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caBIG™ In Vivo Imaging Breakout caBIG™ Annual Meeting April 10, 2006. caBIG™ Annual Meeting: In Vivo Imaging Breakout Introduction by Eliot Siegel, MD In Vivo Imaging Workspace Lead. Formation of the caBIG Imaging workspace somewhat “controversial” last year

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slide2
caBIG™ Annual Meeting: In Vivo Imaging BreakoutIntroduction by Eliot Siegel, MDIn Vivo Imaging Workspace Lead
  • Formation of the caBIG Imaging workspace somewhat “controversial” last year
  • Interesting mismatch between clinical use of imaging in the hospital and outpatient setting and the use of imaging in clinical trials, why is that the case?
    • Difficulty getting images from various sites conducting clinical trials in comparison to text based and other data
    • Lack of optimal quantitative tools to evaluate change in tumor over time on imaging studies
  • Diagnostic imaging is and will continue to play an increasingly critical role as a biomarker for disease from both a clinical and research perspective
introduction
Introduction
  • Unfortunately there are still major problems with images related to clinical trials
    • Each clinical trial group has had to reinvent the wheel which is inefficient and very expensive
      • ACRIN
      • QARC
      • BIRN
      • others
  • Current information systems such as PACS and the EMR are oriented toward clinical care rather than research
introduction4
Introduction
  • Imaging Informatics is an emerging discipline in medicine and will be increasingly important in the future of cancer care
    • We believe that this field of informatics holds the key to making images accessible and also putting a greater degree of rigor on quantitative assessment of change over time which is critical fo the success of imaging as a biomarker
  • Close working relationship between NCICB (NCI-Center for Bioinformatics) NCIA (National Cancer Imaging Archive) and Imaging Workspace
slide5
caBIG™ Annual Meeting: In Vivo Imaging BreakoutIntroduction by Eliot Siegel, MDIn Vivo Imaging Workspace Lead
  • Goals of the workspace
    • Advance imaging informatics on multiple fronts
    • Create, optimize, and validate software tools
      • E.g. extensible imaging platform
    • Model methods to extract meaning from in vivo imaging data and establish databases to test and validate these methods
in vivo imaging workspace
In Vivo Imaging Workspace
  • Structure
    • Eliot Siegel – Workspace Lead
    • Four Special Interest Groups (SIGs):
      • Software
      • Standards and Interoperability
      • Testbed
      • Vocabularies & Common Data Elements.
    • Fifteen Funded Subject Matter Experts (SMEs)
    • More than Seventy Volunteer Participants including participants from industry
    • Participation of NCIA and NCI/CB
    • Small Animal In Vivo Imaging
slide7

caBIG™ Annual Meeting: In Vivo Imaging BreakoutVocabularies and Common Data Elements Special Interest GroupLead by Curt Langlotz, MD, PhD and Daniel Rubin, MD

Imaging VCDE SIG Goals

  • Promote, support, develop, and evaluate standards-based vocabularies, ontologies, and CDEs for radiology and allied imaging fields.
  • Participate in the design of the testbed and provide the vocabulary-related elements required by the testbed .
  • Help develop the standards for creating, storing, and retrieving image metadata and image annotations.
  • Harmonize VCDEs developed in the VCDE SIG with those being created by the VCDE workspace, and will develop VCDE-specific tools and resources that can be deployed on the grid to help realize the strategic vision of the caBIG effort.
outline
Outline
  • Background
    • caBIG history
    • Terminology for imaging
    • ACRIN and imaging clinical trials
  • Proposed imaging VCDE projects
    • Structured image annotation and query software
    • Terminology/CDE development for imaging
    • Natural language processing
nci informatics long range planning circa 1999

Clinical Trial Building Blocks

Clinical Trials

Tools/ Templates

National

Information

Infrastructure

Sharable Information Repositories

Common

Data Elements

“The CII”

NCI Informatics Long Range Planning, circa 1999
importance of common data collection methods circa 1999
Importance of Common Data Collection Methods, circa 1999
  • Serve as building blocks for the CII
  • Allow pooling of data and comparison of results among clinical trials
  • Facilitate enrollment of patients in clinical trials
  • Avoid redundant data collection (capture-once, use-many times principle)
  • Automate and expedite administration of clinical trials
medical vocabularies completeness for radiology
Medical Vocabularies: Completeness for Radiology

Langlotz & Caldwell, J Digit Imaging 15(1S):201, 2002

what is radlex
What is RadLex?

