Presentation Shanoir

Transcription

26/01/2016
SHAring NeurOImaging Resources
Shanoir:SoftwareasaService
EnvironmenttoManagePopulation
ImagingResearchRepositories
Anopensourcewebplatformforneuro-imaging
MotivationsforShanoir
•
Neuro-imaging:largequantityofdata– stillgrowing
– Modalities: MRI, PET, Scanner,…
– Examples: - MRIs tandardclinicalexamination:~1400images (>100Mo)
- MRIclinicalres earchexamination:~4500images(>2G o)
Christian Barillot
VisAGeS Inserm U746– IRISA/Inria Rennes
– Clinical research: multi-centersstudies
➔ Needfor datastorageandarchive
➔ Needfordatastructuration
➔ Needfordatasharingandaccessing
•
Existingsolutions
– CDs:simple solutionbut
•
•
Limitedlifetime(∼ 5years ),Dataintegritynotguaranteed
Phys icals torage
– PACS:PictureArchivingandCommunicationSystem
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•
[email protected]
http://shanoir.org
Local(hos pitals ),regionalorregionalnetworkà limitedacces s
SHANOIR:secureserveraccessiblefromanywebbrowser
FormationFCRIN :«SPECIFICITEDELA
RECHERCHECLIN IQU E
EN IMAG ERIE»
RECHERCHECLIN IQU EEN IMAG ERIE"
Anopensourcewebplatformforpopulationimaging
WhatisShanoir?
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•
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On l i n e
Data d e-i d en ti fi cati o n V i su al i zati o n o f
sto red d ata
an d p ati en t p ri vacy
Do wn l o ad An open source web application designed to:
– ArchiveandIndex
– SearchandRetrieve
neuro-imagingdata
– Share
With:
– auser-f riendlysecure webaccess
– adatabasemodelbuild onanontology 1
(OntoN euroLOG , f
rom the N euroLO G
sto red d ata
Su p p o rt fo r
p ro cessed (d eri ved ) d ata
Do wn l o ad W eb project)
P o rtal
Inorder to:
– Enhancedataavailability andintegrity
– Structure thedata/Managedataprovenance
– Facilitatecollaborative researchworks
– Pool acquisition resources
P ro cessed d ata
Su p p o rt fo r
mu l ti -cen tri c
research stu d i es
C o l l ect n eu ro i magi n g d ata fro m
Ontology:formalrepres entationof
knowledgeas as etofconceptsandthe
relations hips betweenthos econcepts withinadomain.
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NeuroLOG :http:/ / neurolog.i3s.unice.fr/
several so u rces :
• Di co m C D / DV D
• P AC S (vi a Di co m Q& R )
• Ni fti / An a l yze i ma g e fi l es
User access
co n tro l
Su p p o rt fo r cl i n i cal an d n eu ro p:«SPECIFICITEDELA
sych o l o gi cal sco res
FormationFCRIN
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Softwarearchitecture
Dataorganization
Shanoir is organized as a repository of neuroimaging f iles coupled with a relational
database where additional metadata are stored.
ClientTools
WebBrowser
Client
application
ServiceClass
Provider
WebServices
Shanoir
middleware
ShanoirAPI
ShanoirEngine
BackupPACS
JDBCConnector
Datastore
DICOM
Metadata
Relational Database
DataFiles
Environment
• Java Enterprise(JEE)
• JBossApplication
Server (AS)
• Eclipse (asIDE)
• ANT (asbuildtool)
• Subversion
(f orversioncontrol)
JEE frameworks
• JBossRichf aces
• JAX-WS
(f orwebservices)
• JBossSeam
• Java PersistenceAPI
(JPA)withHibernate3
N ifti
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TheStudycardmechanism
Purpose:Alignmentof Ontologyconceptstotheactualimporteddata
•
•
• Study
– Subject
• Examination (date)
– Dataset
– Dataset
– Dataset
– Dataset
– Subject
– Dataset
– Dataset
–…
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Shanoir advantage:
Indexationmechanism
Objectives:
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As s ign inaunique s emantics meta-data that are not natively inthe DICOM format
• e.g.SequenceMRContras t(T1,T2,T2*,DP,..),phys icalparameters oftheMRs equence,MRheadc oil,parallel
acquis itiontechnique,contras tagent(G d,…)
Reduce the workload toas s ign the eta-data for the us er (defined once)
Allow an automatic quality control ofthe conformity of the data to the protocol
Howitworks:
1. The us er defines as et ofconditions bas ed on DICOM tag(s ) value
(e.g.on“Serie Des cription”,“ProtocolN ame”,“EchoTime”,… )
1. Each s etof conditions corres ponds to as et ofrules
2. Ifa s erie fulfils a s etconditions , the corres ponding s et of rules is applied
•
Example :
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If « Serie Des cription »contains « 3DT1G ado »then
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AcquisitionContrast > T1
MrDatasetNature > T1WeightedMRDataset
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–
ContrastAgentUsed
MrSequencePhysics
–
SliceOrientationAtAcquisition
> GADOLINIUM
> Magnetization
>
prepared
spoiled
GRE
sagittal
➥ Inf ormationyoucannotf indinDICOMtags,canbeattached asmetadata.
