1. The cancer Biomedical Informatics Grid™ (caBIG™): In Vivo Imaging Workspace Projects
Fred Prior, Ph.D.
Mallinckrodt Institute of Radiology
Washington University in St. Louis

2. caBIG will facilitate sharing of infrastructure, applications, and data
Common, widely distributed informatics platform
Shared vocabulary, data elements, data models
Common standard for developing applications

4. In Vivo Imaging Workspace
Project 1: Middleware
Project 2: AIM: Annotation and Image Markup
Project 3: Vocabulary
Project 4: XIP: Extensible Imaging Platform
Terminologies & CDEs
Image Annotation
Metadata storage formats
Queries & Analysis
Vocabularies & CDEs
Data Capture
Formats & Tools
Data Re-Use Applications
NLP
Metadata for Images

5. Search for Images
Retrieve Results

6. One of the goals of the In Vivo Imaging Workspace is to facilitate the increasing use of imaging based end points in clinical trials. To achieve this an easily extensible open source platform to support image analysis and visualization was defined as a key priority
The eXtensible Imaging Platform (XIP) is an open source environment for rapidly developing medical imaging applications from an extensible set of modular elements.
This platform will make it easier and less expensive to access specific post-processing applications at multiple sites, simplifying clinical trials, and most importantly, increasing the uniformity of imaging and analysis.
Imaging applications developed by research groups will more easily be accessible within the clinical operating environment, simplifying workflows and speeding data processing and analysis.
Once validated, the software should be readily transitioned into products through streamlined Federal Drug Administration, (FDA), approval processes due to the re-use of already approved libraries and open source development processes.

7. Deliverables XIP.rad XIP.ws
Development and application build environment
Extensive and extensible set of libraries for imaging and visualization
Uses Open Inventor framework
Includes code generating wizards to create new objects and wrap existing libraries
XIP.ws
A reference implementation of a medical imaging workstation developed using XIP.rad
Integrated via middleware into caGRID
Optimized to support basic cancer research use cases
Includes two key components:
XIP.app – a use case specific “plug-in” application integrated via the DICOM WG-23 Interface
XIP.host – the hosting environment that provides XIP.apps access to services such as data stores, remote processing, etc.

8. XIP.ws - Reference Implementation
XIP.app
XIP.host
Standard
XIP
Classes
Custom
XIP
Classes
API (Plug)
API (Socket)

9. Open Inventor
Open Inventor ® ( ) is an object-oriented toolkit offering a comprehensive solution to interactive graphics programming problems.
It presents a programming model based on the Model/View/Controller design pattern and the concept of Pipelines.
C++ modules represent Engines, Nodes and Manipulators
Engines enable the creation of processing pipelines
Nodes support the concept of scene graphs, which are hierarchical structures of objects describing what needs to be visualized in 2D/3D
Manipulators handle input devices, measurements and coordinate transforms in response to user interaction

10. Integrating existing toolkits into
Automatic Wrapper generation for 2D/3D libraries/toolkits such as ITK and VTK
Example: ITK for image processing, segmentation, registration
User can review parsed results and choose to support only the desired data types, hide some methods, exclude some classes, etc.
Wrappers for ITK functions such as Region Growing, Neighborhood, Isolated, Confidence, Watershed, Thresholding, Edge Detection, Laplacian, Gaussian, …
Support for ITK Data Meshes and Vector Fields

11. XIP Framework & Architecture
XIP Application
XIP Development Tools
XIP Modules
Host Independent
XIP Host Adapter API
(Enables rapid development of applications)
ITK
VTK
XIP LIB
. . .
Data Access
Remote Processing
Annotation and Markup
For those of you that were not able to attend Fred Prior’s talk, I’ll first desc
. . .
WG23
WG23
WG23
WG23
Host-Specific Plugin Libraries
caGrid Data Svc.
Analytical Svc.
caGrid
AIM MetaData
. . .
XIP Host
(Can be replaced with any WG23-compatible Host)

12. caGrid Grid Infrastructure for caBIG caGrid Components
Language (metadata, ontologies)
Security
Advertisement and Discovery
Workflow
Grid Service Graphical Development Toolkit (Introduce)
Efficient Bulk Data Transport (IVI middleware)
DICOM compatibility (IVI middleware)

13. gridIMAGE Architecture
Expose algorithms, human markup and
image data as caGrid Services
Here you give an overview of the system and then describe things in detail in the following slides.

14. The caBIG AIM Project An ontology of image annotations
An ontology defines concepts in a domain and the relationships between those concepts
An ontology of image markups
Use of controlled terminologies
RadLex, SNOMED, LOINC, UCUM
Define a set of translatable standards-based representations
Implement this functionality on the caBIG eXtensible Imaging Platform (XIP)

15. An Image, and an Annotation an Image Markup
The pixel at the tip of the arrow [coordinates (x,y)] in this image
[DICOM: ] represents the Ascending Thoracic Aorta [SNOMED:A ]
and an Annotation

16. caDSR, EVS, RadLex, AIM ontology, etc Client access Service accessHW
XIP
Application
Inventor
Application Modules
WG 23 System Services PLUG
WG 23 System Services SOCKET
GRID
CLIENT
SERVICES
DICOM
(DCMTK)
OTHER
VTK
ITK
AIMTK
other OS
NCIA
IDE
RadLex
AIM
NCI
Protégé
EVS
MIDDLEWARE
DICOM Services
IVI Middleware
caGrid
CaBIG
caDSR, EVS, RadLex, AIM ontology, etc
Client access
Service access
Grid Data Service
Grid Analytical Service
AIM Data Service
XIP App
Service
Host
WG23
DICOM Image Sources

17. The caBIG 2007 Annual Meeting
February 5 - 8, 2007
Marriott Wardman Park Hotel, Washington, DC
Plenary sessions; 60 break out sessions; exhibits, demonstrations, and posters; hackathon
Tailored sessions for newcomers February 5 and throughout the conference