NeuroBase: An Information System for Managing Distributed Knowledge and Data Bases in Neuroimaging. Christian BARILLOT DR CNRS

Transcription

1 NeuroBase: An Information System for Managing Distributed Knowledge and Data Bases in Neuroimaging Christian BARILLOT DR CNRS IRISA UMR 6074 CNRS, UR INRIA-Rennes Rennes Vista project Campus de Beaulieu Rennes irisa.fr web: //

2 Context Framework: Concerted Action of the French ministry of research «Technologies for health» Period: Coordinator : Christian BARILLOT Official partners list: VISTA and TeXMex project, IRISA, Rennes (Image processing and indexation) IFR 49 " Functional Neuroimaging» Paris & Orsay (CEA, INSERM U494, CHR Pitié Salpétrière) (clinical and cognitive neuroimaging) CARAVEL Project, INRIA Rocquencourt (data bases) INSERM U438, Grenoble (processing in cognitive neuroimaging) IDM Lab., Univ Rennes I (clinical neuroimaging) TIMC Unit (SIC team), Grenoble (processing & cognition) EPIDAURE project, INRIA Sophia-Antipolis (Image processing)

3 Objectives (1) Specify how to connect and access to information data bases in neuroimaging Applications in neurology and cognitive neuroscience Definition of a data-processing architecture allowing : Access and sharing of experimental neuroimaging results Access and sharing of image processing procedures (on anatomical and functional data) This project mainly concerns the: Elaboration of a reference model for the sharing of heterogeneous and distributed neuroimaging data Specification of a system architecture and an information model (semantic referential of data and image processing methods)

4 Objectives (2) At the end,, such a system must allow the indexation of information accessible from different heterogeneous and distributed data bases for : The search of experiments according to a specific protocol (e.g. allow the retrieval of specific descriptions of experiments, allow the examination of experimental results, and retrieving eventually the related images) The search of similar results (e.g. for the study of anatomofunctional networks) The search of images containing singularities (spatio-temporal particularities for instance) Transverse searches to highlight possible regularities (similarly to a "data mining" type approach) (e.g. possible similarities of the protocol corpus, of the experimental results and the related images, or encore spatio-temporal invariants).

5 Example of a system architecture for sharing of heterogeneous and distributed data Users applications s s Internet Access Accès via Internet Mediation services Common access service (query/retrieve) Services communs d accès using (interrogation/récupération) the «Neurobase» semantic referential Adaptateur Wrapper Adaptateur Adaptateur Adaptateur Wrapper Wrapper Wrapper Heterogeneous & Distributed Information Data Base s Information Base d informations data base Information Base d informations data base Information Base d informations data base Information Base d informations data base

6 Scientific topics Methodologies for conception of probabilistic anatomical and functional brain models (Vista and Epidaure Projects ) Conception and experimentation of functional neuroimaging procedures (IFR 49 and INSERM U438) Ontology in medical informatics and experimental neuroimaging (INSERM U455, IDM team, TIMC-SIC SIC) Information data base, mediation systems and image indexation (Caravel and TeXMeX projects)

7 Long term action: Elaboration of a reference model for the sharing of image data in neuroimaging This covers the modeling of the: Images, regions of interest Acquisition procedures Stimulation procedures (activation paradigms) Indexation processes Interpretations performed on experimental data (labeling of anatomical region or functional responses) Matching procedures between images and patients Image processing procedures for segmentation and quantification

8 Short term work plan Elaboration of a demonstrator based on some existing modules: Le Select ( BrainVISA/Anatomist ( VIsTAL ( Implementation of functionalities such as data wrappers & mediators, medical image processing methods (data access, segmentation, visualization, )) and data flow approaches. registration, This demonstrator will be developed and tested in the context of two test bed applications: Clinical application dealing with epilepsy surgery Cognitive application dealing with the delineation of the visual cortex areas Secondary applications could also be addressed such as brain degenerative diseases in neurology.

9 Work packages for the «Neurobase» Demonstrator Software development Ontologies Interface between «BrainVisa», «LeSelect» and «Data Flow» components. Fusion between distributed components (segmentation, registration and visualization methods). User interaction definition of examples processing data flows (e.g. «brain segmentation»). Ontology instantiation of image processing methods (e.g. «brain segmentation»). Tractability and integration of qualitative criteria. Definition of «Neurobase» semantic referentials (on data and methods). Definition of semantic correspondences Definition of entities/relations terminology Sharing the conceptualization of semantic referentials Selection of a common freeware UML representation tool (eg. ArgoUML

10 List of people involved C. Barillot, I. Corouge,, P. Hellier (VISTA VISTA project, IRISA, Rennes) P. Gros,, L. Amsaleg (TexMeXTexMeX project, IRISA, Rennes) E. Simon, J.P. Matsumoto (CARAVEL project, INRIA, Rocquencourt) H. Benali,, J.P. Bazin (INSERM INSERM U494 - IFR 49, CHR La Pitié Salpetrière re,, Paris) D. Hasboun (IFR IFR 49, CHR La Pitié Salpetrière re,, Paris) M. Pelegrini (INSERM INSERM U483 - IFR 49, CHR La Pitié Salpetrière re,, Paris) D. LeBihan,, D. Papadopoulos,, J-F. J Mangin,, Y. Cointepas (CEA-SHFJ, IFR 49, Orsay) B. Gibaud,, O. Dameron,, X. Morandi (IDM IDM Lab., CHR Pontachaillou, Rennes) M. Dojat,, N. Richard (INSERM INSERM U438, Grenoble) C. Garbay (SIC SIC Team, TIMC, IMAG, Grenoble) G. Malandain (EPIDAURE project, INRIA, Sophia-Antipolis Antipolis) F. Aubry (INSERM INSERM U455 *,, Toulouse) B. Dubois, B. Batrancourt,, S. Kinkingnehun (Neurology Dept. *,, CHR La Pitié Salpetrière re,, Paris) *: Collaborative team partner