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RECHERCHECLIN IQU E
Each Studycardisapplied duringtheDICOMimportanddependsonthestudy,thecenterand
EN IMAG ERIE»
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itsacquisitionequipment.
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ClinicalScoresManagement inShanoir
Clientapplications
• Instrument-basedassessments(i.e.
• Clientapplicationscanqueryandretrievethedata
f romtheShanoir serverthroughweb-services(SOAP).
neuropsychologicaltestssuchasEDSS or
MMS)results inClinical Scores
• Shanoir offers features for hosting such
• Twolibrairies arepublicallyavailabletoimplementthis
f eature:
scores and assign them to the related
stored image data
– ShanoirTk (Javatoolkit)
– QtShanoir (C++client)for:
• Export features are available for
different formats (Excel,CVS,XML…)
• browsing the data inside a graphical widget
• Import derived (processed) data with registration to the source
images, with assignment of specif ic semantic concepts (i.e.
“Processing instrument”)
• QtShanoir has been integrated as aplug-in in MedInria3, f or
advanced image processing software.
• The
“instrument”
database
is
extendable thanks to a user-f riendly
interf ace
RECHERCHECLIN IQU E
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inMedInria
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MedInria :http://med.inria.f r/
:ImportDerivedData
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Ontheright:
• Secureuseraccess
• QueryonShanoir
Objective
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Importprocessed datasets
Register the derived datato thesource one
Align themeta-datato theontology
Allow batchprocess import
Ontheleft:
• Result asatree
• Checkboxes:
Dowload ofwhole
examination(s)or
ofsomesequences
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Shanoir developmentRoadmap
ShanoirUploader
• ShanoirUploader :maketheimport easierand
safer
Hospital
Network
• iShanoir :iOS application forIpad,increase the
portability
• Apache/SOLR integration: makes
query/retrieve easier
RECHERCHECLIN IQU E
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Picture
Archiving and
Communication
Sys tem
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Functionalities
–
Ins talled on the des ktop
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Implemented with JavaW eb Start (JW S)
Atthe MRconsole:
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(1) Query &Retrieve from local PACS
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U pload local data s tored on the PACS (2)
Ons ite Anonymiz ation (3)
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Storing the anonymiz ed data to the
Shanoir s erver (4)
Lateron:connecttotheShanoir
servertocompletetheregistration
ofthedataandresumeimport.
Advantages: Model
Manufacturer
Centricity PACS
– G EH
Easealthcare
yand Fas t
Solutions
McKes
s on Radiology
– Maincare
Can bedone
on packs
ofdata
Agfa
IMPAX
– Can beperformed bya technician
Telemis
Telemis
– Cares
Secured
s
olution
accredited
byVuePACS
Hos pitals tream
Cares tream
ITmanagers
G lobalImaging
G XD5Pacs
RECHERCHECLIN IQU E
P AC S co mp a ti b i l i ty tests (1 1 /2 0 1 5 )
EN IMAG ERIE»
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Shanoir Integration
ShanoirUploader2.0
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Motivation
– Alloweasy indexing andsearchof thedata
– Allowadirect mappingbetweenShanoir
ontologyandSOLRcatalogue
– Alloweasy batchdownload
– Ease InteroperabilitybetweenShanoir
database andothersystem(e.g. FLI-IAM
interoperabilityproject)
G enerate s ecretkeytolink
images &de-identifed
clinical data
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Shanoir Catalogue
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SHAringNeurOImagingResources
WorkinProgress:Shanoir QualityControl
Shanoir@Neurinfo server
Neuri nfo* i s a res earch p latf orm ,
Hos pital N etwork
Anonymous data
from the Un ivers ity of Re nne s I ,
located at the Un ivers ity Hos pita l of
Renne s. It ope rates a Siem ens 3T
Veri oTM MRI a nd a HPC cent er
MRI
SHANOIR
PACS
N ominative data
Study
s upervis ion
and followup
(50TB, 480 co res) a nd u se s Sha no ir
to ma nage and p ubl is h it s data a s
U s ers
wel l a s da ta fro m m ult icent ric
External
Data
Import
Data acces s
DIC OM
studies.
