1. NA-MIC National Alliance for Medical Image Computing http://na-mic.org Slicer3 and the NA-MIC kit Sonia Pujol, Ph.D. Instructor of Radiology Surgical Planning Laboratory Harvard Medical School NA-MIC Workshop – Stanford University, September 3, 2008

2. Sonia Pujol, Ph.D. National Alliance for Medical Image Computing The NA-MIC Kit CMakeCTestDartBatch MakeXNAT 3D SlicerVTKITKNrrdKWidgets

3. Sonia Pujol, Ph.D. National Alliance for Medical Image Computing 3D Slicer Open-source application available for Windows, Linux and Mac 3.2 million lines of code Neuroscience and Image-Guided Therapy

4. Sonia Pujol, Ph.D. National Alliance for Medical Image Computing A joint effort Slicer3 is the result of a joint multi-institutions effort on a national scale: NAC, NCIGT, NA- MIC, mBIRN, fBIRN. Slicer3 strength is built-upon the experience gained with Slicer2. The transition implied 80% of code rewritten. The platform is designed to enable a collaborative development environment.

5. NA-MIC National Alliance for Medical Image Computing http://na-mic.org Three ways to use the NA-MIC kit

6. Sonia Pujol, Ph.D. National Alliance for Medical Image Computing The NA-MIC kit from three user perspectives Clinical researchers Biomedical engineers Algorithm developers

7. NA-MIC National Alliance for Medical Image Computing http://na-mic.org Interact in 3D to enhance data interpretation Clinical researchers

8. Sonia Pujol, Ph.D. National Alliance for Medical Image Computing Visualize User-driven views of anatomical structures

9. Sonia Pujol, Ph.D. National Alliance for Medical Image Computing Visualize User-driven views of anatomical structures Overlay between 2D grey-levels images and 3D anatomical structures

10. Sonia Pujol, Ph.D. National Alliance for Medical Image Computing Visualize User-driven views of anatomical structures Overlay between 2D grey-levels images and 3D anatomical structures Intuitive interaction with the 3D models

11. NA-MIC National Alliance for Medical Image Computing http://na-mic.org Extract relevant information from complex data Biomedical Engineers Inferior occipito-frontal fasciculus extracted from tensor data

12. Sonia Pujol, Ph.D. National Alliance for Medical Image Computing Analyze Advanced analysis of complex data

13. Sonia Pujol, Ph.D. National Alliance for Medical Image Computing Analyze Advanced analysis of complex data Multimodal data fusion

14. Sonia Pujol, Ph.D. National Alliance for Medical Image Computing Analyze Advanced analysis of complex data Multimodal data fusion Clinical parameters extraction

15. Sonia Pujol, Ph.D. National Alliance for Medical Image Computing Analyze Courtesy of Tom Fletcher, University of Utah. Statistical Analysis of Anatomy from Medical Images

16. NA-MIC National Alliance for Medical Image Computing http://na-mic.org #include "itkDiscreteGaussianImageFilter.h" int main ( int argc, char * argv[]) { PARSE_ARGS; typedef itk::Image ImageType; typedef itk::ImageFileReader ReaderType; typedef itk::ImageFileWriter WriterType; ReaderType::Pointer reader = ReaderType::New(); WriterType::Pointer writer = WriterType::New(); reader->SetFileName( FilterInputVolume.c_str() ); writer->SetFileName(FilterOutputVolume.c_str()); typedef itk::DiscreteGaussianImageFilter FilterType; FilterType::Pointer filter = FilterType::New(); Develop plug-ins to extend image analysis capabilities Algorithm Developers

17. Sonia Pujol, Ph.D. National Alliance for Medical Image Computing Create Integrate external executables with the Slicer3 platform

18. Sonia Pujol, Ph.D. National Alliance for Medical Image Computing Create Integrate external executables with the Slicer3 platform Develop plug-ins in C++, Tcl or Python

19. Sonia Pujol, Ph.D. National Alliance for Medical Image Computing Create Integrate external executables with the Slicer3 platform Develop plug-ins in C++, Tcl or Python Build upon the NA-MIC kit to meet your scientific goals

20. Sonia Pujol, Ph.D. National Alliance for Medical Image Computing Discrete Gaussian Filter example C++xml

21. NA-MIC National Alliance for Medical Image Computing http://na-mic.org Translate techniques into skills Clinical researchers Biomedical engineers Algorithm developers

22. Sonia Pujol, Ph.D. National Alliance for Medical Image Computing Learn NA-MIC Training Compendium & Workshops

23. Sonia Pujol, Ph.D. National Alliance for Medical Image Computing Conclusion An end-user application for image analysis An open-source environment for software development A technology delivery platform for community breakthroughs