december 2006 national cancer imaging archive (ncia) october 11, 2007

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%

24

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

27

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.

33

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.