10-30 percent of these concepts are not found in SNOMED-CT

  • Sponsored by the Radiological Society of North America (RSNA)
  • 26 participating organizations
  • 9 committees
  • 92 radiologist participants
  • 5,308 anatomic concepts
lexicon development process

OWL

Iterative Lexicon

Development Process

SNOMED-CT

SNOMED-CT

RadLexProtégé

Database

RadLexweb

site

XML

OWL

RadLex base content

NCI Thesaurus

RadLex Lexicon Development Committees

UMLS Meta-Thesaurus

Lexicon Development Process
boop search

Hierarchy expandsto show results

in context

Term details are shown

BOOP Search

mirc.rsna.org/radlex/service

american college of radiology imaging network acrin
American College of Radiology Imaging Network(ACRIN)
  • NCI-funded imaging clinical trial cooperative group
  • Dozens of trials funded, including some very high profile trials (DMIST, NLST)
  • Tens of thousands of subjects
  • Case report forms containing thousands of potential CDEs
proposed imaging vcde projects
Proposed Imaging VCDE Projects
  • Structured image annotation and query (IRW)
    • Image meta-data standards
    • Image annotation and structured data capture
    • Image query by content from annotated image database
  • Data collection methods for imaging clinical trials, harmonized to RadLex and caDSR/EVS
    • ACRIN data collection elements
    • DICOM elements
    • The imaging “playbook”: Cancer imaging devices, procedures and protocols
  • Natural language processing (NLP)
    • Evaluation of existing tools
    • Adaptation or development of tools for radiology images
image annotation and structured data capture

CAVITARY MASS

Finding: mass

Mass ID: 1

Margins: spiculated

Length: 2.3cm

Width: 1.2cm

Cavitary: Y

Calcified: N

Spatial relationships: Abuts pleural surface; invades aorta

Image Annotation and Structured Data Capture

Capture data once, use it many times

data collection cde example
Data Collection CDE Example
  • Please describe the margins of the mass:
    • Smooth
    • Lobulated
    • Irregular
    • Spiculated
    • Obscured
data collection cde example19

Vocabulary Concepts

Data Collection CDE Example
  • Please describe the margins of the mass:
    • Smooth
    • Lobulated
    • Irregular
    • Spiculated
    • Obscured
reusable common data elements cdes for imaging
Reusable Common Data Elements (CDEs) for Imaging
  • Create caDSR-compatible CDEs from ACRIN data collection methods
  • Identify CDEs specific to cancer imaging research needs
  • Compliant with caDSR, harmonized with RadLex and EVS
    • Associate atoms (terms) and molecules (CDEs)
    • Move from lexicon (lists) toward ontology (knowledge)
  • Coordinate with caBIG VCDE Workspace
the playbook for imaging in cancer research
The “Playbook” for Imaging in Cancer Research
  • Vocabulary for imaging devices, procedures, and protocols
    • (e.g., 7T 18-cm horizontal bore; 4.7T 33-cm bore magnet operating at 200 MHz for 1-H imaging experiments)
  • Common, vendor-independent language to describe experimental imaging instruments.
    • (e.g., “fast spin echo” vs. “turbo spin echo” MRI sequence)
natural language processing
Natural Language Processing
  • Unstructured information will always exist
    • Narrative radiology report archives
    • Peer-reviewed literature
  • Focused extraction from radiology report
    • Anatomy, findings (e.g, nodules and their descriptors), change over time
    • Automatic population of reporting templates
  • Inventory existing NLP tools
  • Select or develop NLP tools to fulfill requirements
vocabulary cde strategy
Vocabulary/CDE Strategy

Metadata storage formats

NLP

Metadata for Images

Image Annotation

Terminologies & CDEs

Queries & Analysis

Data Capture

Formats & Tools

Vocabularies & CDEs

Data Re-Use Applications

standards and interoperability special interest group lead by david channin md and paul nagy phd
Standards and Interoperability Special Interest GroupLead by David Channin, MD and Paul Nagy, PhD
  • Why Standards?
  • Image Standards
  • Workflow Standards
  • Annotation Standards

“The great thing about standards is that there are so many to choose from.” – Dr. Andrew Tanenbaum

why standards
Why Standards?
  • Today, mountains of image data from clinical trials lies fallow.
  • The appropriate use of standards can allow re use of the image data for other purposes than the one immediate trial.
  • Thus enabling discovery in unanticipated ways.
    • Computer Assisted Diagnosis
    • Content Basis Image Retrieval
image standards
Image Standards
  • Clinical Standard Medical Images come in
    • DICOM (Digital Communications in Medicine)
  • Loads of meta data
    • Imaging Physics
    • Frame of reference
    • Patient/Study Information
  • Naming inconsistent for re use
  • Working with UPICT
    • Uniform Protocols in Clinical Trials
    • http://www.upict.org
    • RSNA, FDA, NCI, AAPM, …..
  • Mapping to VCDE (Vocabulary)
workflow standards
Workflow Standards
  • How do we extract the image data from clinical environments?
    • Not a great deal of technical onsite expertise
    • Anonymization of PHI (Pseudonymization)
    • Electronic submission to a repository
  • How do we expose the data to researchers
    • Query of meta data
    • API autonomous access
  • Goal is to allow interoperability at multiple layers in the technology stack of the Image Platform.
workflow comm query standards

