A Grid Environment for Medical Imaging A Grid Environment for Medical Imaging LRMN Sorina POP,...
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A Grid Environment for Medical ImagingA Grid Environment for Medical Imaging
LRMNLRMN
Sorina POP, Tristan GLATARD
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LRMNLRMNSorina POP, Tristan GLATARDSorina POP, Tristan GLATARDCIRA, 2 juin 2009CIRA, 2 juin 2009
SummarySummary
Medical Imaging
Grid environment for medical imaging
Perspectives
Acknowledgments
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LRMNLRMNSorina POP, Tristan GLATARDSorina POP, Tristan GLATARDCIRA, 2 juin 2009CIRA, 2 juin 2009
Medical ImagingMedical Imaging
• CAVIARMyocardium segmentation
Motion estimation
• ThIS/GATEMonte-Carlo simulation
Cancer treatment planning
• SIMRISimulation of MRI
Parellel MPI jobs
ThIS Simulation
Simri
Caviar Caviar
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LRMNLRMNSorina POP, Tristan GLATARDSorina POP, Tristan GLATARDCIRA, 2 juin 2009CIRA, 2 juin 2009
Grid environment for medical imagingGrid environment for medical imaging
• Reliable and responsive grid execution Successful execution of one application on a grid nodeDistant grid node environment and application customization
• Application parallelization MPI (Message Passing Interface) -> SimriSplit the simulation into independent jobs (Monte Carlo) -> Gate
• Execution framework: advanced tools forJob submission, monitoring and retrievalIntegration into service platforms
• High level interface
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LRMNLRMNSorina POP, Tristan GLATARDSorina POP, Tristan GLATARDCIRA, 2 juin 2009CIRA, 2 juin 2009
Reliable and responsive grid executionReliable and responsive grid execution
• DIANERegisters/removes agentsSchedules tasks on agentsStdout/err transfers
• EGEE – gLite Schedules agents on grid sitesTransfer input/result files to/from worker nodes
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LRMNLRMNSorina POP, Tristan GLATARDSorina POP, Tristan GLATARDCIRA, 2 juin 2009CIRA, 2 juin 2009
Execution frameworkExecution framework
• Moteur workflow engineWorkflow execution
• Each application is described as a workflow (using Taverna)
Job submission, input selection and data piping between jobs
• Moteur – DIANE interfaceProvides generic agents
Starts DIANE master and submits DIANE agents
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LRMNLRMNSorina POP, Tristan GLATARDSorina POP, Tristan GLATARDCIRA, 2 juin 2009CIRA, 2 juin 2009
Graphical interface to the gridGraphical interface to the grid
• VBrowserProvides user interface to the grid
Browses input/result files
Launches Moteur
Follows experiment progress (job monitoring)
• Application: the Gate-LabGATE-Lab client (VBrowser plugin)
• Parses simulation (mac) file, zip inputs• Stores inputs on the grid, submits workflow• Keeps track of simulation history
GATE-Lab server• Launches workflow engine• Starts DIANE pilot-job master• Submits agents when necessary
VBrowser
Gate-Lab client
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LRMNLRMNSorina POP, Tristan GLATARDSorina POP, Tristan GLATARDCIRA, 2 juin 2009CIRA, 2 juin 2009
Perspectives (I)Perspectives (I)
• VIP – Virtual Imaging Platform
• GoalEnable heavy simulations: multimodal, dynamicStore and retrieve data (organ models and simulated images)
• Multi-platform executionLarge-scale grids (EGEE, NorduGrid)Local clusters (Creatis, IN2P3)GPU
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LRMNLRMNSorina POP, Tristan GLATARDSorina POP, Tristan GLATARDCIRA, 2 juin 2009CIRA, 2 juin 2009
Perspectives (II) Perspectives (II)
• Distributed database for medical imagingStorage, sharing, indexing and search on metadata
Technologies• iRODS
– Access and uniform management of heterogeneous data distributed among different sites
• MDM (Medical Data Manager)– Management of distributed DICOM images, high security level
Medical Images Database
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LRMNLRMNSorina POP, Tristan GLATARDSorina POP, Tristan GLATARDCIRA, 2 juin 2009CIRA, 2 juin 2009
AcknowledgementsAcknowledgements
• University of Lyon, CREATIS-LRMN• Hugues Benoit-Cattin, David Sarrut, Patrick Clarysse
• I3S, CNRS• Johan Montagnat
• University of Amsterdam, Academic Medical Centre• Silvia D. Olabarriaga
• CERN• Jakub T. Mosciki