The cancer Biomedical Informatics Grid

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The cancer Biomedical Informatics Grid (caBIG)
In Vivo Imaging Workspace Projects

• Fred Prior, Ph.D.
• Mallinckrodt Institute of Radiology
• Washington University in St. Louis

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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

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In Vivo Imaging Workspace

• Project 1 Middleware
• Project 2 AIM Annotation and Image Markup
• Project 3 Vocabulary
• Project 4 XIP Extensible Imaging Platform

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Retrieve Results
Search for Images
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• 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.

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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.

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XIP.ws - Reference Implementation
XIP.app
Standard XIP Classes
Custom XIP Classes
API (Plug)
API (Socket)
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Open Inventor

• Open Inventor (http//oss.sgi.com/projects/inven
  tor/ ) 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

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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

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XIP Framework Architecture
XIP Application
XIP Modules Host Independent
XIPDevelopmentTools
XIP Host Adapter API
XIP LIB
ITK
VTK
. . .
(Enables rapiddevelopment ofapplications)
Remote Processing
Annotation and Markup
Data Access
. . .
Host-Specific Plugin Libraries
XIP Host
(Can be replaced with any WG23-compatible Host)
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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)

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gridIMAGE Architecture
Expose algorithms, human markup and image data
as caGrid Services
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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

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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)

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An Image,
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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