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

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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

Transcript of NA-MIC National Alliance for Medical Image Computing National Alliance for Medical Image Computing:...

Page 1: NA-MIC National Alliance for Medical Image Computing  National Alliance for Medical Image Computing: NAMIC Ron Kikinis, M.D. .

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

Page 2: 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 http://na-mic.org

Overview

• Introduction

• Core 1

• Core 2

• Core 3

• Support Cores

• Slicer Demo

Page 3: 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 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

Page 4: 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 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)

Page 5: 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 http://na-mic.org

Introduction

• What is our problem?

• What is our science?

Page 6: 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 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

Page 7: 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 http://na-mic.org

What is our science?

• Computational tools for image analysis (algorithms)

• Software engineering methods and applications for image analysis (tools)

Page 8: 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 http://na-mic.org

Structure

Page 9: 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 http://na-mic.org

Overview

• Introduction

• Core 1

• Core 2

• Core 3

• Support Cores

• Slicer Demo

Page 10: 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 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)

Page 11: 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 http://na-mic.org

Overview

• Introduction

• Core 1

• Core 2

• Core 3

• Support Cores

• Slicer Demo

Page 12: 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 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

Page 13: 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 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

Page 14: 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 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

Page 15: 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 http://na-mic.org

ITK today

• Over 20,000 registered downloads

• Mailing lists– ITK Users: >1000 subscribers – ITK Developers: >210 subscribers

Page 16: 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 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

Page 17: 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 http://na-mic.org

Overview

• Introduction

• Core 1

• Core 2

• Core 3

• Support Cores

• Slicer Demo

Page 18: 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 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

Page 19: 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 http://na-mic.org

Overview

• Introduction

• Core 1

• Core 2

• Core 3

• Support Cores

• Slicer Demo

Page 20: 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 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

Page 21: 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 http://na-mic.org

Training

Page 22: 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 http://na-mic.org

Dissemination: Events

Page 23: 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 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

Page 24: 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 http://na-mic.org

The Philosophy

Open Source

+

Open Data

=

Open Science

Page 25: 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 http://na-mic.org

The Open Source Model

• Enabling technology for translational research

• Compatible with both research and commercialization

Page 26: 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 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

Page 27: 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 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.

Page 28: 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 http://na-mic.org

For More Information

www.na-mic.org