Post on 01-Apr-2015
NA-MICNational Alliance for Medical Image Computing http://na-mic.org
National Alliance for Medical Image Computing: NAMIC
Ron Kikinis, M.D.
http://na-mic.org
National Alliance for Medical Image Computing http://na-mic.org
Overview
• Introduction
• Core 1
• Core 2
• Core 3
• Support Cores
• Slicer Demo
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
National Alliance for Medical Image Computing http://na-mic.org
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 http://na-mic.org
Introduction
• What is our problem?
• What is our science?
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
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)
National Alliance for Medical Image Computing http://na-mic.org
Structure
National Alliance for Medical Image Computing http://na-mic.org
Overview
• Introduction
• Core 1
• Core 2
• Core 3
• Support Cores
• Slicer Demo
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 Methods1. Quantitative DTI Analysis
2. Cross-Sectional Shape Analysis2. Stochastic Flow Models
Figure 3: a) A rendering of a cortical surface, extracted from MRI, shows a degree of noise that significantlyaffects successive processing. b) A feature-preserving, PDE-based filter smooths away small-scale noisewhile preserving sharp features such as the concave regions of the sulci.
(a) (b)
National Alliance for Medical Image Computing http://na-mic.org
Overview
• Introduction
• Core 1
• Core 2
• Core 3
• Support Cores
• Slicer Demo
National Alliance for Medical Image Computing http://na-mic.org
Core 2GE
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’s
1. Software Architecture
2. Software Process
3. Software Quality1. Graphical programming interfaces
2. Coordinate pre-compiled tools
3. Data format interpreters
1. DBP Applications1. Grid Middleware
2. Data Grid2. Application Methodology
Distributed Computing
Applications
3. Data Mediation 3. Application Quality Assurance
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
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
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
National Alliance for Medical Image Computing http://na-mic.org
National Library of MedicineSegmentation and Registration Toolkit
$12 million over 6 yearsLeading edge algorithmsOpen Source Software
www.itk.orgwww.itk.org
National Alliance for Medical Image Computing http://na-mic.org
Overview
• Introduction
• Core 1
• Core 2
• Core 3
• Support Cores
• Slicer Demo
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
National Alliance for Medical Image Computing http://na-mic.org
Overview
• Introduction
• Core 1
• Core 2
• Core 3
• Support Cores
• Slicer Demo
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 PI’s also have strong scientific credentials
• Collaboration history through BIRN and ITK
National Alliance for Medical Image Computing http://na-mic.org
Training
National Alliance for Medical Image Computing http://na-mic.org
Dissemination: Events
National Alliance for Medical Image Computing http://na-mic.org
NA-MIC-Organization StructureExternal Advisory
Committee
GovernanceCommittee
Stephen Wong
PI: Core 7 (Management)
Ron Kikinis
Chair, GovernanceTask Force
Steve Pieper
Chair, UtlizationTask Force
e
Eric GrimsonChair, IP
Task Force
Randy GollubChair, Data Sharing
Task Force
Bill Lorensen
Chair, Process ChangeMgt Task Force
Stephen Wong
Chair, Project ChangeMgt Task Force
Will Shroeder
Chair, IT Task Force
Utilization TFProject
ManagementOffice
Governance
TF
IntellectualProperty TF
Data Sharing TF
InformationTechnology TF
Project ChangeManagement TF
Process ChangeManagement TF
NAMIC Cores 1- 6
Eric Grimson
PI: Core 1 (Algorithms)
Bill Lorensen
PI: Core 2 (Engineerg)
Steve Potkins, MarthaShenton
PIs: Core 3 (DrivenBiological Projects)
Will Shroeder
PI: Core 4(Service)
Randy Gollub
PI: Core 5 (Training)
Steve PieperPI: Core 6
(Dissemination)
Randy Gollub
Chair, TrainingTask Force
Traing &Education TF
Steve Pieper
Chair, Content MgtTask Force
ContentManagement TF
Steve Potkin
Chair, Image GeneticsTask Force
ImagingGenetics TF
Ron Kikinis: NAMIC PI
Stephen Wong: Co-PI
National Alliance for Medical Image Computing http://na-mic.org
The Philosophy
Open Source
+
Open Data
=
Open Science
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
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
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.
National Alliance for Medical Image Computing http://na-mic.org
For More Information
www.na-mic.org