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PIV 2017: Gestion des données
scientifiques en imagerie in vivo

07.12.2017



FLI-IAM, entry	
  and	
  access	
  point	
  to	
  resources	
  for	
  
medical	
  imaging	
  research	
  
Michael Kain	
  
France	
  Life	
  Imaging	
  	
  (FLI)	
  -­‐	
  
Informa:on	
  Analysis	
  and	
  Management	
  (IAM)	
  
Your	
  service	
  desk	
  for	
  research	
  in	
  medical	
  imaging	
  
	
  
2017-­‐12-­‐07	
  
PIV	
  2017:	
  Ges:on	
  des	
  données	
  
scien:fiques	
  en	
  imagerie	
  in	
  vivo	
  
1	
  
•  Intro	
  
–  Phase	
  1	
  +	
  2	
  
–  Architecture	
  
–  Products	
  
•  Interoperability	
  
–  CARMIN-­‐API	
  
–  OAK	
  –	
  Open	
  App	
  Catalog	
  
•  Example:	
  Challenges	
  MICCAI	
  2016	
  
•  Future	
  
Agenda	
  
2017-­‐12-­‐07	
  
PIV	
  2017:	
  Ges:on	
  des	
  données	
  
scien:fiques	
  en	
  imagerie	
  in	
  vivo	
  
2	
  
•  France	
  Life	
  Imaging	
  (FLI)	
  is	
  a	
  large-­‐scale	
  research	
  infrastructure	
  project,	
  aimed	
  
at	
  establishing	
  a	
  coordinated	
  and	
  harmonized	
  network	
  of	
  biomedical	
  imaging	
  
in	
  France	
  
•  Its	
  mission	
  is	
  to:	
  
–  coordinate	
  na:on-­‐wide	
  research	
  ac:vi:es	
  concerned	
  with	
  in	
  vivo	
  imaging	
  and	
  combine	
  
the	
  skills	
  to	
  push	
  the	
  current	
  technological	
  barriers	
  
–  provide	
   scien:sts	
   a	
   convenient	
   access	
   to	
   a	
   complete	
   range	
   of	
   imaging	
   technologies	
  
(150	
   imaging	
   systems)	
   and	
   integrated	
   services;	
   in	
   addi:on,	
   the	
   infrastructure	
   will	
   be	
  
open	
  to	
  collabora:ons	
  with	
  industrial	
  partners	
  
•  This	
   project	
   was	
   selected	
   in	
   2012	
   by	
   the	
   call	
   “Inves:ssements	
   d’Avenir	
   -­‐	
  
Infrastructure	
  en	
  Biologie	
  et	
  Santé”	
  
•  37	
  million	
  Euros	
  for	
  8	
  years	
  
•  Nodes	
  (see	
  next	
  slide)	
  and	
  work	
  packages:	
  
–  Molecular	
  Imaging	
  Agents	
  
–  Instrumenta:ons	
  &	
  Innova:ons	
  Technologiques	
  
–  Imagerie	
  Interven:onnelle	
  
–  Traitement	
  et	
  Analyse	
  en	
  Imagerie	
  Mul:modale	
  
–  Forma:on	
  
•  hdp://francelifeimaging.fr	
  
France	
  Life	
  Imaging	
  (FLI)	
  -­‐	
  1	
  
2017-­‐12-­‐07	
  
PIV	
  2017:	
  Ges:on	
  des	
  données	
  
scien:fiques	
  en	
  imagerie	
  in	
  vivo	
  
3	
  
2017-­‐12-­‐07	
  
PIV	
  2017:	
  Ges:on	
  des	
  données	
  
scien:fiques	
  en	
  imagerie	
  in	
  vivo	
  
4	
  
France	
  Life	
  Imaging	
  (FLI)	
  -­‐	
  2	
  
•  Objec:ves	
  of	
  the	
  Node:	
  “Build	
  an	
  in-­‐vivo	
  image	
  management	
  infrastructure”	
  for	
  
