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MammoGrid. European federated mammogram database implemented on a GRID infrastructure presented by Salvator Roberto Amendolia / CERN on behalf of the MammoGrid Consortium HealthGrid Forum Brussels, 20 th September, 2002. MammoGrid Consortium. CERN (Technical Coordinator)

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Mammogrid

MammoGrid

European federated mammogram database implemented on a GRID infrastructure

presented by Salvator Roberto Amendolia / CERN

on behalf of the MammoGrid Consortium

HealthGrid Forum

Brussels, 20th September, 2002


Mammogrid consortium

MammoGrid Consortium

  • CERN (Technical Coordinator)

    • Vitamib (France) - subcontractorFinance/Admin

  • Mirada Solutions (UK) – Medical Image Analysis S/W

  • Univ of Oxford (UK) – Medical Vision Laboratory

  • Univ of Pisa (I) – Medical Physics section

  • Univ oF Sassari (I) – Maths & Physics Dept

  • Univ West of England (UK) – Computing Research

  • Univ of Cambridge (UK) – Addenbrookes Hospital

  • Univ Hospital of Udine (I) – Inst of Diagnostic Imaging

    • Ospedale Valdese Torino (I) - Breast Screening Unit - subcontr.

    • Zybert Computing Ltd. (UK) -Subcontractor for GRIDserver

      Project kick-off meeting CERN 18th-19th September 2002

HealthGrid Forum - Brussels


Mammogrid objectives

MammoGrid Objectives

  • To evaluate current Grids technologies and determine the requirements for Grid-compliance in a pan-European mammography database.

  • To implement the MammoGrid database, using novel Grid-compliant and Federated-Database technologies that will provide improved access to distributed data and will allow rapid deployment of software packages to operate on locally stored information.

  • To deploy enhanced versions of a standardization system that enables comparison of mammograms in terms of intrinsic tissue properties independently of scanner settings, and to explore its place in the context of medical image formats (DICOM).

  • To develop software tools to automatically extract image information that can be used to perform quality controls on the acquisition process of participating centres (e.g. average brightness, contrast).

HealthGrid Forum - Brussels


Mammogrid objectives cont

MammoGrid Objectives (cont.)

  • To develop software tools to automatically extract tissue information that can be used to perform clinical studies (e.g. breast density, presence, number and location of micro-calcifications) in order to increase the performance of breast cancer screening programs.

  • To use the annotated information and the images in the database to benchmark the performance of the software described in points 3, 4 and 5.

  • To exploit the MammoGrid database and the algorithms to propose initial pan-European quality controls on mammographic acquisition and ultimately to provide a benchmarking system to third party algorithms.

HealthGrid Forum - Brussels


Mammography diagnosis and grid

Mammography Diagnosis and GRID.

GRID opens up the possibility of addressing important clinical needs in radiology:

  • Data sharing among clinicians for second review diagnosis.

  • Image Based epidemiological studies

  • Computer Aided Quality Control in Acquisition and Diagnosis

  • Validation of Computer Aided Diagnosis Systems

HealthGrid Forum - Brussels


A grid infrastructure is ideal

A GRID INFRASTRUCTURE IS IDEAL

The databases to statistically validate image based clinical hypothesis are:

  • Populated by large number of cases

  • Contain large files (1 mammogram 10Mb+)

  • Geographically distributed repositories

  • Heterogenous database formats

  • Need to be accessible to co-workers

    Development and validation of medical image analysis solutions demands:

  • Computationally expensive simulations.

  • Repeated runs for optimal parameter tuning.

  • Statistical test rigs.

  • Remote execution and maintenance

    Services (e.g. security) must be system-resident, invisible, generic

HealthGrid Forum - Brussels


Mammo grid philosophy

Mammo GRID Philosophy

  • Project concentrates on applying emerging GRID technology rather on developing it.

  • It plans to implement a ‘lightweight’ (but fully functional) GRID and study its usage in hospitals

  • It will draw heavily on other Grids projects e.g. DataGrid

  • It will deliver a prototype federated database of mammograms in hospitals in the UK and Italy

  • It will investigate :

    • the role of Grids-based meta-data for resolving queries

    • the use of standardised mammogram to resolve image and population variability

    • Health data security using a novel ‘Grid box’

    • the infrastructure needed for CADe

  • It will provide rapid feedback from the Hospital community

  • And should inform the next generation of HealthGrids developments

HealthGrid Forum - Brussels


Hep vs mammogrid

HEP vs Mammogrid

  • Similarities

    • Large number of big files

    • Files can be sensibly organized in directory tree

    • Need to replicate and move file copies between sites

    • Need to execute commands on the node which hosts data locally

  • Difficulties

    • Complexity of co-working in medical environment

    • Lack of trained IT personnel

    • Confidentiality

HealthGrid Forum - Brussels


Problem

Problem

  • Typical next generation HEP experiment

    • Large scale simulation & reconstruction effort

    • Heavily distributed processing and event storage

      • ~1000 scientists in ~100 of institutions

    • Complex analyses of distributed data

    • Large files (one event up to 2GB)

      10^9 files/year (x n, n>2)

      2 PB/year

  • Experiment lifetime

    • 20-25 years

  • GRID

    • Widely accepted as a solution

HealthGrid Forum - Brussels


The challenge in hep

The challenge in HEP

Can we provide, building on top of available public domain and open source components and standards, a functional distributed computing infrastructure to the community of our users which will remain operational even if underlying technologies keep changing?

