Open-Source Cracks Open 3D Imaging Biomedicine Tools

These programs are now more easily accessible to those without advanced computer knowledge.

When you imagine uses for open-source 3D imaging software, medical applications don’t immediately spring e to mind. But at The Scientific Computing and Imaging Institute and The Center for Integrative Biomedical Computing at the University of Utah, the focus is precisely on how to apply 3D imaging and visualization to help advance medical treatments and therapies. Even better, they have gone on to develop 15 different open-source software programs that do everything from processing images to rendering complicated 3D models. The researcher team includes biologists, bio-engineers, computer scientists, mathematicians, and medical doctors among others, so it’s clear that they’ve thought about a lot of angles that might be missed by those focused in on just one research area.

Here are two examples of the open-source software anyone can download and what it can do. Seg3D is a tool allows users to explore images comprised of 3D volumes using “volume rendering and orthogonal slice view windows.” But what are the practical applications? For one, it can be used to simulate bone growth, as illustrated in these images, under electric stimulation. The study is built upon other clinical trials that showed bone growth improve with electric stimulation. Using the simulation offered by Seg3D, which includes generating accurate skeletal, as well as neuromuscular segment models, the study was able to expand upon earlier clinical findings significantly.

ImageVis3D is a volume-rendering program that has three design goals. It strives to be simple with a flexible user interface. Scalability means users can use laptops and “high end graphics workstation[s]” to “explore terabyte sized data sets.” And interactivity means that the program itself can be reused and extended in parts by other developers. If that isn’t enough, they’ve made a mobile app for it.


Torso model using ImageVis3D, image via

Like Seg3D, this program also is used for biomedical simulation of 3D volumes. Without getting too technical, it combines the processes of most other simulation studies used in biomedicine, called image-based geometric modeling. The problem with this type of simulation is that it requires a lot of computer technical skill and knowledge not readily accessible by users in biomedicine. Therefore, the developers combined the complexity of IBGM with a bottom-up software development approach that focuses on “standalone software systems for tasks that are ubiquitous across many projects.” Translation: more general, easier-to-use software. The result is a set of tools that are easily accessible to those unfamiliar with complicated computer knowledge but that can render complex biomedical models. Its accessibility is supported by a mobile app for the program.

Every one of these 15 programs allows researchers to investigate and potentially solve some very complex medical conditions. And they are all free. The labs only ask that users acknowledge the software in their publications so the researchers can continue receiving grant funding. It’s that easy.

Sherin Wing writes on social issues as well as topics in architecture, urbanism, and design. She is a frequent contributor to Archinect, Architect Magazine and other publications. She is also co-author of The Real Architect’s Handbook. She received her PhD from UCLA. Follow Sherin on Twitter at @xiaying

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