Open Source Research Tool

By Cindy Atoji

Sept. 30, 2008 | The virtual operating room may be a step closer to reality, thanks to the latest version of 3D Slicer, a new generation of freeware that has already been used for brain mapping, image guided surgery, virtual colonoscopy, and other biomedical research. The aptly named “Slicer” provides different views of the same subject on demand, such as vivid 3-D images of the brain, created from the raw data of two-dimension magnetic resonance (MR) images.

“3D Slicer has powerful visualization and analysis capabilities, intended to enable research using diagnostic medical images,” says Harvard Medical School Professor Ron Kikinis, a research radiologist who has led the project since its inception over a decade ago. The free, open source software, version 3.2 of 3D Slicer, has been funded primarily by the National Institutes of Health, with contributors from over a dozen research groups, including those who are using Slicer for advanced medical computing projects on brain tumor, prostate cancer, autism, and schizophrenia.

“As a research platform, Slicer is less structured and restricted than conventional medical device software,” says Kikinis, who says that the newly released version has plug-in capabilities that can interoperate with research PAC systems, and can handle a variety of formats, including DICOM (Digital Imaging and Communications in Medicine) formatted files.

Consisting of more than 550 thousand lines of code, mostly C++, 3D Slicer is a massive software project developed and maintained by scientists from multiple U.S. and international groups. While source code is available, says Kikinis, pre-compiled versions of Slicer are available for Windows, Linux, and Mac operating systems.

Although there have been no commercial uses of 3D Slicer yet, Kikinis says, he expects such releases soon. “Everything we distribute—Slicer, and the underlying libraries and tool kits—are all free of patented code so there are no strings attached. This was done specifically to encourage adoption and use of commercial entities into medical products.” The software is not FDA approved, and is for research, not clinical use, says Kikinis.

Slicer began as an open source collaboration between the MIT Artificial Intelligence Lab and Brigham and Women’s Hospital, as a way of integrating various aspects of image-guided medicine into a single environment. 3D Slicer is now routinely used at Brigham for pre-surgical cases, including MRI data to build 3-D models of the brain and to highlight tumors. The 3D Slicer package includes tools of analysis for Computed Tomography (CT) and MR, which include generating 3-D models, image analysis, aligning data obtained in different imaging modalities, and anatomical labeling of tissue types.

With over 10,000 downloads of 3D Slicer 3.2 already, Kikinis hopes open source availability will spark new research and development of improved methods for analysis of MRI and CT medical images. “I think we have a solid engine,” he says. “We are focusing on building application packages on top of the infrastructure, so the value of these application packages will improve over time.”


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