Scheduled Workflow

Charge Posting

-

Patient Info. Recon-ciliation

Post-Processing Workflow

Presentation of Grouped Procedures

Reporting Workflow

KeyImageNotes

Simple Image & Numeric Reports

Consistent Present-ation of Images

NMImage

EvidenceDocs

Access to Radiology Information

Portable Data for Imaging

Radiology Audit Trail Option on ITI-Audit Trail and Node Authentication

Basic Security

Teaching File and Clinical Trial Export

Workflow Comm/Query Standards

IHE Radiology

  • LAN Based – DICOM Q/R | C-Store | GPWL
  • Internet based – IHE RHIO – Registry/Repository using EbXML/SOAP
  • Internet - DICOM WG23 utilizing OGSA
standards and interoperability special interest group lead by david channin md and paul nagy phd29
Standards and Interoperability Special Interest GroupLead by David Channin, MD and Paul Nagy, PhD

Annotations and Image Markup – In conjunction with Vocabulary

Courtesy Dr. David Clunie

annotations and markup
Annotations and Markup
  • Goal is to create a knowledge representation (OWL) for annotations in markup to enable semantic web applications.
  • Provide practical presentation states in DICOM Structured Reports and XML RIDER.
  • Create tools in the Imaging Platform to author this markup.
imaging software sig goals and objectives
Imaging Software SIG: Goals and Objectives
  • The goal of the Software SIG is to create and adapt open source software tools to promote and enhance the use of imaging in cancer research. The SIG will focus on tools for image acquisition, management and analysis for use in clinical trials.
    • specifically tools for enhancing lesion detection, characterization and change determination.
  • The SIG will define requirements for these projects and write requirements specifications and/or white papers.
  • The SIG will define use cases and test plans for each project and guide and track the development team that is tasked with implementation.
  • The SIG will participate in the validation of software and/or algorithms resulting from each project using the IVI test bed
viewing annotation and analysis software
Viewing, Annotation and Analysis Software
  • To facilitate the increased use of imaging based end points in clinical trials the SIG has identified the need for an easily extensible open source platform to support image analysis and visualization.
  • To address this need a development program will been undertaken to create an eXtensible Imaging Platform (XIP)
extensible imaging platform
eXtensible Imaging Platform
  • The XIP is a
    • Collection of software classes, algorithms and sample applications for building imaging applications valuable to research
    • Method for rapidly prototyping "medical imaging workstation" applications from a re-usable, extensible set of modular elements
  • Researchers will be able to rapidly develop and evaluate new approaches to medical imaging problems, and use them in a translational research setting.
  • Grid technology in general, and caGrid in particular, makes it possible to let users to choose between grid components and locally available components.
    • Analytic services (CAD algorithms, algorithms for quantifying changes in consecutive imaging studies, algorithms associated with a 3-D visualization pipeline etc).
    • Data sources might or might not be DICOM based.
    • Both data and algorithms can be physically distributed.
current status
Current Status
  • Imaging Software SIG has developed a requirements specification for the XIP
  • An RFP has been drafted
  • The SIG is working to define appropriate milestones and demonstration projects
change detection analysis
Change Detection & Analysis
  • The In Vivo Imaging Workspace is assessing current status of change detection & analysis technology for cancer imaging
  • Detecting and quantifying change in lesions over time represents a critical unmet need in the Cancer Research Community
slide36

Baseline

Follow-up

slide37

Baseline

Follow-up

change analysis and validation
Change Analysis and Validation
  • Working on definition of SIG’s role in larger NCI activity. It has been suggested by NCI that a major contribution would be the development of basic change analysis algorithms, and evaluation methods.
    • Algorithms for “binary outcome” determination and for change quantification
    • Databases with known truth for validation studies
    • Databases containing multiple segmentation results on the same images using different approaches
  • Utilize the “plug-in” application interface for the XIP to provide a “sand box” in which algorithms may be implemented and evaluated
testbed special interest group lead by joel saltz md phd and stephan erberich phd
Testbed Special Interest GroupLead by Joel Saltz, MD, PhD and Stephan Erberich PhD

