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INSTRUCT Image Processing Centre for Microscopy

INSTRUCT Image Processing Centre for Microscopy. European Infrastructure for Structural Biology. ESFRI= Infrastructure for science. Integrated Imaging. Resolution range. Thickness range. I 2 PC. Transmission EM. SCOPE. Single particles. Icosahedral particles. Electron

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INSTRUCT Image Processing Centre for Microscopy

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  1. INSTRUCT ImageProcessing Centre forMicroscopy

  2. EuropeanInfrastructureforStructuralBiology

  3. ESFRI=Infrastructureforscience

  4. IntegratedImaging Resolution range Thickness range I2PC Transmission EM

  5. SCOPE Single particles Icosahedral particles Electron crystallography Helical particles Electron Tomography X-Ray Tomography

  6. Image processing Organization FUNCTIONS Project support Standarization User support Training New algorithm development

  7. BENEFITS High-Throughput 3D-Microscopy Standarization of Image processing workflow Reduction of the Learning curve Increase of reproducibility Reduction of Processing time User support Objectivecomparison Of algorithms Software interoperability Project support Access to the latest And best algorithms Minimization of Analysis errors Image processing training

  8. Personnel Director: JMC Staff plan 2011/12 Tech. Director CSIC: COSS Tech. Director UAM: RM Admin (June-12) Research team Infrastructure team Service team Associate scientists AQ JO Tech3 (June-12) JJFR JMRT JRM Tech4 (June-12) JMB JB JJV Tech5 (June-12) CSM AZP JC FPI (Oct-11) AP PostDoc(Dec-11) JV Col

  9. I2PC

  10. I2PC

  11. Users: Structural biologists Workflow platform Single Particles Electron Tomography Electron Crystallography Imaging modalities … High-Performance Computing Computational resources SCIPION

  12. ExternalCollaborations • Dr. Chiuis at theScientificcommittee of Instruct. • Dr. Baumeister, Dr. Frank and FEI at theScientificcommittee of I2PC • 2009: Visit COSS and RM to AMI • 2010: Visit RM, JMC to NCMI • 2010: VisitFEI to I2PC • 2011: Visit SL toI2PC • 2011: Visit HS toI2PC • 2011: VisitBC to I2PC • 2011: Visit COSS and AQ to AMI • 2012: DeveloperWorkshop(*.*) • 2012: NCMI-I2PC Benchmark

  13. ExecutionLayerSimplicity • WorkFlows • DistributedSystem Data Abstraction

  14. DistributedSystem Worker Host 2 Worker Host 1 SCIPION client Web Services Database

  15. DistributedSystem Worker Host 2 SCIPION client Worker Host 1 Web Services Database

  16. DistributedSystem

  17. ExecutionLayerSimplicity • WorkFlows • DistributedSystem Data Abstraction

  18. Data Abstraction Wrappers I/O ParametersOntology • ProcessOntology Logical & PhysicalTypesOntology

  19. ProcessOntology

  20. ProcessOntology

  21. Logical & PhysicalTypesOntology Set of Micrographs Micrograph Stackwithsampling Imagewithsampling Microscope Image Stack SamplingRate ScipionMicroscope tiff ccp4 spi xmipp img spi A/pixel

  22. Logical & PhysicalTypesOntology

  23. Logical & PhysicalTypesOntology

  24. Task I/O ParametersOntology

  25. Task I/O ParametersOntology

  26. ExecutionLayerSimplicity • WorkFlows • DistributedSystem Data Abstraction

  27. WorkFlows BPMN

  28. WorkFlows

  29. WorkFlows Sync BPMN + Data Web ServiceWorkFlow Management Async Async REST Sync Worker Host Web Service Executer

  30. WorkFlows • WorkFlow Repository • WorkFlow Engine • WorkFlow Queue • WorkFlow Monitor • Can disconnect • Customized WorkFlow Worker Host 2 SCIPION client Worker Host 1 Web Services

  31. WorkFlows • DistributedSystem Data Abstraction ExecutionLayerSimplicity

  32. Execution Layer Web Service XML Scipion Monitor ScipionLauncher EMAN ScipionExecuter XmippScipionExecuter Spider ScipionExecuter Outputs

  33. Execution Layer Web Service XML

  34. Workingdirconfig • Log Fileconfiguration • Executepreruncommandsifexist • Queue or FrontEnd • Launcher • Executer • Monitor • Parameter parsing • Task Execution • Execution monitoring

  35. Roles/Community & Privilege

  36. http://sourceforge.net/projects/scipion/

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