Harvard IIC

Slicing Up the Universe with Mac OS X

The Perseus molecular cloud complex in 12CO as displayed in OsiriX. The color scale represents the intensity of the gas emission.

The Astronomical Medicine project (or “AstroMed” for short) has shown rousing levels of initial success, giving astronomers new perspectives on star formation by utilizing the third dimension to visualize velocity data along with spatial information at varying wavelengths. The AstroMed roadmap now includes two visualization applications (3D Slicer and OsiriX), which were designed to view medical imagery such as magnetic resonance imaging (MRI) scans. The project’s goal is to abstract and generalize the visualization process to create multi-discipline solutions, appropriate for use in geophysical studies, atmospheric sciences, astronomy, and medicine.

Halle says, “In the initial experiment, there were lots of little turns and file format conversions, because this really was a medical imaging program — but by looking at areas that are star-forming regions with this tool, you can see a pattern where young stars are being formed, then you can see these same patterns in other locations that no one has ever reported. All of a sudden people can make new scientific discoveries because nobody had ever looked at the data in this way.”

“Mac is the easiest way to get a high-quality UNIX development environment complete with OpenGL on your desktop.”

Developing UNIX-based Applications in Mac OS X

3D Slicer is built on a set of open source tools dating back to before Mac OS was UNIX-based. As Apple transitioned to Mac OS X, the choice to build the operating system on open source tools frameworks including OpenGL created a developer-friendly environment poised to become a force in cross-discipline computing environments.

Halle adds, “The UNIX-like programming interface is stronger with every new release of Mac OS X. It continues to become easier for us to get the full functionality of 3D Slicer on the Mac and make it faster and more convenient for people to use.

“The researchers we work with all come from a UNIX programming environment so it is very easy for people to move transparently to the Mac and get the best of all worlds. I can use the GNU C compiler, I can use Emacs; but then if I want to do a user interface that really works well, I can use Xcode and Interface Builder to extend things. We start from a foundation which is cross platform, but the pieces that 3D Slicer is built on can be incorporated into a tool with a really nice Cocoa interface.”

3D Slicer continues to be developed as a cross-platform solution, supported and tested on approximately 50 different combinations of compilers, hardware architectures, and operating systems. Mac is Halle’s platform of choice, “If you are on a Mac, you can submit changes to the code and it gets compiled on each machine 3D Slicer supports. The great thing about using Mac is that it’s so accessible right out of the box — you install your development environment CD and everything is just there and it works. I think that is one of the greatest features — Mac is the easiest way to get a high-quality UNIX development environment complete with OpenGL on your desktop.”

Advancing Science through Technology

Advances in computational science and technology have catapulted us into a golden era in scientific computing. The work being done by the IIC to bring focus and collaboration between disparate disciplines with disparate data types is uncovering universal applicability of computational tools.

Goodman ponders the future of science imaging, “We don’t really know if the software of the future is some giant monolithic program, a 3D Photoshop with statistical and Mathematica — like features built in, or whether it is really a new a way to use existing and future packages together in a seamless pipeline.”

Regardless of the direction this journey takes, the importance of the right people asking the right questions, using the right technology, is paramount to the advancement of science.

Computers and technology are now a core part of both the questions and the answers — the Harvard IIC’s focus on cross-discipline collaboration is bringing together peers at the top of their field.

Halle says, “All of these sciences have developed their own procedures with their own algorithms in their own ecosystems. There is such a potential windfall for science if we can put them all together — that is really what Harvard IIC is all about. Computer scientists and scientists can work together as peers, each with their own strengths, to make innovations that nobody has even dreamed of before.”

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