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The ca ncer B iomedical I nformatics G rid ™ (caBIG ™ ): In Vivo Imaging Workspace Projects

The ca ncer B iomedical I nformatics G rid ™ (caBIG ™ ): In Vivo Imaging Workspace Projects

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The ca ncer B iomedical I nformatics G rid ™ (caBIG ™ ): In Vivo Imaging Workspace Projects

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  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

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

  4. Retrieve Results Search for Images

  5. 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.

  6. 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.

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

  8. 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

  9. 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

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

  11. 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) caGrid

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

  13. 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

  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 Markup and an Annotation 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] An Image,

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

  17. The caBIG2007 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