HealthGrid Forum - Brussels


One hep solution

One HEP solution

  • AliEn framework

    • Lightweight, simplified but fully functional GRID implementation

    • Distributed file catalogue with support for replication

    • Strong (certificate) based authentication

    • Resource broker

    • Possibility to submit and execute commands in the system

  • It makes extensive use of Open Source components and the latest internet standards (SOAP, Web services, OpenSSL, OpenLDAP, Globus, MySQL, perl, CPAN)

  • AliEn provides coherent interface and shields user from rapid changes in underlying technology

  • On mid to long term, ALICE experiment remains committed to integrate AliEn with DataGRID solutions as they become available

  • Given the worldwide nature of ALICE computing, AliEn will be interfaced to other GRID solutions (U.S., Asia, Japan..)

HealthGrid Forum - Brussels


Alien and open source

AliEn and Open Source

Benefits of development based on OpenSource

components are more than obvious…

HealthGrid Forum - Brussels


Some alien features

Some AliEn features

  • Authentication module which supports various authentication methods (including Globus/GSI)

  • Distributed file catalogue built on top of RDBMS with user interface that mimics the file system

  • Secure file transport and replication Service

  • Task queue which holds commands to be executed in the system (commands, inputs and outputs are all registered in catalogue)

  • Computing and Storage elements

  • Metadata catalogue

  • Monitoring framework

  • C/C++/perl API

  • Web portal

  • EDG compatible authentication and JDL

HealthGrid Forum - Brussels


Grid of grids

AliEn stack

iVDGL stack

EDG stack

GRID of GRIDs

AliEn User Interface

HealthGrid Forum - Brussels


Mammogrid

Healthcare Institute

University Database

Hospital Italy

Local

Query

Local

Query

Local

Query

Local

Query

Query

Result

GRID

Clinician’s Workstations

Massively distributed data

AND distributed analyses

Local

Analysis

Local

Analysis

Local

Analysis

Local

Analysis

  • Knowledge is stored alongside data

  • Active (meta-)objects manage various versions of data and algorithms

  • Small network bandwidth required

Hospital UK

Shared meta-data

Analysis-specific data

Federated System Solution

HealthGrid Forum - Brussels


Mammogrid workpackages

MammoGrid Workpackages

  • WP 1Project Management

  • WP 2User Requirements Specifications

  • WP 3Information System Architecture and Grid Compliance

  • WP 4Local Node Implementation

  • WP 5 Integration Environment

  • WP 6 Standardisation Software

  • WP 7 Acquisition Control Software for a Grid deployment scenario.

  • WP 8 Software for CAD Diagnosis and QC in a Grid deployment scenario.

  • WP 9 Pilot Study 1: Breast Density Measurements in a Grid deployment Scenario

  • WP10 Pilot Study 2: CAD for Quality Control in a Grid deployment scenario

  • WP11 Dissemination & Exploitation

HealthGrid Forum - Brussels


Mammogrid implementation

Project Management

WP 1 - CERN (Vitamib)

GRID/DB

infrastructure

Integration

test bed

Information infrastructure

Use case/

validation

User

Req’s

& Specs

WP 3 - CERN/UWE

specifications

H/W

local node implem.

WP 5 - CERN

WP 4 - Mirada

WP 2

CERN/UWE

Hospitals

WP 9&10

Cambridge

Udine

Application S/W

Standardisation

S/W.

WP 7&8 - Oxford,

Pisa/Sassari

WP 6 - Mirada

Dissemination & Exploitation

WP 11 - All

MammoGrid Implementation

HealthGrid Forum - Brussels


Main deliverables milestones

Main Deliverables/milestones

  • User Requirements Specification and Technical System Specification (months 3, 6)

  • Prototype GRID-compliant database and information infrastructure (first release m. 18, final rel. m. 36)

  • Packaged medical imaging workstation with interface to GRID, secure GRID box, (month 12)

  • Grid compliant SMF software (month 12)

  • Application software (CADe etc.) (months 12, 24, 36)

  • Clinical Trial results (month 24, 36)

HealthGrid Forum - Brussels


Dissemination clustering

Dissemination & Clustering

  • “GRID related” dissemination efforts

    • CERN/UWE members of Global Grid Forum, GGF and of the Object Management Group, OMG

    • CERN already in GRIDSTART for dissemination and closely working with DataGrid. UWE to join.

