«Shanoir : une solu/on pour la ges/on de données distribuées en imagerie in- vivo» Jus/ne Guillaumont Isabelle Corouge
Shanoir: a solu-on for neuro- imaging data management Jus/ne Guillaumont, Isabelle Corouge VisAGeS U746 INSERM- INRIA, IRISA UMR CNRS 6074 - Rennes shanoir- contact@lists.gforge.inria.fr h?p://shanoir.org 2
Neuro- imaging: large quan/ty of data s/ll growing Modali/es: MRI, PET, Scanner, Examples: - MRI standard clinical examina/on: ~ 1400 images (> 100Mo) - MRI clinical research examina/on: ~ 4500 images (> 2Go) Clinical research: mul/- centers studies Need for data storage and archive Need for data structura/on Need for data sharing and accessing Exis/ng solu/ons CDs: simple solu/on but SHAring NeurOImaging Resources Mo-va-ons Limited life/me ( 5 years), Data integrity not guaranteed Physical storage PACS: Picture Archiving and Communica/on System Local (hospitals), regional or regional network à limited access SHANOIR: secure server accessible from any web browser Funded by ADT INRIA developed by VisAGeS Inserm- Inria U746 (5 engineers since 2008) 3
What is Shanoir? An open source web applica/on designed to: Archive and Index Search and Retrieve neuro- imaging data Share With: a user- friendly secure web access a database model build on an ontology 1 (OntoNeuroLOG, from the NeuroLOG 2 project) In order to: Enhance data availability and integrity Structure the data / Manage data provenance Facilitate collabora/ve research works Pool acquisi/on resources 1 Ontology: formal representa/on of knowledge as a set of concepts and the rela/onships between those concepts within a domain. 2 NeuroLOG: h?p:// neurolog.i3s.unice.fr/ 4
The User Side 5
Shanoir is in service in several projects Neurinfo (2009): MRI research facility OFSEP (2011): French MS- observatory FLI (2014): large- scale research infrastructure project Projects 6
SHANOIR @Neurinfo MRI Hospital Network NominaEve data Users Research PACS Study supervision and follow- up h2p://www.neurinfo.org Data access Anonymous data SHANOIR External Data Import DICOM Centers Users (ac/ve) Studies Subjects Examina/ons Datasets 31 52 60 2228 3157 114 441 Raw data (dicom) 1588 GB Processed data (niii) Meta- data Contacts Février 2015 1511 GB 20 GB elise.bannier@irisa.fr isabelle.corouge@irisa.fr 7
SHANOIR @OFSEP Observatoire Français de la Sclérose en Plaques Mul-ple sclerosis (MS) = 1 person / 1,000 à 80,000 pa/ents in France But with very good network: OFSEP 28 university hospital neurology departments 18 regional health care networks selected by the French Ministry of Higher Educa/on and Research aier the call for proposals "Cohortes 2010" (ANR) is a na/onal project with 10M on 10 years maintains and develops exis/ng and new cohorts (35,000 pa/ents in total) to answer specific ques/ons enriches exis-ng clinical data with biological samples, socio- economic data and neuro- images 8
OFSEP s goal 40,000 pa/ents 1 brain MRI every 3 years 1 spine MRI every 6 years During 10 years SHAring NeurOImaging Resources SHANOIR @OFSEP Observatoire Français de la Sclérose en Plaques à 200,000 MRI with several MR models v ~ 300 acquisi/on sites v device diversity : currently 14 different MR models à Standard na/onal MR protocol à SHANOIR plaqorm Contact jus-ne.guillaumont@inria.fr 9
FLI: large- scale research infrastructure project Selected by the call "Inves/ssements d Avenir" for "Infrastructure en Biologie et Santé" In coopera/on with: CEA CNRS Inria Inserm SHAring NeurOImaging Resources SHANOIR @FLI France Life Imaging Aims at establishing a coordinated and harmonized network of biomedical imaging in France 10
SHANOIR @FLI- IAM Node Informa/on Analysis and Management 11
SHANOIR @FLI- IAM Node Informa/on Analysis and Management à "Build an in- vivo image management infrastructure" for: The Clinician: to conduct large and/or clinical and preclinical research studies involving new innova/ve in- vivo medical imaging and new innova/ve therapeu/c procedures The Pharma: to provide pharma and CRO companies high technological computa/onal solu/ons in medical imaging The medical imaging community: to allow experimenta/on and valida/on of new innova/ve medical imaging solu/ons Strengths: Based on high technological exper/se and experience From data management solu/ons: CATI, SHANOIR, ArchiMed From medical image processing solu/ons: medinria, BrainVisa, VIP plaqorm From large na/onal clinical Cohorts: CATI, OFSEP Contacts chris-an.barillot@inria.fr michael.kain@inria.fr 12
So^ware architecture Shanoir is organized as a repository of neuroimaging files coupled with a rela/onal database where addi/onal metadata are stored. Environment Java Enterprise (JEE) JBoss Applica/on Server (AS) Eclipse (as IDE) ANT (as build tool) Subversion (for version control) Metadata Niii DICOM JEE frameworks JBoss Richfaces JAX- WS (for SOAP web services) JBoss Seam Java Persistence API (JPA) with Hibernate 3 13
Communica-on with client applica-ons DBMS Server Side Network SHANOIR Client Libraries Client Side + ShanoirTK SHANOIR Business Server QtShanoir MedInria + Network Access Storage Plugin Core 14
4 Client applica-ons Client applica/ons can query and retrieve data from any Shanoir server through web- services (SOAP). 4 client applica/ons have been developed: ShanoirTk (Java client command- line app) QtShanoir (C++ client app) QtShanoir has been integrated as a plug- in in MedInria 3, an advanced image processing soiware New: ShanoirUploader (Java client app) New: ishanoir (ios client app) 3 MedInria: h?p://med.inria.fr/ 15
QtShanoir in MedInria* On the right: Secure user access Query on Shanoir On the len: Results in a tree Checkboxes: Download of whole examina/on(s) or of some sequences * h2p://med.inria.fr/ 16
ShanoirUploader New PACS Shanoir Uploader Picture Archiving and CommunicaEon System (1) Query Retrieve (2) Anonymisa-on (3) Func-onali-es Download the data stored in a PACS, accessible via the local network Local anonymisa/on Upload the data on Shanoir server Asynchronous usage: Import (4) No wai/ng /me for the user Planned to deliver a completely automated import of data 17
ShanoirUploader New 18
ishanoir Shanoir Client for ios, iphone or ipad Func-onali-es Shanoir account configura/on Selec/on of data on the Shanoir server Download data from the Shanoir server Data transfer to viewers, like Osirix New 19
Development Roadmap Embedded quality control Automa/c control of sequence parameters during the import Automa/c control of intervals between two MRIs for OFSEP protocol < 3 years for the brain MRIs < 6 years for the spine MRIs [MRI brain - spine] < 1 month GUI: storage and visualiza/on of results of automa/c controls of visual controls Reapplica-on of a study- card on already imported data (in case of an error during acquisi/on or applica/on/configura/on of previous study- card) Adapt NifTI conversion on local MRI specifici-es (enhanced dicom ) Repor-ng/Sta-s-cs Size of data Results and progress of quality control 20
Shanoir is an open source soiware plaqorm designed to archive, structure, manage, visualize and share neuroimaging data with an emphasis on mul/- centric collabora-ve research projects. Thank you for your a?en/on! Do you have any ques/ons? 21
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Study- Card mechanism 23