Methods and tools for a collaborative environment supporting - - PowerPoint PPT Presentation

Methods and tools for a collaborative environment supporting experiments in neuroscience

Focus K3D Workshop on Anatomical Models – Nice – June 17 2009

Andrea Schenone

Department of Communication, Computer and System Sciences University of Genova

Focus K3D Workshop on Anatomical Models - Nice - 16-17/06/2009

Neuroscience

neurology psychology cognitivism biophysics mathematics engineering

domain issues

biology genomics proteomics computer science modeling machine learning Scientific paradigms Methods and algorithms Data and techniques

Focus K3D Workshop on Anatomical Models - Nice - 16-17/06/2009

data issues

data managing computing models imaging genetics signals neuro psychological tests machine learning

Neuroscience

• ntologies

Formats Schemas Procedures Semantics

Focus K3D Workshop on Anatomical Models - Nice - 16-17/06/2009

technology issues

data managing computing security privacy formats schemas web access certification authorization distributed data collaborative tools hpc grid cloud

Neuroscience

Methods Tools Software environments

Focus K3D Workshop on Anatomical Models - Nice - 16-17/06/2009

Experiments in neuroscience

Multiscale approach Multimodal analysis Multicentric data Collaborative tools Extensibility requests Scalability issues Complexity

Focus K3D Workshop on Anatomical Models - Nice - 16-17/06/2009

Clinical applications

Computer Assisted Diagnosis Support to surgery Time series analysis Clinical Trials

Collaborative environments in neuroscience

Research applications

Retrospective analysis Algorithms testing Models validation Activation studies Definition of biological markers Statistical models

All these challenges need a lot of requirements to be satisfied

Focus K3D Workshop on Anatomical Models - Nice - 16-17/06/2009

Our tentative solution

XTENS (eXTensible Environment for NeuroScience)

Web/Grid Portal Repository Application Multipurpose Taxonomic Structure (process, event) Complete description of relationships between data and actions

Focus K3D Workshop on Anatomical Models - Nice - 16-17/06/2009

XTENS architecture

Relationships

Decoupling repository and application Portal Web-based access Multimodal / multicentre data management Local / remote visualization Decoupling hardware and software Software as a Service approach Distributed data management Virtualizing devices

Focus K3D Workshop on Anatomical Models - Nice - 16-17/06/2009

XTENS architecture

Technology

Repository Domain: * Repository portal * Database * Grid Storage Xengine Framework Application Domain: * Application portal * External applications * Hardware devices * Grid-portal with plugins EnginFrame Data & computational Grid Advanced hardware resources

Focus K3D Workshop on Anatomical Models - Nice - 16-17/06/2009

XTENS schema

Need for data extensibility XCEDE schema (XML-based Clinical and Experimental Data Exchange) BIRN (Biomedical Informatics Research Network) Projects Subjects Operators Visits Locations Studies Acquisitions Results Other

Models

Focus K3D Workshop on Anatomical Models - Nice - 16-17/06/2009

XTENS schema

Process:

structured sequence of events

Event:

single step of the process

Conditional sub-processes Detailed logs

Focus K3D Workshop on Anatomical Models - Nice - 16-17/06/2009

XTENS schema Application Specific Taxonomic Structure

Specific configurations depending on different applications Relationships between data and actions

Focus K3D Workshop on Anatomical Models - Nice - 16-17/06/2009

XTENS interface

Visits

Focus K3D Workshop on Anatomical Models - Nice - 16-17/06/2009

XTENS interface

Subjects

Focus K3D Workshop on Anatomical Models - Nice - 16-17/06/2009

XTENS interface

Studies

Focus K3D Workshop on Anatomical Models - Nice - 16-17/06/2009

XTENS interface

History

Focus K3D Workshop on Anatomical Models - Nice - 16-17/06/2009

Application

Collaborative environment in support to epilepsy surgery

Drug resistant epilepsy Ablation of the epileptogenic zone Surgical planning Collaborative environment Multimodal imaging Visualization tools Registration and segmentation methods Time series analyses

Partner: Niguarda Hospital - Milan

Focus K3D Workshop on Anatomical Models - Nice - 16-17/06/2009

Application

Collaborative environment in support to epilepsy surgery

Electrodes implantation for SEEG acquisition Implant planning for trajectories Mapping of positions and signals

• n the reference space

Analysis of SEEG traces Definition of surgical targets Surgical planning Retrospective studies with a large number of cases Mapping on atlases Model of epileptic seizures

Focus K3D Workshop on Anatomical Models - Nice - 16-17/06/2009

Application

Collaborative environment in support to epilepsy surgery Requirements

Distributed data Imaging & signals Extensible repository Safe web access Multimodal correlation Interactive/Remote visualization Computational requests Metadata management

Focus K3D Workshop on Anatomical Models - Nice - 16-17/06/2009

Models

Brain

Focus K3D Workshop on Anatomical Models - Nice - 16-17/06/2009

Models

Vessels

Focus K3D Workshop on Anatomical Models - Nice - 16-17/06/2009

Models

Electrodes

Focus K3D Workshop on Anatomical Models - Nice - 16-17/06/2009

Models

Segmentation Registration Integration Mapping

Details in: Corradi et al. HealthGrid 2009 Thanks

Focus K3D Workshop on Anatomical Models – Nice – June 17 2009

Focus K3D Workshop on Anatomical Models - Nice - 16-17/06/2009

XTENS architecture

Semantic integration with external sources Interface to PACS/RIS Data access protected also by robot certificates