The cancer Biomedical Informatics Grid™ (caBIG™):

In Vivo Imaging Workspace Projects

Fred Prior, Ph.D.Mallinckrodt Institute of RadiologyWashington University in St. Louis

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

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 CaptureFormats & Tools

Data Re-Use Applications

NLPMetadata for Images

Search for Images Retrieve Results

• 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.

Deliverables• XIP.rad

– 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.

XIP.ws - Reference Implementation

XIP.hostXIP.host

API (Socket)API (Socket)

API (Plug)API (Plug)

XIP.appXIP.app

Custom Custom XIP XIP

ClassesClasses

StandardStandardXIPXIP

ClassesClasses

Open Inventor• Open Inventor ® (http://oss.sgi.com/projects/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

Integrating existing toolkits into

• 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

• 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.

XIP Framework & Architecture

XIP Application

(Can be replaced with any WG23-compatible Host)

XIP Host Adapter API

XIP

LIB

ITK

VTK

. .

.

Host-Specific Plugin Libraries

Rem

ote

Pro

cess

ing

caG

rid

Analy

tica

l S

vc.

Data

A

ccess

caG

rid

D

ata

S

vc.

An

nota

tion

an

d M

ark

up

AIM

Meta

Data

. .

..

. .

XIP ModulesHost Independent

WG23

XIPDevelopment

Tools

XIP Host

WG23 WG23 WG23

(Enables rapiddevelopment of

applications)

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)

gridIMAGE ArchitectureExpose algorithms, human markup and

image data as caGrid Services

DICOM Interoperability• Interoperability Library

– Translate between DICOM and caBIG data models, and DICOM QR and caBIG query language

• DICOM Data Service

– Exposes existing DICOM QR aware data resources (PACS, etc) as caGrid compliant service

• VirtualPACS

– Allows DICOM-aware clients (review workstation, etc) to access DICOM caGrid data services over the grid

• caGrid-based security for data transport, authentication, and authorization

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)

An Image, an Image Markup

The pixel at the tip of the arrow [coordinates (x,y)] inthis image[DICOM: 1.2.814.234543.23243]represents the Ascending Thoracic Aorta[SNOMED:A3310657]

and an Annotation

HW

XIPApplication

InventorApplication Modules

WG 23 System Services PLUG

WG 23 System Services SOCKET

GRIDCLIENT

SERVICES

DICOMSERVICES(DCMTK)

OTHERSERVICES

VTK ITK AIMTK other

OS

NCIA

XIPIDE

RadLex

AIM

NCI

ProtégéEVS

XIP

MIDDLEWARE

DICOM

DICOM Services

IVI MiddlewarecaGrid

CaBIG

caDSR, EVS, RadLex, AIM ontology, etc

Client accessService access

Grid Data Service

Grid Analytical Service

AIM Data Service

XIP App

ServiceHost

WG23

DICOM Image

Sources

The caBIG 2007 Annual Meeting

• February 5 - 7, 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