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Society for Imaging Informatics in Medicine (SIIM) 2011 Abstract

Title: New tools for integrating clinical images into research studies



The Informatics for Integrating Biology and the Bedside (i2b2, available at http://www.i2b2.org) software suite enables the repurposing of healthcare data for clinical research [1].  The i2b2 software provides clinical investigators with the tools necessary to integrate medical record and clinical research data in the genomics age, a software suite to construct and integrate the modern clinical research chart (CRC). The i2b2 open-source software is designed to support two general use cases within the mission of repurposing electronic health records for research.  One is to enable queries that can browse through all the enterprise data to find cohorts of patients that are of interest for further research while preserving patient privacy.  A second is to use the data provided by the medical record to do a “deep dive” into the phenotype of a set of patients (possibly identified from the first use case) in support of genomic, outcomes, and environmental studies.  While the i2b2 core software enables such access to a vast majority of medical information, it does not support medical images.  Yet many current and future clinical research studies rely on medical images for quantitative metrics for diagnosis, prognosis and treatment response.  Images are used to quantify disease burden such as tumor volume, inflammation, hemorrhage, and infarction.  Serial imaging is used to quantify the outcome of interventions, such as changes in tumor size or loss of brain tissue.  Importantly, medical images are providing an ever increasing number of sensitive diagnostic approaches to disease, such as the use of susceptibility weighted and diffusion tensor MR imaging in the evaluation of brain trauma. 


Here we describe a software plug-in (a “cell” within the i2b2 “hive”) that allows clinical images to be retrieved from a hospital’s clinical Picture Archiving and Communication System (PACS).  The i2b2 plug-in utilizes a widely available, open-source imaging informatics platform (XNAT [2], available at http://www.xnat.org) in order to manage the images obtained from the PACS.


The images that become available through XNAT can be navigated through a user interface and accessed by external applications via web services.  Using an application programming interface (API), research tools have been adapted to compute and extract novel information from the clinical images using XNAT.  These tools include Freesurfer (developed at the Athinoula A. Martinos Center for Biomedical Imaging at the Massachusetts General Hospital), which allows brain MRIs to be automatically segmented into anatomic regions, and 3DSlicer (developed by the National Alliance for Medical Image Computing), which allows non-rigid image registration models to be computed from conventional MR images. In addition, any medical imaging software that conforms to the DICOM standard can be interfaced with the XNAT research image repository using the XNAT Gateway application as a secure bridge



Ordinarily, i2b2 works by copying all the relevant patient clinical data into a research database called the Clinical Research Chart (CRC).  This works well for the non-imaging data, but the approach is not optimal for images due to the complexities inherent in the storage, indexing, and retrieval processes.  Furthermore, obtaining images from a clinical PACS can be a complex affair.  Leadership at four of the primary Harvard Medical School-affiliated academic healthcare centers (Brigham and Women’s Hospital, Massachusetts General Hospital, Children’s Hospital Boston, and Beth Israel Deaconess Medical Center) were appropriately concerned that retrieval of medical images from the clinical PACS for research purposes might interfere with and hence compromise their clinical mission.  Indeed, a tool that might pull tens of thousands of images from the clinical PACS could cause a serious clinical performance impediment.  Therefore, a contract was put into place with the software that guaranteed only a governed number of images would be pulled at a specific rate at specific (off-peak) times.  Furthermore, audit trails and security protocols were added to comply with the Health Insurance Portability and Accountability Act (HIPAA), where standard DICOM interfaces fail to offer appropriate assurances. 


In addition to ensuring an appropriate interface to clinical systems, the software should be usable by clinician scientists working in a hospital environment, to best promote its adoption and widespread use. For most in our target user community, a streamlined workflow, expressed clearly, simply, and with adequate feedback is required. Our software user interface (UI) is intuitive, guiding a user through querying for studies by multiple criteria, managing query results, requesting clinical data and monitoring retrieval status, previewing retrieved data, and transferring data to XNAT. The presentation layer is designed to also permit flexible navigation among workflow steps, and to be compatible with existing i2b2 UI paradigms.


Although the software does not need the i2b2 CRC to function, the system is much more effective when patient queries utilizing the CRC can direct the download of imaging studies for specific phenotypes.  The imaging studies can then be specified and transferred to XNAT, where they are analyzed and annotated. These annotations can be returned to the CRC for further querying and analysis with the rest of the phenotypic and genotypic data.



