NA-MIC National Alliance for Medical Image Computing National Alliance for Medical Image Computing: NAMIC Ron Kikinis, M.D.

National Alliance for Medical Image Computing Overview Introduction Core 1 Core 2 Core 3 Support Cores Slicer Demo

National Alliance for Medical Image Computing 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

National Alliance for Medical Image Computing NIH NCBC’s 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)

National Alliance for Medical Image Computing Introduction What is our problem? What is our science?

National Alliance for Medical Image Computing 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

National Alliance for Medical Image Computing What is our science? Computational tools for image analysis (algorithms) Software engineering methods and applications for image analysis (tools)

National Alliance for Medical Image Computing Structure

National Alliance for Medical Image Computing Overview Introduction Core 1 Core 2 Core 3 Support Cores Slicer Demo

National Alliance for Medical Image Computing 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

National Alliance for Medical Image Computing Overview Introduction Core 1 Core 2 Core 3 Support Cores Slicer Demo

National Alliance for Medical Image Computing 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 API’s1. 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

National Alliance for Medical Image Computing 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

National Alliance for Medical Image Computing Slicer Today 460K Lines of Code –Cross-Platform Tcl/Tk GUI –VTK/ITK Based C++ Computing –> 7000 Registered Downloads –>230 on slicer-users –>150 on slicer-devel

National Alliance for Medical Image Computing ITK today Over 20,000 registered downloads Mailing lists –ITK Users: >1000 subscribers –ITK Developers: >210 subscribers

National Alliance for Medical Image Computing National Library of Medicine Segmentation and Registration Toolkit $12 million over 6 years Leading edge algorithms Open Source Software

National Alliance for Medical Image Computing Overview Introduction Core 1 Core 2 Core 3 Support Cores Slicer Demo

National Alliance for Medical Image Computing 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

National Alliance for Medical Image Computing Overview Introduction Core 1 Core 2 Core 3 Support Cores Slicer Demo

National Alliance for Medical Image Computing Support Cores (# 4-7) Service, Training Dissemination Crucial support for the scientific and engineering enterprise Support core PI’s also have strong scientific credentials Collaboration history through BIRN and ITK

National Alliance for Medical Image Computing Training

National Alliance for Medical Image Computing Dissemination: Events

National Alliance for Medical Image Computing NA-MIC-Organization Structure

National Alliance for Medical Image Computing The Philosophy Open Source + Open Data = Open Science

National Alliance for Medical Image Computing The Open Source Model Enabling technology for translational research Compatible with both research and commercialization

National Alliance for Medical Image Computing 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

National Alliance for Medical Image Computing 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.

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