december 2006 national cancer imaging archive (ncia) october 11, 2007
TRANSCRIPT
December 2006
National Cancer Imaging Archive (NCIA)
https://imaging.nci.nih.gov
October 11, 2007
Summary
• Overview
• Review of Functionality
• Architecture
• Object Model
• Grid Services
• NCIA Installation
• Questions and Demonstration
3
Overview
What is NCIA?
• National Cancer Imaging Archive
• Searchable repository of in vivo cancer images in DICOM format
• Publicly available at no cost over the Internet
• Open source (Java J2EE based)
• In addition to images, NCIA contains:
• Non-image files (PDF, image markup)
• Annotation data provided by a curator
Goals of NCIA
• Provide a resource for sharing image sets and related information
• Enable collaboration during clinical trials involving imaging
• Support research and development of imaging biomarkers
• Create an environment for distributed image reads
• Education
• Support Computer Aided Detection (CAD) algorithm testing and development
• Facilitate partnerships among organizations (Cooperative Groups)
• Standardization and Interoperability
6
Review of Functionality
Image Submission
• Medical Imaging Resource Center (MIRC)
• MIRC Field Center and MIRC Server solution addresses two barriers to image sharing across the Internet
• DICOM protocol typically blocked at firewalls
• Removal of Protected Health Information (PHI) through a configurable de-identification process at submitting site
• MIRC Field Center is installed both at NCI and at partner institutions
• Images submitted via HTTPS by MIRC Field Center
• Images sent to NCI via FTP
• NCI provides Tier 1 and Tier 2 support for institutions submitting images to the NCIA instance at the NCI
• Email and Telephone support available
Image Submission (continued)
• External organizations can verify a successful image submission to the NCIA using the Verify Submission Tool
Image Submission (continued)
• Images are checked for quality using the online NCIA QC Tool, available to administrative users
Image Repository
• Archive currently contains over 2 million DICOM images plus annotation files and curation data
• Data Access• Web portal available for accessing repository• caGrid access• caCORE generated toolkit API• Cedara visualization and markup• Node-to-Node communication
• Online searching for cases/images based on criteria such as Image Modality, Slice Thickness, Collection, curation data, etc.
• Users can download DICOM data bundled with annotation files and curation data.
• Web portal system operates based on “shopping cart” feature
• Federated searches and image downloads enabled via the implementation of the NCIA data service
Search for ImagesBasic Search Functionality
• User can select Modality, Slice Thickness, Collections, etc.
Search for Images
Advanced Search Options
Search Results – Patient List
Search Results
Search criteria shown above
Search results shown below, organized by Subject
Search Results – Studies for Patient
Studies
Studies shown below, organized by de-identified Study ID
Search Results
DICOM Image Thumbnails
•Image Thumbnails viewable for each series
•Any individual images can be added to the data basket for download
Download Images
Downloading DICOM files in Data Basket
Data Download
Image Visualization Third Party Tool
• A third party tool was needed to demonstrate the following capabilities:• Image visualization• Image markup persistence• Support for central reads
• Stop gap solution until an XIP based application is operational
• Cedara software was chosen• Delivered a customized version of I-Response that operates in
conjunction with the Cedara ISG Server.• Communication with the I-Response and ISG is done over HTTP.
Image Visualization Controls
I-Response Workstation
I-Response Workstation
21
Object Model
Object Model
• Object model based on DICOM standard• Basic Hierarchy
• TrialDataProvenance – site that collected images for a collection• Patient – Person being imaged• Study – Grouping of one or more Series taken at one visit• Series – Grouping of images• Image – A digital in vivo image• Annotation – A non-image file associated with a series
Object Model
• Object model run through Semantic Integration Workbench (SIW) and also annotated
• caBIG Silver compatibility review:
• Completed Kickoff meeting for the VCDE, Oct. 4th
• Kickoff meeting for the VCDE Architecture Workspace, Oct. 12th
• Object model in Production caDSR by Oct. 19th
Project
Total DE Identified to Date
Total CDEs to
date New DE% DE reuse
DEC Reuse
% DEC Reuse
VD Reuse
% VD Reuse
NCIA Data Model DICOM CDEs 86 86 0 100% 10 12% 74 86%NCIA Data Model Non-DICOM CDEs 21 21 21 0% 0 0% 0 0%NCIA Total CDEs 107 107 21 80% 10 9% 74 69%
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Architecture
Image Submission and Federated Search (2.4)
Fir
ewal
l
De-
ID
MIRCField
Center
MIRC Storage Service
MIRC DICOM Service
MIRC Database Service (Adapter)
Fir
ewal
l
MIRC (Tomcat)
Image Submission
Database
Hibernate
NCIA caCORE API
Data Manager
Data Manager
CSM API
ProcessorsQuery, Result set, User Registration, Lookup Manager, CSM, Export
HibernateHibernate
MDB(Image zipping, Curation Data
