Medical Imaging Informatics Bench to Bedside (mi2b2)

Shawn Murphy MD, Ph.D.

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.

Enable i2b2 to be used for Image Analysis in CTSC by connecting BIRN/XNAT

PACS

BIRN/XNAT

DICOMCFIND

DICOMCGET

DICOMCSTORE

i2b2

RequestImages with

Accession #’s

Query is doneTo find patients

StudyImages

Derive newdata from images

What is the “Informatics for Integrating Biology and the Bedside” (i2b2) project?

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

i2b2 software is used across the country

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

United States International

i2b2 Hive allows queries to return various types of patients

AB

C

shared / central

Clinical Research Chart

“Hive” of software services and core CRC

cells

remote

local

Project Task: Enable queries to find patients associated with medical images using i2b2

i2b2 project portal

AB

C

shared / central

Clinical Research Chart

“Hive” of software services and core CRC

cells

remote

local

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

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

Project Task : Enable automated requests for medical images to PACS and copy to XNAT

PACS

XNAT

DICOMCFIND

DICOMCGET

DICOMCSTORE

i2b2

RequestImages with

Accession #’s

Query is doneTo find patients

StudyImages

Derive newdata from images

What is BIRN/XNAT?

An open source BIRN imaging informatics 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.

XNAT Connects multiple applications throughout BIRN

BIRN Mediator (BIRN-CC)LONI Pipeline (UCLA)3D Slicer (NAMIC)

Project Task: enable progressive annotations to images in i2b2

Slicer:Data

visualization analysis

XNATEnterprise

DataRepository

(CRC)

FileRepository

IdentityManagement

OntologyManagement

CorrelationAnalysis

De -Identification

Of dataNatural

LanguageProcessing

AnnotatingGenomicData #1

ProjectManagement

WorkflowFramework

AnnotatingGenomicData #2PACS PACS

i2b2 HIVE

Dr X Desktop Pediatric

rare disease

Dr YDesktop

Alzheimer

Dr ZDesktop

Chronic pain management Dr W

Desktop Quantitative

cancer biomarkers

Resulting i2b2-XNAT-PACS Integration

17

Annotated imaging data can be added back to i2b2 Enterprise Repository

i2b2 DB Project 1

i2b2 DB Project 2

i2b2 DB Project 3

of Project 3

of Project 2

Shared dataof Project 1

[ Enterprise SharedData ]

Ontology

Consent/Tracking

Security

Allowing queries for imaging data to be made across i2b2 distributed “Shared Health Research Information Network”

Central “aggregator” broadcasts query to local hospital

“adaptors”, which return aggregate counts

SHRINEadapter

SHRINEadapter

SHRINEadapter

I2b2 QueryAggregator

Hospital 1i2b2

Hospital 2i2b2

Hospital 3caBIG

mi2b2: Implementation

i2b2 & Catalyst leadership: Shawn Murphy & Randy GollubProject lead architect: Chris HerrickProject 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 GaoDissemination: Valerie HumbletXNAT team: Dan Marcus, Tim Olson, John PaulettWiki page: Posting of all Meeting minutes, agendas, etchttp://www.na-mic.org/Wiki/index.php/CTSC:ARRA_supplement

http://catalyst.harvard.edu