NA-MIC National Alliance for Medical Image Computing National Alliance for Medical Image...

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NA-MIC National Alliance for Medical Image Computing http://na-mic.org National Alliance for Medical Image Computing: NAMIC Ron Kikinis, M.D. http://na-mic.org Slide 2 National Alliance for Medical Image Computing http://na-mic.org Overview Introduction Core 1 Core 2 Core 3 Support Cores Slicer Demo Slide 3 National Alliance for Medical Image Computing http://na-mic.org NIH Roadmap National Centers for Biomedical Computing (NCBC) will develop and implement the core of a universal computing infrastructure... The centers will create innovative software programs and other tools that enable the biomedical community to integrate, analyze, model, simulate, and share data on human health and disease. 7 National Centers for Biomedical Computing Funded for 5 years with the option for a second cycle Slide 4 National Alliance for Medical Image Computing http://na-mic.org NIH NCBCs Center for Computational Biology (CCB) Informatics for Integrating Biology and the Bedside (i2b2) Multiscale Analysis of Genomic and Cellular Networks (MAGNet) National Alliance for Medical Imaging Computing (NA-MIC) The National Center for Biomedical Ontology (NCBO) Physics-Based Simulation of Biological Structures (SIMBIOS) National Center for Integrative Biomedical Informatics (NCIBI) Slide 5 National Alliance for Medical Image Computing http://na-mic.org Introduction What is our problem? What is our science? Slide 6 National Alliance for Medical Image Computing http://na-mic.org What is our problem? Diagnostic Imaging produces data in increasing quantity and of increasing complexity Image Computing is about extraction of relevant information from images Slide 7 National Alliance for Medical Image Computing http://na-mic.org What is our science? Computational tools for image analysis (algorithms) Software engineering methods and applications for image analysis (tools) Slide 8 National Alliance for Medical Image Computing http://na-mic.org Structure Slide 9 National Alliance for Medical Image Computing http://na-mic.org Overview Introduction Core 1 Core 2 Core 3 Support Cores Slicer Demo Slide 10 National Alliance for Medical Image Computing http://na-mic.org Core 1 Harvard Georgia TechUNC UtahMIT Segmentation Registration Foundational Methods Structural Features and Statistics Connective Features and Statistics 1. Shape and Atlas Based Segmentation 2. Statistical Shape Analysis 3, DTI Connectivity Analysis 1. Diffusion-based Registration 2.Group Effect Maps 3. Automatic Segmentation 1. DTI Processing 2. Surface Processing 3. PDE Implementations 1. Combined Statistical/PDE Methods 1. Quantitative DTI Analysis 2. Cross-Sectional Shape Analysis 2. Stochastic Flow Models Slide 11 National Alliance for Medical Image Computing http://na-mic.org Overview Introduction Core 1 Core 2 Core 3 Support Cores Slicer Demo Slide 12 National Alliance for Medical Image Computing http://na-mic.org Core 2 GE IsomicsUCSD UCLAKitware Software Integration Software Engineering Software Quality Software Engineering Tools Data Access Tools 1. Cross-platform Build 2. Cross-platform Distribution 3. Cross-language APIs1. Software Architecture2. Software Process3. Software Quality1. Graphical programming interfaces 2. Coordinate pre-compiled tools 3. Data format interpreters1. DBP Applications 1. Grid Middleware 2. Data Grid 2. Application Methodology Distributed Computing Applications 3. Data Mediation3. Application Quality Assurance Slide 13 National Alliance for Medical Image Computing http://na-mic.org NA-MIC Kit Application 3D Slicer Toolkits ITK, VTK, KWWidgets, LONI pipeline Software Engineering Tools Cmake, Ctest, Dart2 Doxygen, CableSwig, Valgrind, StyleCheck, SourceNavigator, Ctags, Bug Tracking, CVS, Subversion, Dart, Version Control, Python, TCL/TK, Java, C/C++, OpenGL Slide 14 National Alliance for Medical Image Computing http://na-mic.org Slicer Today 460K Lines of Code Cross-Platform Tcl/Tk GUI VTK/ITK Based C++ Computing www.slicer.org > 7000 Registered Downloads >230 on slicer-users >150 on slicer-devel Slide 15 National Alliance for Medical Image Computing http://na-mic.org ITK today Over 20,000 registered downloads Mailing lists ITK Users: >1000 subscribers ITK Developers: >210 subscribers Slide 16 National Alliance for Medical Image Computing http://na-mic.org National Library of Medicine Segmentation and Registration Toolkit $12 million over 6 years Leading edge algorithms Open Source Software www.itk.org Slide 17 National Alliance for Medical Image Computing http://na-mic.org Overview Introduction Core 1 Core 2 Core 3 Support Cores Slicer Demo Slide 18 National Alliance for Medical Image Computing http://na-mic.org Core 3.1: Harvard, Dartmouth Fronto-temporal connections Cognitive and behavioral data Core 3.2: UCI, Toronto Brain regions involving DLPFC Clinical, cognitive, genetic data Core 3 Slide 19 National Alliance for Medical Image Computing http://na-mic.org Overview Introduction Core 1 Core 2 Core 3 Support Cores Slicer Demo Slide 20 National Alliance for Medical Image Computing http://na-mic.org Support Cores (# 4-7) Service, Training Dissemination Crucial support for the scientific and engineering enterprise Support core PIs also have strong scientific credentials Collaboration history through BIRN and ITK Slide 21 National Alliance for Medical Image Computing http://na-mic.org Training Slide 22 National Alliance for Medical Image Computing http://na-mic.org Dissemination: Events Slide 23 National Alliance for Medical Image Computing http://na-mic.org NA-MIC-Organization Structure Slide 24 National Alliance for Medical Image Computing http://na-mic.org The Philosophy Open Source + Open Data = Open Science Slide 25 National Alliance for Medical Image Computing http://na-mic.org The Open Source Model Enabling technology for translational research Compatible with both research and commercialization Slide 26 National Alliance for Medical Image Computing http://na-mic.org The Open Data Model Massive effort in social engineering (aka This is MY data, why should I share it?) Provides data sets and problems for algorithm developers E.g. BIRN develops data-sharing technology used as template by other efforts Slide 27 National Alliance for Medical Image Computing http://na-mic.org Challenges Imaging community is in the early stage of learning about large-scale research Everybody needs infrastructure, but who will pay for it? Translational research and software engineering is expensive and difficult. The traditional academic reward system does not work. A pure business approach does not work either. Slide 28 National Alliance for Medical Image Computing http://na-mic.org For More Information www.na-mic.org