Upload)
Retrieval
(Researchers)
DICOMHTTP
HTTPS
Cancer Centers /
Academia /Industry
DataAccessLayer
HTTPS, FTP
caGrid Clients
Java Server Faces (JSF)
Cedara I-Response client
Verify Submission Tool QC Tool
* … 1
Cedara ISG Server
Grid Client
Query Portal
Online Search
Generic Grid Services
NCIA GridServices
NCIA Nodes
Image Submission and Federated Search (3.0)
Fir
ewal
l
De-
ID
MIRCField
Center
MIRC Storage Service
MIRC DICOM Service
MIRC Database Service (Adapter)MIRC Database
Service (Adapter)
Fir
ewal
l
MIRC (Tomcat)
Image Submission
Database
Hibernate
NCIA caCORE API
Data Manager
Data Manager
CSM API
ProcessorsQuery, Result set, User Registration, Lookup Manager, CSM, Export
HibernateHibernate
MDB(Image zipping,Curation Data
Upload)
Retrieval
(Researchers)
DICOMHTTP
HTTPS
Cancer Centers /
Academia /Industry
DataAccessLayer
HTTPS, FTP
BDTBDT
caGrid Clients
Java Server Faces (JSF)
Cedara I-Response client
Verify Submission ToolVerify Submission Tool QC ToolQC Tool
* … 1
Cedara ISG Server
Cedara ISG Server
Grid Security
Grid Security
Grid Client
Query Portal
Online Search
Generic Grid Services
NCIA GridServices
NCIA Nodes
NCIA Grid Broker
NCIA Grid Broker
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Grid Services
caGrid Services
• New NCIA caGrid Services (release 3.0)
• Middleware enabled applications can be used to issue queries to the NCIA repository
• Exposes NCIA caCORE API over caGrid
• Generated using caGrid tools (toolkit, Introduce, GAARDS,etc.)
• Query via Common Query Language (CQL)
• Features
• Image retrieval via Bulk Data Transport (BDT)
• Leverages grid security
• Domain objects returned
caGrid Services (continued)
• Additional Data Service generated with caCORE Toolkit
• Implemented to enhance performance between NCIA caGrid Nodes
• What does a grid-enabled NCIA mean to you?
• Other caGrid enabled applications have the ability to pull down metadata and images from NCIA nodes using Bulk Data Transport
• Those institutions with NCIA nodes will be able to provide search and download capabilities to other applications connected to the caGrid
• Sample CQL Query• Find Patient with Patient Name = “John Doe” AND Patient ID = “12345”
<Target name="gov.nih.nci.ncia.domain.Patient">
<Group logicRelation="AND">
<Attribute name=”patientName” predicate="EQUAL_TO” value=”John Doe”/>
<Attribute name=”patientId” predicate="EQUAL_TO” value=”12345”/>
</Group>
</Target>
Grid Security Implementations
• Release 3.0• NCIA maintains an internal database of users through its custom CSM
implementation. • Each user in the NCIA user table is provided with x509 certificates
• Release 3.1• Upgrade to CSM 3.2, integration with NCI LDAP• External Authentication mechanism and localized authorization scheme
• NCIA will pull certificate from issuing authority, OSU Dorian Server, to validate credentials.
31
NCIA Installation
NCIA Installation
• To install your own NCIA• Download the NCIA download bundle from the NCICB Download Center, http://
ncicb.nci.nih.gov/download/#NTools• Follow the installation guide and setup instructions available on the NCIA GForge
site, https://gforge.nci.nih.gov/plugins/scmcvs/cvsweb.php/ncia-docs/install%20guides/?cvsroot=ncia
• Hardware requirements are documented and are available from GForge, https://gforge.nci.nih.gov/plugins/scmcvs/cvsweb.php/ncia-docs/NCIA%20Hardware%20Requirements/?cvsroot=ncia
• The NCICB will soon be offering installation and configuration assistance to those institutions installing a local grid-enabled NCIA
• Image markup storage and retrieval requires server license• A separate ISG server license is required from Cedara to operate and integrate the
image markup storage and retrieval functionality.
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Questionsand
Demonstration
34
Backup Slides
Release 3.0
• Code restructuring that reflects best practices for software design and separation of concerns that will help prevent careless mistakes from turning into critical production issues.
• Sophisticated caGrid access interface that allows us to take quality of service into account when making calls to our grid partners.
• Upgrade to latest and greatest version of MIRC (T32) and reorganization of the MIRC CVS module so we can tag the code base without confusing everyone.
• Totally redesigned MIRC database adapter that will prevent duplicate image submission, handles exceptions correctly, and is designed to grow without becoming a burden to maintain.
• Markup persistence with Cedara IRW.
• New NCIA pure DICOM object model featuring:
• Increases CDE reuse from 9% to 80%
• Currently being reviewed for silver compatibility
• Bulk Data Transport
• Grid Security
• Major cleanup of over 85,000 duplicate image records which fixes critical download issues.
• Documented, repeatable process for installation of NCIA grid nodes on MS SQLserver.
• Incorporation of new build and deployment documentation and comprehensive documentation of NCIA configuration in all 4 tiers.
• Standardized and working dual file system configuration for QA and STAGING tiers of NCIA.• Critical bug fix support of the production system.