–  Clinician:	
  to	
  conduct	
  clinical	
  and	
  preclinical	
  research	
  studies	
  involving	
  new	
  innova:ve	
  in-­‐vivo	
  medical	
  
imaging	
  and	
  therapeu:c	
  procedures	
  
–  Pharma:	
  to	
  provide	
  pharma	
  and	
  CRO	
  companies	
  high	
  
technological	
  computa:onal	
  solu:ons	
  in	
  medical	
  imaging	
  
–  Companies	
  and	
  startups:	
  
–  Medical	
  imaging	
  community:	
  to	
  allow	
  experimenta:on	
  and	
  
valida:on	
  of	
  new	
  innova:ve	
  medical	
  imaging	
  solu:ons	
  
•  Strengths:	
  based	
  on	
  exis?ng	
  high	
  technological	
  exper:se	
  and	
  experience	
  
–  From	
  data	
  management	
  solu:ons:	
  ArchiMed,	
  CATI,	
  SHANOIR,	
  …	
  
–  From	
  medical	
  image	
  processing	
  solu:ons:	
  BrainVisa,	
  medInria,	
  VIP	
  +	
  Bou:ques,	
  …	
  
–  From	
  large	
  na:onal	
  clinical	
  Cohorts:	
  CATI,	
  OFSEP,	
  …	
  
•  Mul:ple	
  research	
  labs	
  involved,	
  around	
  10	
  	
  
•  3	
  Work	
  groups:	
  "Interoperability	
  and	
  data	
  management",	
  "Processing	
  and	
  
workflow"	
  and	
  "Preclinical	
  imaging"	
  	
  
•  hdps://portal.fli-­‐iam.irisa.fr/services	
  
Informa:on	
  Analysis	
  
and	
  Management	
  (IAM)	
  -­‐	
  1	
  
2017-­‐12-­‐07	
  
PIV	
  2017:	
  Ges:on	
  des	
  données	
  
scien:fiques	
  en	
  imagerie	
  in	
  vivo	
  
5	
  
Phases	
  of	
  FLI-­‐IAM	
  
2017-­‐12-­‐07	
  
PIV	
  2017:	
  Ges:on	
  des	
  données	
  
scien:fiques	
  en	
  imagerie	
  in	
  vivo	
  
6	
  
Today	
   Goal	
  
Publicly	
  funded	
   Self-­‐financing	
  Par:ally	
  publicly	
  funded	
  
Phase	
  1	
   Phase	
  2	
  (2-­‐3	
  years)	
   Phase	
  3?	
  
Beginning	
  
of	
  2018	
  
Beginning	
  
of	
  2020/21	
  
2	
  Mio.	
  €	
  
for	
  research	
  ins:tutes	
  
1,2	
  Mio.	
  €	
  
for	
  sub-­‐contrac:ng	
   ?	
  
Business	
  model	
  
Prototype	
  development	
  
 	
  
FLI@Interoperability	
  
Shanoir	
  
Archi	
  
Med	
  
CATI-­‐
DB	
  
Retrieve	
  
Query	
  
Registra:on	
  
Register	
  
Standalone	
  
Compute/Display	
  
	
  	
  
CARMIN-­‐API	
  
Server	
  
Download	
  
VIP +
Boutiques
OAK
Open App
Catalog
HPC	
  
FLI-­‐IAM	
  
Compu?ng	
  
Components	
  
FLI-IAM image processing
clients and viewers
	
  	
  
Execute	
  
Information
System and
Search Engine
Metadata
Catalogs
SingleSignOn
Auth.service
FLI-­‐IAM	
  
Web	
  
Portal	
  
FLI-­‐IAM	
  
Distributed	
  
Archive	
  
Black
Board
FLI-­‐IAM	
  Architecture	
  
2017-­‐12-­‐07	
  
PIV	
  2017:	
  Ges:on	
  des	
  données	
  
scien:fiques	
  en	
  imagerie	
  in	
  vivo	
  
7	
  
CARMIN-­‐API	
  Client	
  
FLIWS
medInria
DTM	
  
•  Image	
  Databases:	
  
–  ArchiMed	
  
–  CATIDB	
  
–  Dopamin	
  
–  Shanoir	
  (Shanoir	
  Classic,	
  
Shanoir	
  Small	
  Animal,	
  
Shanoir-­‐NG)	
  
–  (XNAT)	
  
•  Image	
  importers/
uploaders:	
  
