grid services for medical image processing and …miccai.irisa.fr/Program/description/Johan-Montagnat...MICCAI tutorial on grid services for medical image processing and registration

Johan MontagnatI3S, CNRS

http://www.i3s.unice.fr/~johan/

Introduction

MICCAI tutorial on

grid services for medical image processing and

registration

MICCAI tutorial on grid services for medical image processing and registration Johan Montagnat 2

Agenda

Grids, a tool for compute and data-intensive medical imaging applicationsJohan MontagnatMammography analysis on gridsMike BradyBiomedical Informatics Research NetworkRon KikinisIXI e-Science projectDerek HillCoffee breakThe case of medical image registrationDaniel RueckertRound table: our vision of grid technology for medical image registration, trends and problems, opened discussion, call for participationX. Pennec, D. Hill, J. MontagnatLunch

9h

9h30

9h50

10h10

10h3010h50

11h20

12h20


What are grids?

The myth: providing unlimited computing power by letting the user transparently access to infinite Internet resources.

Early grid adoptersData storage: napsterComputation: SETI@homeInformation: web

The infamouselectrical network analogy

Client-server technology}


What are grids?

Assembling resourcesStorageComputingNetwork

Federating usersLarge scale user communities (Virtual Organizations)Ease exchanges

Pushing standardsCommunication protocolsData representation and formatsComputation control languages

The real grid potential is in sharing resources, data, and knowledge.


New bottles around old wine?

Scalability/Extensibility problemsLoad balancingParallelizationDecentralizationFault toleranceSecurity...

Distributed computing has addressed these kind of problems for decades!

New wineInteroperability high level interfaces, standardsAuthentication and autorization certificates and policies

Peer-to-Peer (P2P) or agent technologies matureAlternative to the client-server approach


The new factors empowering grids

Faster networksGrowth of network bandwidth vs growth of computing/storage: cheapest data exchanges

Cheap PCsSuccessful development of cluster computingSome degree of standardization of hardware and software

Standardization bodiesW3C http://www.w3c.org/ (HTTP(S), *ML, SOAP, WSDL...)OASIS http://www.oasis-open.org/ (WS, security...)Global Grid Forum http://www.ggf.org/ (OGSA, WS-RF...)...

Grid marketingIndustry adoption


All is becoming gridified

Overuse of “grids”grid = parallelismgrid = cluster computinggrid = just name itgrid or gridS?

Over-expectationsin grids deployment schedulein grids capabilitiesin transparency of grids from the user point of view

PCs clusters are:cheap... but administrators are notable to deal with embarrassingly parallel applications

Supercomputers and dedicated systems have their own playground


From PCs to supercomputers

Several kind of grids:network of computersnetwork of clustersnetwork of supercomputers

Single PC capabilitiespowerful, yet limited capabilities of a each hostgeneral purpose network connection

Parallelismtrade-off between splitting and network overhead

Supercomputerslowest communications overhead, large splitting

Global GridNetwork of clusters and supercomputersResource brokering among available resources

Medical imagingcommunity


Grids are emerging technologiesSome components available

User authenticationHigh performance data transferData managers with replication and metadataResource brokering...

Still a lot to be donePerformance issues in scalabilityHigh level representation of dataTransparency of the underlying infrastructure...

Medical data processing is very complexThis community has one of the most challenging requirements listConfidentiality of data and security requirementsParallel processing, interactive jobs, emergency situations...


SemanticsToo much information kills information

To find some information on the web: googleTry “Mike Brady” keyword...

Semantic webCommon framework that allows data to be shared and reused across applicationsGive explicit meaning to informationResource Description Framework

Semantic gridsPropagate to grids what may become the web

Ontologies, OWLFormally describe the meaning of terminology used in a domainEnable processing of information rather than just delivery to humans


Real grid enabled applications

Very few decentralized, scalable algorithmssuch as Domain Name Service

How does Google backup the web?6 centers20000 PCsLoad distribution

Embarrassingly parallel applicationsEasily distributed computationsJust bring in more CPU and bandwidth

More to learn from P2P and agent technologies

Lot done in the field of data managementWhat about computations, knowledge extraction?

Client/Server

Client/Server

Client/Server

Client/Server

Client/Server


Application areas

High Energy PhysicsPb of data generated per sec as the output of the Large Hadron Collider

AstronomyAstronomy images

Earth ObservationSatellite images

GeophysicsSismic data revealing underground structure

Aeronautics, industryFinite Element Modeling, etc.

