering is based on creating time-varying composites of light layers in order to simulate the effect of twinkling Christmas lights and flickering candles. The scene has 30 lights, one inside each teapot. Light layers are created during rendering by saving the contribution of each light into its own image. This produced 30 images/layers. Each light produced 4,000 samples per pixel. That adds up to 120,000 samples per pixel after compositing. Laura allowed up to 10 diffuse light bounces and 200 specular bounces.

For more information on the project, visit

miriah DYACongratulations to Miriah Meyer, who receive this year's University of Utah Distinguished Alumni Award. To celebrate the founding of the University of Utah in 1850, the Alumni Association each year recognizes alumni and honorary alumni who have excelled professionally, served the local and national communities, and supported the university in its mission.

A reception and dinner will be held Friday, March 3rd at the Little America Hotel in Salt Lake City. Tickets for the reception are available through the University of Utah Alumni Association.
scix adSCI Institute Technical Exchange (SCI X) was created to strengthen the interactions between the SCI Institute and other academic researchers, and also those companies conducting or wishing to conduct research with the University and inspire them to increase their collaborative efforts in research and new product development. 

SCI X is intended to provide its guests access to unique resources and expertise found within the SCI Institute, creating an expanded relationship between the SCI  Institute and our past, present and future academic and industry collaborators.

F1.mediumAn image of the ulnar-mammary syndrome, visualized with FluoRender, was chosen for the cover of Disease Models and Mechanisms. CIBC Collaborator, Gabrielle Kardon's article can be found here in it's entirety.

Development of a subset of forelimb muscles and their attachment sites requires the ulnar-mammary syndrome gene Tbx3.
Mary P. Colasanto, Shai Eyal, Payam Mohassel, Michael Bamshad, Carsten G. Bonnemann, Elazar Zelzer, Anne M. Moon, Gabrielle Kardon

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.

fluorender 2 20We are excited to announce the latest release of FluoRender, version 2.20, which incorporates improvements, bug fixes, and new features.

You can download FluoRender here

New Features:

  • Clustering algorithms. Three clustering algorithms for segmentation are added: expectation-maximization on Gaussian mixture, DBSCAN, and k-means. Users can use these methods in the "Component" window.
  • Improved tracking algorithms. Tracking accuracy has been improved. We improved the algorithm for generating the track map and incorporated clustering algorithms to automatically segment during tracking. Users can also adjust a series of parameters in the "Tracking" window to fine tune the tracking.
  • A new 4D script for tracking sparse particles. The 4D script allows users to track selected features in a time sequence. No initial segmentation is required for it to work. It can be used to track sparse and small features conveniently.
  • A density setting for component generation. The density setting has been added in the basic component generation. Its concept is based on the clustering algorithm DBSCAN. However, its implementation is based on the synthetic brainbows algorithm, which uses GPU to compute segmentation of dense data sets.
  • Render view output enlargement. The option has been added when the render view is captured and saved as an image. Users can set an output image size larger than the render view size.
  • 4D script list. The list of built-in 4D scripts has been added to the "Record/Export" panel. Users can easily select and switch 4D scripts without browsing to the actual files.

Fire2016 PanelAlex Lex, Bei Wang Phillips, and Chris Johnson were chosen to present at the Future in Review Conference held at the Stein Eriksen Lodge in Park City, Utah.

What is Future in Review? Hosted by Mark Anderson, founder and publisher of the Strategic News Service™, the Future in Review® (FiRe) conference exposes world experts and participants to new ideas in a manner that produces an accurate portrait of the future in technology, including the global economy, cloud computing, biology and medical diagnostics, policy, netbooks, space travel, sustainability, and other fields that contribute to technology outcomes. (Strategic News Service and the SNS weekly global report have been accurately predicting the technology industry's future since 1995.)

This year's theme was titled "The Power of Flows."
Photo courtesy of Kris Krüg

Charles Hansen 591x394Utah engineers co-developing space simulation software for planetariums and home computers.

Sept. 7, 2016 – If space is the final frontier, OpenSpace could become the final frontier in space simulation software.

Computer scientists from the University of Utah will be working with researchers from New York University's Tandon School of Engineering and the American Museum of Natural History (AMNH) to develop OpenSpace, an open-source 3-D software for visualizing NASA astrophysics, heliophysics, planetary science and Earth science missions for planetariums and other immersive environments. The software also will be developed for use in schools and on home computers.

sciencenodeChris Johnson speaks with ScienceNode on visualizations as a collaborative process of discovery, and a crucial step on path to knowledge.

Read the full article here.
fluorender 2 19We are excited to announce the latest release of FluoRender, version 2.19.4, which incorporates improvements, bug fixes, and new features.

Download FluoRender

In this release, we mainly improved the usability of a series of functions for 4D analysis, including the component analyzer, 4D scripts, paint brush tools, and format supports. We have also made a series of video tutorials and published them on YouTube.