–  ArchiMed	
  Desktop	
  Client	
  
–  ShanoirUploader	
  
•  Processing	
  plaMorms:	
  
–  CATI	
  
–  FLIWS	
  
–  VIP	
  +	
  Bou:ques	
  
Products	
  
2017-­‐12-­‐07	
  
PIV	
  2017:	
  Ges:on	
  des	
  données	
  
scien:fiques	
  en	
  imagerie	
  in	
  vivo	
  
8	
  
•  Viewers/local	
  processings:	
  
–  BrainVisa	
  
–  medInria	
  
•  Pipelines/processings:	
  
–  Preclinical	
  
–  Bordeaux	
  -­‐	
  Func:onal	
  
connec:vity	
  
–  Marseilles/Paris	
  -­‐	
  Sulcal	
  
Morphometry	
  
–  24	
  MICCAI	
  2016	
  Challenger	
  
Pipelines	
  
•  Others:	
  
–  Open	
  App	
  Catalog	
  (OAK)	
  
–  CARMIN	
  API,	
  +	
  clients	
  below:	
  
•  carmin-­‐widget.js	
  (browser)	
  
•  Janicule	
  (desktop)	
  
•  Portal	
  client	
  (backend)	
  
–  Dicomifier	
  
–  SegPerfAnalyzer	
  (SPA)	
  
–  Data	
  Trans	
  Module	
  (DTM)	
  
–  Portal,	
  based	
  on	
  LifeRay	
  
•  Single-­‐Sign-­‐On	
  module	
  
–  Common	
  catalog	
  
–  Automated	
  test	
  cases	
  	
  
Installa:ons	
  of	
  ShanoirUploader	
  in	
  France	
  
within	
  the	
  OFSEP	
  project	
  
2017-­‐12-­‐07	
  
PIV	
  2017:	
  Ges:on	
  des	
  données	
  
scien:fiques	
  en	
  imagerie	
  in	
  vivo	
  
9	
  
•  Our	
  main	
  goal:	
  interoperability	
  
•  We	
  believe	
  that	
  the	
  long-­‐:me	
  life:me	
  of	
  today	
  sovware	
  systems	
  are	
  defined	
  
by	
  the	
  interoperability	
  between	
  the	
  systems	
  and	
  their	
  environment	
  
•  Plays	
  between	
  the	
  following	
  standards/formats	
  (and	
  more):	
  
–  DICOM	
  (Digital	
  Imaging	
  and	
  Communica:ons	
  in	
  Medicine)	
  and	
  PACS	
  (Picture	
  
Archiving	
  and	
  Communica:on	
  System)	
  
–  DICOM	
  De-­‐iden:fica:on,	
  Pseudonymiza:on	
  and	
  Anonymiza:on	
  
–  DICOMWeb:	
  WADO-­‐URI,	
  -­‐WS	
  or	
  -­‐RS,	
  QIDO-­‐RS,	
  STOW-­‐RS	
  
–  NIfTI	
  (Neuroimaging	
  Informa:cs	
  Technology	
  Ini:a:ve)	
  
–  NRRD	
  (Nearly	
  Raw	
  Raster	
  Data)	
  
–  XDS	
  (Cross-­‐Enterprise	
  Document	
  Sharing)	
  
–  HL7	
  CDA	
  (Clinical	
  Document	
  Architecture)	
  
–  HL7	
  FHIR	
  (Fast	
  Healthcare	
  Interoperability	
  Resources)	
  
–  BIDS	
  (Brain	
  Imaging	
  Data	
  Structure)	
  
–  NIDM	
  (The	
  Neuroimaging	
  Data	
  Model)	
  
–  Medical	
  Health	
  Record	
  (DMP,	
  EHR,	
  PHR,	
  openEHR)	
  
Interoperability	
  -­‐	
  1	
  
2017-­‐12-­‐07	
  
PIV	
  2017:	
  Ges:on	
  des	
  données	
  
scien:fiques	
  en	
  imagerie	
  in	
  vivo	
  
10	
  
•  Within	
  the	
  following	
  legal	
  environments:	
  
–  France:	
  
•  CNIL,	
  e.g.	
  Agrément	
  d’hébergement	
  de	
  données	
  de	
  santé	
  (ou	
  «	
  agrément	
  HDS	
  »)	
  
