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Medical Imaging Informatics Bench to Bedside (mi2b2)

Medical Imaging Informatics Bench to Bedside (mi2b2). Shawn Murphy MD, Ph.D. PRINCIPAL AIM FOR CTSC-BIRN PROPOSAL.

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Medical Imaging Informatics Bench to Bedside (mi2b2)

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  1. Medical Imaging Informatics Bench to Bedside (mi2b2) Shawn Murphy MD, Ph.D.

  2. PRINCIPAL AIM FOR CTSC-BIRN PROPOSAL • The purpose of this Administrative Supplement project is to develop and disseminate additions to the Informatics for Integrating Biology and the Bedside (i2b2)-based projects to hospitals that will allow clinical imaging data from sophisticated medical imaging modalities such as MRI, PET, ultrasound and high-speed CT to be used for secondary research purposes.

  3. Enable i2b2 to be used for Image Analysis in CTSC by connecting BIRN/XNAT Query is done To find patients Derive new data from images i2b2 BIRN/XNAT Request Images with Accession #’s Study Images PACS DICOM CFIND DICOM CGET DICOM CSTORE

  4. One of 7 roadmap projects funded by the National Center for Biomedical Computing Open source software for the collection, querying, and analysis of clinical data, trials data, genotypic data, and imaging annotations Software supports large enterprise repositories and specific-purpose project repositories What is the “Informatics for Integrating Biology and the Bedside” (i2b2) project?

  5. Beth Israel Deaconness Hospital, Boston, MA Boston University School of Medicine, Boston, MA Brigham and Women's Hospital, Boston, MA Children's Hospital, Boston, MA Denver Children's Hospital, Denver, CO Cincinnati Children's Hospital, Cincinnati, OH Cleveland Clinic, Cleveland, OH Weil Medical College of Cornell, NYC, NY Group Health Cooperative Massachusetts General Hospital, Boston, MA Maine Medical Center, Portland, ME Marshfield Clinic, Wisconsin Morehouse School of Medicine, Atlanta, GA Oregon Health & Science University, Portland, OR Ohio State University Medical Center, Columbus, OH Philadelphia Children's Hospital, Philadelphia, PA Renaissance Computing Institute, Chapel Hill, NC Tufts New England Medical Center, Boston, MA University of California Davis, Davis, CA University of California San Francisco, SF, CA University of Massachusetts Medical School, Worcester, MA University of Michigan Medical Center, Ann Arbor, MI University of Pennsylvania School of Medicine, Philadelphia, PA University of Rochester Medical Center, Rochester, NY University of Texas Health Sciences Center Houston, Houston, TX University of Texas Health Sciences Center San Antonio, SA, TX University of Texas Health Sciences Center Southwestern, Utah Health Science Center, Salt Lake City, UT University of Washington, Seattle, WI Georges Pompidous Hospital, Paris, France University of Goettingen, Goettingen, Germany University of Pavia, Pavia, Italy University of Seoul, Seoul, Korea i2b2 software is used across the country United States International

  6. i2b2 Hive allows queries to return various types of patients B A C local shared / central “Hive” of software services and core CRC cells remote Clinical Research Chart

  7. Project Task: Enable queries to find patients associated with medical images using i2b2 i2b2 project portal B A C local shared / central “Hive” of software services and core CRC cells Billing Codes remote HL7 Clinical Research Chart

  8. Human Subject Privacy Plan • Follow common plan as for other clinical data types • All patients at a site are added to enterprise repository with HIPAA notification that their data may be used for research upon registration. • General queries produce only aggregated numbers that are obfuscated to prevent identification of individuals • Submit IRB proposal for specific hypothesis & detailed data request for specific set of patients • PI of approved study given identifiable data in secure transfer • IRB can audit all data transfers

  9. Queries can be is performed to return sets of patients with images

  10. Project Task : Enable automated requests for medical images to PACS and copy to XNAT Query is done To find patients Derive new data from images i2b2 XNAT Request Images with Accession #’s Study Images PACS DICOM CFIND DICOM CGET DICOM CSTORE

  11. What is BIRN/XNAT? • An open source BIRN imaginginformatics platform. • Core features: • DICOM workflow • Web interface • Extensible data model • RESTful web services API • Pipeline processing • Built on various open source Java (Jakarta Turbine, Maven, Restlets, dcm4che) and Javascript (YUI) technologies.

  12. XNAT Connects multiple applications throughout BIRN • BIRN Mediator (BIRN-CC) • LONI Pipeline (UCLA) • 3D Slicer (NAMIC)

  13. Project Task: enable progressive annotations to images in i2b2

  14. Resulting i2b2-XNAT-PACS Integration XNAT Enterprise Dr Y Desktop Alzheimer Dr Z Desktop Chronic pain management Dr X Desktop Pediatric rare disease Dr W Desktop Quantitative cancer biomarkers Slicer: Data visualization analysis PACS PACS Annotating Genomic Data #2 Project Management File Repository De - Identification Of data Ontology Management Identity Management Natural Language Processing Data Repository (CRC) Workflow Framework Annotating Genomic Data #1 Correlation Analysis 17 i2b2 HIVE

  15. Annotated imaging data can be added back to i2b2 Enterprise Repository i2b2 DB Project 1 [ Enterprise Shared Data ] i2b2 DB Project 2 Shared data of Project 1 Ontology Consent/Tracking of Project 2 i2b2 DB Project 3 Security of Project 3

  16. Allowing queries for imaging data to be made across i2b2 distributed “Shared Health Research Information Network” SHRINE adapter Hospital 1 i2b2 Hospital 3 caBIG I2b2 Query Aggregator SHRINE adapter SHRINE adapter Hospital 2 i2b2 Central “aggregator” broadcasts query to local hospital “adaptors”, which return aggregate counts

  17. mi2b2: Implementation i2b2 & Catalyst leadership: Shawn Murphy & Randy Gollub Project lead architect: Chris Herrick Project lead scientist: Steve Pieper Hospital Departments of Radiology IT leaders: Ramin Khorasani / Kathy Andriole (BWH) Keith Dreyer / Darren Sack (MGH) Robert Lenkinski / Jesse Wei (BIDMC) Daniel Nigrin / Richard Robertson / Bill Tellier / Paul Lamonica (CHB) Programmers: Wensong Pan, Yong Gao Dissemination: Valerie Humblet XNAT team: Dan Marcus, Tim Olson, John Paulett Wiki page: Posting of all Meeting minutes, agendas, etc http://www.na-mic.org/Wiki/index.php/CTSC:ARRA_supplement

  18. http://catalyst.harvard.edu

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