SIG Goals

  • Design and implement core middleware compliant with caGrid, DICOM and IHE
  • Addresses the need for high performance data transport on the grid, and dynamic algorithm deployment to reduce the need to data movement.
  • Develop software development environments to help developers use middleware to develop applications
  • Work with cooperative groups to leverage testbed capabilities in support of translational research
  • Responsibility for coordination of GridCad application
testbed special interest group lead by joel saltz md phd and stephan erberich phd40
Testbed Special Interest GroupLead by Joel Saltz, MD, PhD and Stephan Erberich PhD

Testbed: Consists of vivo imaging caGrid standards, reference middleware stack implementation supporting grid based applications. The testbed is designed to support each individual application as well as to demonstrate interoperability between applications

Testbed Projects: Middleware, Coordination of Application Projects, Cooperative group outreach

middleware testbed for multi center clinical trials cooperative cancer group use case scenario
Middleware Testbed for multi-center clinical trials:Cooperative Cancer Group use case scenario
  • ACQUISITION
    • Image acquisition and handling at trial site (Image transfer techniques, HIPAA, firewalls, MIRC)
    • Quality assurance
  • REVIEW AND ANALYSIS
    • Image Warehousing, access control, and central review
    • Access to correlative and image meta data via caGrid
    • Annotation and Markup in caGrid
    • Quantitative analytic tools
  • DISCOVERY
    • Integrated caGrid supported discovery of image, molecular, pathology information
slide42

Testbed development focus application: gridCAD — A Novel Use of Grid Computing to Support Human Markup and Execution of Multiple CAD Systems

Tony Pan, Joel Saltz, Tahsin Kurc, Stephen Langella,

Shannon Hastings, Scott Oster, Ashish Sharma, Metin Gurcan

Department of Biomedical Informatics

The Ohio State University Medical Center, Columbus OH

Eliot Siegel, Khan M. Siddiqui

University of Maryland School of Medicine, Baltimore, MD

benefits
Benefits
  • Facilitate research and clinical decision support with large number of subjects and multiple CAD algorithms.
    • Parameter studies, clinical and preclinical trials, etc
  • Provide a client to support remote human markup of nodules
  • Enable better algorithm development and validation through the use of many distributed, shared image datasets
  • Support remote algorithm execution – reduce data transfer and avoid the need to transmit PHI
  • Reduce overall processing time and algorithm development cycle through remote compute resource recruitment and CAD compute farms
  • Scalable and open source — caGrid 1.0
gridcad architecture
gridCAD Architecture

Expose algorithms, human markup and

image data as caGrid Services

future direction
Future Direction
  • Location independence
    • Move algorithms to data
    • Move data to algorithms
    • Move both data and algorithms to compute servers
    • Currently supported – ongoing collaborations to deploy these capabilities
  • Security and Privacy
    • Encryption and Just-In-Time anonymization for the image data services
  • Scaling and Deployment
    • High performance image transfer mechanisms
    • Greater number and variety of CAD vendors
    • Additional application areas, including CAD for other diseases and in vitro image analysis
cog nant cooperative group application
COG/NANT Cooperative Group Application
  • COG Phase-I Consortium (23 medical center) and NANT (14 medical centers) are now actively engaged in the caBIG testbed.
  • Grid based analysis of perfusion imaging studies: DCE-MRI analysis deployed as an analytic service
  • Grid based evaluation of joint prognostic value of perfusion studies, pathology, molecular clinical data
in vivo imaging workspace involvement in rsna 2006 eliot siegel md
In Vivo Imaging Workspace involvement in RSNA 2006Eliot Siegel, MD,

6

Workstations:

SIG 1

Testbed

Architecture

3

Workstations:

SIG 3

Vocabulary

2

Workstations:

caBIG demo

1 spy,

Rembrandt

2

Workstations:

NCI

CIP demo

Projects

IDRi

Theme Park Directory & Purpose

6

Workstations:

SIG 2

Software

3

Workstations:

SIG 4

Standards

2

Workstations:

NCIA

RIDER

4

Workstations:

Allies

Pharma

Device

?CRO

q a and wrap up lead by eliot siegel md in vivo imaging workspace lead
Q&A and Wrap UpLead by Eliot Siegel, MD, In Vivo Imaging Workspace Lead
  • Engage in projects that further the strategic goals of the Imaging Workspace and caBIG™ program.
  • Identify synergies with the other caBIG™ workspaces.
  • Partner with external organizations within the caBIG™ community, (ex.; ACRIN, NCIA), to further Imaging Workspace and caBIG™ program goals
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