•  ANSM	
  
–  Europe:	
  
•  GDPR	
  (General	
  Data	
  Protec:on	
  Regula:on),	
  applies	
  on	
  25.	
  May	
  2018	
  
–  USA:	
  
•  HIPAA	
  (Health	
  Insurance	
  Portability	
  and	
  Accountability	
  Act)	
  
•  Title	
  21	
  CFR	
  Part	
  11	
  by	
  FDA	
  
•  Work	
  started	
  on	
  that	
  road:	
  
–  Common	
  catalog,	
  unified	
  meta-­‐data	
  search	
  index	
  over	
  all	
  image	
  databases	
  
–  Unified	
  access	
  to	
  processing	
  playorms:	
  CARMIN-­‐API	
  
–  OAK:	
  open	
  app	
  catalog	
  for	
  processing	
  applica:ons	
  of	
  medical	
  images	
  
–  VIP	
  +	
  Bou:ques:	
  exchange/execute	
  pipelines	
  encapsulated	
  in	
  Docker	
  images	
  (local/cluster)	
  
•  S:ll	
  a	
  very	
  long	
  way	
  to	
  go:	
  
–  Traceability	
  of	
  access	
  to	
  data	
  and	
  systems	
  
–  Assure	
  security	
  on	
  the	
  most	
  high	
  level	
  
–  Open	
  and	
  unified	
  access	
  for	
  (commercial)	
  viewers,	
  e.g.	
  Osirix,	
  to	
  databases	
  in	
  FLI-­‐IAM	
  
–  Integrate	
  all	
  databases	
  compa:ble	
  with	
  ShanoirUploader	
  and	
  name	
  to	
  FLI-­‐IAM	
  Uploader	
  
–  Unified	
  data	
  exchange	
  between	
  research	
  databases	
  
Interoperability	
  -­‐	
  2	
  
2017-­‐12-­‐07	
  
PIV	
  2017:	
  Ges:on	
  des	
  données	
  
scien:fiques	
  en	
  imagerie	
  in	
  vivo	
  
11	
  
•  CARMIN:	
  a	
  Common	
  web	
  API	
  for	
  ReMote	
  pipeline	
  Invoca:on	
  
•  Unifies	
  the	
  remote	
  access	
  to	
  pipeline	
  hos:ng	
  playorms	
  
•  Core	
  API	
  features:	
  
–  Authen:ca:on	
  (username+password	
  or	
  API-­‐Key)	
  
–  Playorm	
  informa:on	
  
–  List	
  of	
  available	
  pipelines	
  and	
  pipeline	
  informa:on:	
  e.g.	
  Params	
  
–  Input	
  data	
  upload	
  
–  Pipeline	
  execu:on	
  
–  Output	
  data	
  download	
  
•  Implemented	
  in:	
  
–  FLIWS	
  
–  CATI	
  
–  VIP	
  
–  Coming	
  soon:	
  CBRAIN?	
  
Interface	
  to	
  processing	
  playorms	
  
2017-­‐12-­‐07	
  
PIV	
  2017:	
  Ges:on	
  des	
  données	
  
scien:fiques	
  en	
  imagerie	
  in	
  vivo	
  
12	
  
•  Centralized,	
  open	
  app	
  catalog	
  for	
  
processing	
  applica:ons	
  of	
  medical	
  images	
  
•  Based	
  on	
  CARMIN,	
  /pipelines	
  (1	
  method)	
  
OAK	
  –	
  the	
  open	
  app	
  catalog	
  
2017-­‐12-­‐07	
  
PIV	
  2017:	
  Ges:on	
  des	
  données	
  
scien:fiques	
  en	
  imagerie	
  in	
  vivo	
  
13	
  
•  Connect	
  to	
  the	
  OAK:	
  
–  Open	
  for	
  all	
  partners	
  to	
  work	
  on	
  the	
  app	
  catalog	
  
–  Playorm	
  owners:	
  
•  Implement	
  one	
  interface	
  in	
  REST:	
  /pipelines,	
  that	
  gives	
  back	
  a	
  list	
  of	
  
your	
  public	
  available	
  pipelines	
  (you	
  keep	
  control	
  of	
  all	
  your	
  code)	
  