By adhering to the DICOM standards for query and retrieval of images we believe our work will have broad applicability at many research hospitals.  The Harvard hospitals represent a microcosm in which equipment from different PACS vendors, different policies on-line, near-line, and off-line storage, and different radiology IT infrastructures can all be accommodated early in the design and implementation process.  The result should be a system that can be deployed with minimal changes at other institutions.


The National Center for Research Resources (NCRR) funding enabled the development of this software plug-in for i2b2 that allows clinical images to be retrieved from a hospital’s clinical Picture Archiving and Communication System (PACS).  The i2b2 plug-in utilizes the widely available, open-source imaging informatics platform XNAT, supported by the Biomedical Informatics Research Network (BIRN), in order to manage the images obtained from the PACS.  Many National Institute of Heath Clinical-Translational Science Center awarded entities use the i2b2 software suite to enable the repurposing of healthcare data for clinical research, and we expect the ability to add clinical images from the hospital PACS to broadly serve the community.




The imaging plug-in for i2b2 will become available shortly as an open source addition to the software platform.  Development is supported by both NCRR (1 UL1 RR 025758-01) and the BIRN (1 U24 RR 025736-01) funding.







[1] Murphy, S. N., G. Weber, et al. (2010). "Serving the enterprise and beyond with informatics for integrating biology and the bedside (i2b2)." J Am Med Inform Assoc 17 (2): 124-130.

[2] Marcus, D. S., T. R. Olsen, et al. (2007). "The Extensible Neuroimaging Archive Toolkit: an informatics platform for managing, exploring, and sharing neuroimaging data." Neuroinformatics 5 (1): 11-34.



Primary Author:

First Name:  Shawn

Middle Name/Initial:  N

Last Name:  Murphy

Degree:  MD, PH.D.

Title:  Medical Director, Partners Healthcare Reseach Computing

Department:  Information Systems

Organization:  Partners HealthCare

Address:  One Constitution Center, 261

City:  Charlestown

State/Province:  MA

Zip Code:  02129

Phone:  617-643-5876

Fax:  617-643-5280

Email:  snmurphy@partners.org

SIIM Member?   Yes      No


Secondary Authors:

Author 2:

First:  Daniel


Last:  Marcus

Degree:  Ph.D.

Title:  Director, Neuro-informatics Research Group

Organization:  Washington University, St. Louis, St. Louis, MO

Author 3:

First:  Christopher

Middle:  D.

Last:  Herrick

Degree:  MBA

Title:  Senior Technical Architect, Information Systems

Organization:  Partners HealthCare System, Inc., Charlestown, MA


Author 4:

First:  Timothy


Last:  Olsen

Degree:  MCS

Title:  Lead Developer XNAT, Neuroinformatics Research Group

Organization:  Washington University St. Louis, St. Louis, MO

Author 5:

First:  Randy

Middle:  L.

Last:  Gollub

Degree:  MD, Ph.D.

Title:  Associate Director of Psychiatric Neuroimaging Research and Director of the Center for Biomedical Imaging  

Organization:  Massachusetts General Hospital, Boston, MA


Author 6:

First:  Steven

Middle:  D.

Last:  Pieper

Degree:  Ph.D.

Title:  CEO

Organization:  Isomics, Inc., Cambridge, MA

Author 7:

First:  Yanbing


Last:  Wang

Degree:  MSc

Title:  Software Developer, Information Systems

Organization:  Partners HealthCare System, Inc., Charlestown, MA

Author 8:

First:  Wendy


Last:  Plesniak

Degree:  Ph.D.

Title:  Research Fellow

Organization:  Brigham and Women’s Hospital, Boston, MA


Author 9:

First:  Darren


Last:  Sack

Degree:  BS, RT®

Title:  Corporate Manager, Enterprise Medical Imaging

Organization:  Partners HealthCare System, Inc., Boston, MA

Author 10:

First:  Jesse


Last:  Wei

Degree:  MD

Title:  Director, Radiology Informatics

Organization:  Beth Israel Deaconess Medical Center, Boston, MA

Author 11:

First:  Katherine

Middle: P.

Last:  Andriole

Degree:  Ph.D.

Title:  Assoc Professor of Radiology

Organization:  Brigham and Women’s Hospital, Boston, MA

Author 12:

First:  Paul


Last:  Lamonica

Degree:  BA

Title:  Sr. Pacs Systems Analyst, Neuroimaging Center


Children’s Hospital, Boston, MA