3D Slicer is an open-source (BSD-style license) platform for medical image segmentation, registration, visualization and analysis. It represents a practical integration of innovations from a multitude of fields including medical image analysis, cross-platform software development, collaborative software development and extensible platform design. Kitware has been closely involved in many of these innovations. In particular, 3D Slicer builds upon ITK, VTK, CMake, CDash, CTK and MIDAS.
Slicer is funded by grants associated with the National Alliance for Medical Image Computing (NA-MIC) and the Neuroimaging Analysis Center (NAC) and has an extensive community behind it. The lead institute for these multi-institutional centers is Brigham and Women’s Hospital (BWH). Other funded participants include the University of Utah, GE Corporate Research, the University of North Carolina at Chapel Hill, Georgia Tech, Johns Hopkins, MIND Institute, MIT, MGH, UCLA, and many others.
To date, 3D Slicer contains 95+ modules that cover a large range of applications including tractography, endoscopy, tumor volume estimation, image guided surgery and more. Special attention has been given to documenting each module and creating tutorials that cover many of the most common use-cases for Slicer. Over 400 publications acknowledge funding from one or more Slicer-related grants. Those publications span a wide range of medical, biomedical, pharmaceutical, and other basic and applied science domains.
Version 4.0 of 3D Slicer is a systematic rewrite of the Slicer platform. The main Slicer application now adheres to high programming standards (e.g., unit tests and a clean model-view-controller design) and has adopted Qt for its GUI. Compared to Slicer 3.X, Slicer 4.0 has cut the number of lines of code necessary for most features by 70 percent. Slicer 4.0 is faster, more stable, more extensible, and more developer and user friendly than Slicer 3.X. Tcl is gone and has been replaced by Python and CMake’s Superbuild. The modules’ user interface can be effortlessly generated using Qt Designer to allow the programmer to focus on algorithms.
Slicer 4.0 alpha (developer) was release in early September. The Beta release is scheduled for December 2010 and the full Slicer 4.0 release is scheduled for February 2011. However, much of the Slicer 4.0 platform is already complete. We are encouraging our friends to begin using Slicer 4.0 now to ensure it achieves the lofty, yet practical goals we have set.
To learn more about the NA-MIC community, visit na-mic.org, to download Slicer, visit slicer.org and to browse the collection of Slicer-related publications (hosted on MIDAS), visit slicer.org/publications.
Contrast enhanced CT (with the stereotactic frame of a gamma-knife device), anatomical MRI and diffusion tensor MRI have been registered and segmented to produce this image. Fiber tracking allows the clinician to examine brain connectivity. Neurosurgeons use such fused views to determine tumor margins and surgical paths. This image was generated using 3D Slicer. In particular, 3D Slicers’ affine registration module, DTI fiber tracking module, and connected component segmentation module were used. All of these modules are built using VTK and ITK and are available as open-source as part of the 3D Slicer distribution. This image was generated by Andras Jakab, University of Debrecen, Medical School and Health Science Center, Hungary. This image won 2nd place in the 2008 Best Biomedical Visualization Contest hosted by Kitware.