•  1	
  week	
  of	
  integra:on	
  work	
  (maximum)	
  
•  Add	
  your	
  playorm	
  to	
  the	
  website	
  and	
  your	
  pipelines	
  come	
  into	
  the	
  catalog	
  
–  Pipeline	
  developers/developing	
  companies:	
  
•  Contact	
  us	
  and	
  we	
  integrate	
  your	
  pipelines	
  
•  Send	
  us	
  a	
  GitHub	
  link	
  to	
  your	
  private	
  docker	
  image	
  
•  We	
  never	
  access	
  to	
  any	
  source	
  code,	
  we	
  do	
  not	
  even	
  have	
  
to	
  see	
  inside	
  the	
  docker	
  image	
  
•  Implement	
  your	
  CARMIN	
  interface	
  
•  What	
  we	
  provide:	
  hdps://github.com/fli-­‐iam/CARMIN	
  
–  Swagger	
  defini:on	
  of	
  the	
  REST	
  interface:	
  to	
  create	
  your	
  code	
  
–  carmin-­‐client.js	
  in	
  JavaScript	
  for	
  web	
  portals	
  
–  Janicule,	
  C++	
  desktop	
  client	
  to	
  connect	
  to	
  CARMIN	
  
OAK	
  –	
  the	
  open	
  app	
  catalog	
  
2017-­‐12-­‐07	
  
PIV	
  2017:	
  Ges:on	
  des	
  données	
  
scien:fiques	
  en	
  imagerie	
  in	
  vivo	
  
14	
  
•  3 usage scenarios identified for FLI-IAM
–  Software as a Service (SaaS)
•  1.a: turn-key service
•  1.b: resource service
–  Platform as a Service (PaaS)
•  Show case: organization of two scientific challenges
–  Storage + Computing as a Service (SCaaS)
•  MICCAI 2016
–  Medical Image Computing and Computer Assisted Intervention
–  SATELLITE EVENTS: Challenges MSSEG + PETSEG
–  15	
  challengers	
  /	
  23	
  pipelines	
  integrated	
  
–  5	
  engineers	
  hired	
  for	
  the	
  challenges	
  
–  More	
  than	
  25	
  task	
  force	
  mee:ngs	
  organized	
  since	
  October	
  2015	
  
–  More	
  than	
  600	
  emails	
  exchanged	
  between	
  
challengers	
  and	
  pipeline	
  integrators	
  
(1-­‐2	
  weeks	
  average	
  :me	
  of	
  pipeline	
  integra:on)	
  
–  Around	
  85	
  man-­‐months	
  of	
  work	
  
Example:	
  Challenges	
  MICCAI	
  2016	
  
15	
  
PIV	
  2017:	
  Ges:on	
  des	
  données	
  
scien:fiques	
  en	
  imagerie	
  in	
  vivo	
  
2017-­‐12-­‐07	
  
People network for MSSEG	
  
16	
  
PIV	
  2017:	
  Ges:on	
  des	
  données	
  
scien:fiques	
  en	
  imagerie	
  in	
  vivo	
  
2017-­‐12-­‐07	
  
Key numbers - 2	
  
17	
  
Defini:on/
Planning/Orga,	
  
11	
  
Recruitment,	
  1	
  
Data	
  
Prepara:on,	
  22	
  
Portal,	
  6	
  
Shanoir/DTM,	
  
15	
  
VIP/Bou:ques,	
  3	
  
Pipeline	
  
Integra:on,	
  13	
  
Evalua:on/
SPA,	
  10	
  
Tes:ng/QC,	
  4	
  
Man-­‐months	
  
PIV	
  2017:	
  Ges:on	
  des	
  données	
  
scien:fiques	
  en	
  imagerie	
  in	
  vivo	
  
2017-­‐12-­‐07	
  
Architecture for challenges	
  
	
  