...


Sharing to get stronger

Unlike electrical power, adding computers is not equivalent to add volts

Distributed computing conjecture : a parallel machine performance is lower than the sum of individual processors performance

Humans are selfishEvery user want to use other's resources without seeing others using its resources

The real grid potential is in sharingdatasets: to create virtual databases, esp. for rare dataalgorithms: to foster reusability and comparisonsresources: to face computation picksenforce standards


Medical data on grids

Data storage and archival10 Tb of medical images/hospital/yearNeed for long term archival (20 to 70 years)

DatasetsLarge scale data setsStatistics, epidemiologyRare diseasesPersonalized atlases construction

Data representationMedical imagesMetadataOntologies


Security of medical applications

Authentication and AuthorizationCertificate authorities issuing certificate pairsAsymmetric certificate based authenticationAuthorization policies enforcement

Data access control at individual levelPhysiciansPatientsResearchers

DelegationGranting access rights

Encryption for data storage and transferBest effort privacy protectionKey-based data encryption

owner


Biomedical computing

Embarrassingly parallel applications

databases processingbioinformatics

Parallel computationscostly processings

Interactive computationsresources reservationuser supervision and validation

Emergency situationsresources preemption

Algorithms warehouse


Standardization

Medical data representationFile level: DICOM, Analyse...Database level: Data storage and mediatorsInter-sites: ontologies

Algorithms reusabilityImage formatsInput/outputParameters

Unique opportunity to enforce standards


Medical algorithms assessment

Sharing dataCommon datasets

Sharing algorithmsTesting others algorithms

Sharing proceduresCommon test suites

Sharing computing resourcesLarger assessment studies

Empowering testing and comparisons

Seq1 > dcscdssdcsdcdsc bscdsbcbjbfvbfvbvfbvbvbhvbhsvbhdvbhfdbvfd

Seq2 > bvdfvfdvhbdfvb bhvdsvbhvbhdvrefghefgdscgdfgcsdycgdkcsqkc

…

Seqn > bvdfvfdvhbdfvb bhvdsvbhvbhdvrefghefgdscgdfgcsdycgdkcsqkchdsqhfduhdhdhqedezhhezldhezhfehflezfzejfv


Grid infrastructures in Europe

EGEEhttp://www.eu-egee.org/27 countries, 70 partnersProduction platform8000 PCs to be deployed in 2 yearsLCG2 middleware (Globus+DataGrid based)

DEISAhttp://www.deisa.org/consortium of supercomputing centersBuild a distributed terascale computing facilityTight coupling of supercomputing centers by high bandwidth networks


References and related events

HealthGrid associationhttp://www.healthgrid.org/HealthGrid conference (next event in Oxford, 2005)

BIRN: Biomedical Informatics Research Network http://www.nbirn.net/

TeraGrid: http://www.teragrid.org/

UK e-Science: http://www.rcuk.ac.uk/escience/ myGrid: http://www.mygrid.org.uk/, In silico biologyIXI: http://www.ixi.org.uk/, medical imaging

French ACI-GRID, http://www-sop.inria.fr/aci/grid/public/

Mammogrid, http://mammogrid.vitamib.com/

GEMSS, http://www.ccrl-nece.de/gemss/

Crossgrid, http://www.eu-crossgrid.org/

...


Conclusions

Grids are emerging technologiesEarly adoptersEvolving field

Yet, they are addressing medical imaging challenges

Standards and tools arisingSome successful applications deployedThe tool creates the need: new applications will emerge from grid infrastructures

Need to federate the biomedical communityStrengthen the communityDeploy large scale infrastructures

Need standardsTo enable flexibility and interoperability


Meeting follow-up

http://www.i3s.unice.fr/~johan/miccai/


Agenda

Grids, a tool for compute and data-intensive medical imaging applicationsJohan MontagnatMammography analysis on gridsMike BradyBiomedical Informatics Research NetworkRon KikinisIXI e-Science projectDerek HillCoffee breakThe case of medical image registrationDaniel RueckertRound table: our vision of grid technology for medical image registration, trends and problems, opened discussion, call for participationX. Pennec, D. Hill, J. MontagnatLunch

9h

9h30

9h50

10h10

10h3010h50

11h20

12h20

Documents

grid services for medical image processing and …miccai.irisa.fr/Program/description/Johan-Montagnat...MICCAI tutorial on grid services for medical image processing and registration