Transcript Slicer3 and the NA-MIC kit NA-MIC National Alliance for Medical Image Computing -mic.org

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
Les joueurs de cartes – Paul Cezanne (1839-1906)- Metropolitan Museum of Arts, New-York
NA-MIC Workshop – MICCAI 2008, September 10, 2008
The NA-MIC Kit
3D Slicer
CMake
VTK
ITK
CTest
Dart
Nrrd
KWidgets
Batch Make XNAT
Funded by the NIH Roadmap for Biomedical Image Computing
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
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, NAMIC, 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.
Sonia Pujol, Ph.D.
National Alliance for Medical Image Computing
NA-MIC
National Alliance for Medical Image Computing
http://na-mic.org
Three ways to use the NA-MIC kit
The NA-MIC kit from three
user perspectives
• Clinical researchers
• Biomedical engineers
• Algorithm developers
Sonia Pujol, Ph.D.
National Alliance for Medical Image Computing
NA-MIC
Clinical
researchers
National Alliance
for Medical
Image Computing
http://na-mic.org
Interact in 3D to
enhance data
interpretation
Visualize
•User-driven views of
anatomical structures
•Overlay between 2D
grey-levels images and
3D anatomical structures
•Intuitive interaction with
the 3D models
Sonia Pujol, Ph.D.
National Alliance for Medical Image Computing
NA-MIC
Biomedical
National Alliance
for MedicalEngineers
Image Computing
http://na-mic.org
Extract relevant
information from
complex data
Inferior occipito-frontal fasciculus extracted from tensor data
Analyze
•Advanced analysis of
complex data
•Multimodal data fusion
•Clinical parameters
extraction
Sonia Pujol, Ph.D.
National Alliance for Medical Image Computing
Analyze
Statistical Analysis of Anatomy from Medical Images
Courtesy of Tom Fletcher, University
of Utah.
Sonia Pujol, Ph.D.
National Alliance for Medical Image Computing
NA-MIC Algorithm Developers
National Alliance for Medical Image Computing
http://na-mic.org
N
K
ln p( X |  ,  , )   In {  k N xn | k ,  k }
n 1
k 1
Develop plug-ins to extend
image analysis capabilities
#include "itkDiscreteGaussianImageFilter.h"
int main ( int argc, char * argv[])
{
PARSE_ARGS;
typedef itk::Image< short, 3 > ImageType;
typedef itk::ImageFileReader< ImageType > ReaderType;
typedef itk::ImageFileWriter< ImageType > WriterType;
ReaderType::Pointer reader = ReaderType::New();
WriterType::Pointer writer = WriterType::New();
reader->SetFileName( FilterInputVolume.c_str() );
writer->SetFileName(FilterOutputVolume.c_str());
typedef itk::DiscreteGaussianImageFilter <ImageType, ImageType> FilterType;
FilterType::Pointer filter = FilterType::New();
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
Sonia Pujol, Ph.D.
National Alliance for Medical Image Computing
Discrete Gaussian Filter
example
C++
Sonia Pujol, Ph.D.
National Alliance for Medical Image Computing
xml
Clinical researchers
NA-MIC
National Alliance
for Medicalengineers
Image Computing
Biomedical
http://na-mic.org
Algorithm developers
Translate
techniques
into skills
Learn
NA-MIC Training
Compendium &
Workshops
Sonia Pujol, Ph.D.
National Alliance for Medical Image Computing
Learn
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
Sonia Pujol, Ph.D.
National Alliance for Medical Image Computing