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09/2014
Shanoir@OFSEP server
Centers
27
31
42
U s ers (active)
(53)
118 (52)
178 (66)
Studies
53
60
70
Subjects
1706
2228
2833
Examinations
2268
3157
4005
-
114 441
151582
Datas ets
Raw data
(Dicom)
Proces s ed data
(N ifti)
1126 G B
1434 G B
1588 G B
(1 .1 TB )
(1 .4 TB )
(1 .5 TB )
989 G B
1331 G B
1758 G B
(0 .9 TB )
(1 .3 TB )
(1 .7 TB )
http:/ / www.neurinfo.org
OFSEP is a nationwide , clin ical, cohort,
representing about half of the MS patients
population l iving in France, for a
longitudina l follow-up (clinical, bi ological
and neuroimaging data). Shanoir has been
chosen to be the OFSEP neuroimaging data
management platf orm
DatavolumeonShanoir(Go)
09/2015
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:http:/ / www.neurinfo.org
Anopensourcewebplatformforpopulation imaging
SHANOIR @Neurinfo
09/2013
* Neurinfo
2years ß
RECHERCHECLIN IQU E
EN IMAG ERIE»
2 000
1 750
1 500
1 250
1 000
750
500
250
0
B rain M R imagin g p ro to col
Sp in al co rd M R imagin g p ro to col
(At l east o n e every 3 years)
(At l east o n e M R I every 6 years)
R e co mme n d e d
§
Sagi ttal en h an ced 3 D T1
Axi al DW I wi th ADC m
ap
Axi al 2 D TSE T2 /DP o r 3D T2
Gad o l i n i u m i njecti o n (0.1 mmo l /kg)
3 D FLAIR (o r 2D FLAIR i f
n ot
avai l ab l e)
C o n trast-en h an ced 3 D T1
§
Axi al 2 D T2 GR E
§
§
§
ð
DICOMvolume
§
à 30GB/month
à 360GB/year
RECHERCHECLIN IQU E
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C o n tacts
§
Sagi ttal T2
In case o f l esi o n o ccu rren ce
§
Axi al T2 GR E
§
Axi al T1 TSE wi th gad o l i n i um
i n jecti o n
R e co mme n d e d for firstan d differe ntial diagn o sis
e lise .b an n ie r@ irisa.fr
isab e lle .co ro u ge @ irisa.fr
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§
Sagi ttal T1 wi th gad o l i n i um
i n jecti o n
Ad van ce d se q u e nce s
§
DTI ≥ 1 5 d i recti o n s( rep l ace th e
DW I)
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§
Sagi ttal STIR
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Shanoir@FLI-IAM
Variabilitywithincenters
Siemens
Philips
GE
10%
11
17
35%
55%
Dif f erentsoftwareversionsinstalledonthe
machines
à Installationof theprotocolonthemachine
• Dif f erentPACSmodels
à Possibledif f icultyof communicationwith
ShanoirUploader
Manufacturer
G EHealthcare
Maincare Solutions
Agfa
Telemis
Cares tream
G lobalImaging
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3
2
2
1
1
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FLI - I AM
App St or e
Stan d alo n e C o mp u te /Disp l
ay
Model
Centricity PACS
McKes s on Radiology
IMPAX
Telemis
Cares tream VuePACS
G XD5Pacs
FLI-IAM
Computing
Components
Deri ved DB
Sto re
FLI@ C o mp u ti n g
Bla ck
Bo a rd
API CARMIN
F LI-IA M i ma ge
p ro ce ssi n g cl i ent
Submis s ion
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*https :/ / project.inria.fr/ fli/ en
Sh an
o ir
FLI-IAM
W eb
portal
M et adat a
Cat alogs
I nf or m at ion
Syst em and
Sear ch Engine
Qu ery
R etri eve
Arch i M ed
C ATI
-DB
FLI-IAM
Dis tributed
Archive
FLI@ In tero p erab i l i ty
XDS/XCA
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Thank you foryour attention!
Shanoir Majorfunctionalities
•
•
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•
VIP
Wo rk fl o w
Ma na g em
en
t
Si ng l e Sig n
On Au th .
s e rv i c e
3
•
FLI* is re search i nfrastr ucture aim ing to bui ld an organ ise d an d stand ardi zed
netw ork for i n-vivo i maging in France. The I AM n ode is a con sort ium of teams
that set up an infrastructure of in-vivo image storage and processing.
Register
1
1
1
1
1
1
1
1
31
Foreach center,we have:
• Dif f erentMRmodels
HP C
2
2
2
2
Manufacturer - Model
Siemens - Aera 1,5T
Philips - Achieva 3T
G eneralElectric - DISCOVERY MR750w 3T
Philips - Ingenia 1,5T
Siemens - Avanto 1,5T
Siemens - Skyra 3T
G eneralElectric - Signa HDxt 3T
Philips - Achieva 1,5T
Philips - Ingenia 3T
Siemens - Es pree 1,5T
Siemens - Spectra 3T
Siemens - Symphony Tim1,5T
Siemens - Trio 3T
Siemens - Verio 3T
Execu te
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Dataorganization
Studycardmechanism
Clinicalscores
Clientsapplications
Undergoinglargescaleprojects
• Neurinfo imagingplatform (31 sitesconnected)
• OFSEP’s cohort in MS(35sitesconnected)
• FranceLife Imaging (FLI-IAM) nationalinfrastructure for
in-vivoimaging FormationFCRIN :«SPECIFICITEDELA
RECHERCHECLIN IQU E
EN IMAG ERIE»
Shanoir is an open source software platform designed to
archive, structure, manage, visualize and share neuroimaging data
with an emphasis on multi-centric collaborative research projects
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RECHERCHECLIN IQU E
EN IMAG ERIE»
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Presentation Shanoir

Transcription

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