    • Pursue relationship with EU funded GRID projects (e.g. CROSSGRID, BIOGRID, GEMSS)

    • Develop relationship with NDMA project (USA)

  • “Clinical dissemination”

    • Advisory Group (Oxford, Torino, IMIM & GEIE-LINC) to give visibility to future MammoGrid partners.

  • “Medical Image Analysis dissemination”

    • Academic dissemination through targeted conferences and journals in computer science & medical informatics

HealthGrid Forum - Brussels


Exploitation

Exploitation

  • Mirada

    • Establish SMF as a standard for breast density measurement.

    • Establish SMF as a standard for mammogram data exchange.

    • Prototype SMF based review workstation for CADiagnosis.

  • CERN/UWE

    • Study the spinning-out of GRID/database technologies to address needs in healthcare

  • Oxford

    • Develop patentable technologies for medical image analysis products.

    • Transfer of technology agreement with Mirada.

  • Pisa/Sassari

    • Develop patentable technologies for medical image analysis products.

HealthGrid Forum - Brussels


Mammogrid added value previous ec projects mammogrid

Distributed network of medical images DB (Medimedia)

GroupWare collaborative platform (Horizon)

Remote consultation/diagnostic, (Europath)

Case-by-case security implementations

Point-to-point connectivity on the Web

Multiple federated mammogram databases

Clinicians tele- and co-working in new and innovative groupings (‘virtual organisations’)

Distributed and ubiquitous analysis and diagnosis

Security handled by services’ on the Grid’

Massive connectivity and datasets with massive available compute power

MammoGrid Added ValuePrevious EC projects MammoGrid

HealthGrid Forum - Brussels


Ediamond uk and gp calma i

eDiamond (UK) and GP-CALMA (I)

  • similar approach, one UK based, one Italy based, one Europe wide

  • synergy!!

  • Different areas of application

    • Teaching & CPD eDiamond

    • Tele-diagnosis GP-CALMA

    • Quality control MammoGrid

    • Epidemiology MammoGrid

    • Algorithm development: data mining eDiamond

    • CADe development GP-CALMA

HealthGrid Forum - Brussels


Grid which one

GRID - which one?

  • One year ago GRID projects were still in their infancy

  • Globus Toolkit™

    • Open source toolkit for building GRID infrastructure and applications

    • APIs, SDKs, and tools which implement Grid protocols & services

  • Components Globus Toolkit™ are used in many current GRID (including EU DataGrid) projects but…

    • toolkit is only a toolkit

    • someone has to do integration work

  • Emerging new technologies and standards

    • Web services, W3 standard protocols..

    • B2B solution, not specifically designed to support massive distributed computing

HealthGrid Forum - Brussels


Web services

“Web Services”

  • Geneva, May 2001:

    • Instead of using Globus toolkit or waiting for DataGRID to deliver re-packaged version of Globus, we decided to try different path and use Web Services and related standards as a backbone of our GRID implementation

  • Web Services - components

    • WSDL: Web Services Description Language

      • Interface Definition Language for Web services

    • SOAP: Simple Object Access Protocol

      • XML-based RPC protocol; common WSDL target

    • UDDI: Universal Desc., Discovery, & Integration

      • Directory for Web services

  • GGF in Toronto, February 2002 :

    • Web Services declared as a key element of new OGSA (Open Grid Services Architecture) initiative

HealthGrid Forum - Brussels


Mammogrid

OGSA

I

HealthGrid Forum - Brussels


Alien open source components

AliEn Open Source Components

  • SASL/OpenSSL/OpenCA as authentication protocol

  • Globus/GSS as an implementation of authentication compatible with other Grid projects

  • ClassAds language for job description (compatible with EU DataGrid)

  • OpenLDAP for configuration management

  • Apache for Web Portal

  • MySQL as relational database backend

HealthGrid Forum - Brussels


Conclusions on alien

Conclusions on AliEn

  • After just one year of development with limited resources, AliEn has become a lightweight, simplified but fully functional GRID implementation

  • Adding AliEn interface between our application and external GRID infrastructure

    • Allows us early prototyping of GRID technology

    • Enables massive distributed production

    • Protects users from rapid changes in technology

  • It makes extensive use of Open Source components and the latest internet standards (SOAP, OpenSSL, OpenLDAP, Globus, MySQL,

  • These components and modules are interchangeable and easily replaceable by other (possibly non-OpenSource) components offering the same functionality

HealthGrid Forum - Brussels


Mammogrid

(…)

In our current picture, GridBox will act as adapter between GRID (services) and Mirada Workstation

It is possible to define an abstract interface (API to be used by Mirada Workstation) for which we will provide an implementation based on AliEn.

If there is clear benefit for our project, we could consider using

WebSphere as UDDI service

DB2 as relational DB backend

However, this has not been planned and would require additional effort.

HealthGrid Forum - Brussels


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