18	
  
Portal	
  FLI-­‐IAM	
  
Shanoir	
  
VIP/Bou?ques	
  
Database	
  for	
  
medical	
  images	
  
Processing	
  
plaMorm	
  
DTM	
  
SFTP	
  
PIV	
  2017:	
  Ges:on	
  des	
  données	
  
scien:fiques	
  en	
  imagerie	
  in	
  vivo	
  
2017-­‐12-­‐07	
  
VIP/Boutiques: tool integration
Tool description
(JSON)
Tool implementation
Workflow Management System
for Science Automation
http://pegasus.isi.edu
Virtual Imaging Platform
VIP
http://vip.creatis.insa-lyon.fr
Your tool ?
Niak / PSOM
http://boutiques.github.io
http://cbrain.mcgill.ca
2017-­‐12-­‐07	
  
•  We	
  did	
  a	
  market	
  study	
  (TMTG)	
  at	
  the	
  beginning	
  of	
  2017	
  
•  Organiza:on	
  of	
  phase	
  2	
  
–  How	
  will	
  FLI-­‐IAM	
  be	
  structured?	
  
•  As	
  structure	
  itself,	
  and	
  in	
  rela:on	
  to	
  FLI,	
  phase	
  2	
  (in	
  valida:on)	
  
•  Partners,	
  research	
  and	
  industrial	
  (ongoing	
  exchanges)	
  
•  Poten:al	
  service	
  customers	
  (ongoing	
  presenta:ons)	
  
–  Order	
  of	
  services	
  to	
  propose?	
  
•  First	
  service	
  offer	
  to	
  start:	
  Shanoir	
  Small	
  Animal	
  
•  What	
  else	
  aver?	
  
•  Some	
  of	
  the	
  next	
  steps	
  to	
  prepare:	
  
–  More	
  interoperability!!!	
  
–  Agrément	
  d’hébergement	
  de	
  données	
  de	
  santé	
  (ou	
  «	
  agrément	
  HDS	
  »)	
  
–  Service	
  for	
  clinical	
  research	
  studies:	
  hos:ng	
  of	
  electronic	
  health	
  records	
  
–  Project	
  OpenAIRE:	
  integrate	
  open	
  science	
  directly:	
  
•  DOI	
  (digital	
  object	
  iden:fier)	
  managment	
  within	
  databases	
  and	
  processing	
  playorms	
  
within	
  FLI-­‐IAM	
  
•  Any	
  ideas	
  or	
  proposals:	
  please	
  contact	
  me	
  J	
  
Future	
  
PIV	
  2017:	
  Ges:on	
  des	
  données	
  
scien:fiques	
  en	
  imagerie	
  in	
  vivo	
  
20	
  2017-­‐12-­‐07	
  
Thank	
  you	
  for	
  your	
  aVen?on!	
  
2017-­‐12-­‐07	
  
PIV	
  2017:	
  Ges:on	
  des	
  données	
  
scien:fiques	
  en	
  imagerie	
  in	
  vivo	
  
21	
  

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M kain fli-iam_piv_2017_c

  • 1. PIV 2017: Gestion des données scientifiques en imagerie in vivo
 07.12.2017
 
 FLI-IAM, entry  and  access  point  to  resources  for   medical  imaging  research   Michael Kain   France  Life  Imaging    (FLI)  -­‐   Informa:on  Analysis  and  Management  (IAM)   Your  service  desk  for  research  in  medical  imaging     2017-­‐12-­‐07   PIV  2017:  Ges:on  des  données   scien:fiques  en  imagerie  in  vivo   1  
  • 2. •  Intro   –  Phase  1  +  2   –  Architecture   –  Products   •  Interoperability   –  CARMIN-­‐API   –  OAK  –  Open  App  Catalog   •  Example:  Challenges  MICCAI  2016   •  Future   Agenda   2017-­‐12-­‐07   PIV  2017:  Ges:on  des  données   scien:fiques  en  imagerie  in  vivo   2  
  • 3. •  France  Life  Imaging  (FLI)  is  a  large-­‐scale  research  infrastructure  project,  aimed   at  establishing  a  coordinated  and  harmonized  network  of  biomedical  imaging   in  France   •  Its  mission  is  to:   –  coordinate  na:on-­‐wide  research  ac:vi:es  concerned  with  in  vivo  imaging  and  combine   the  skills  to  push  the  current  technological  barriers   –  provide   scien:sts   a   convenient   access   to   a   complete   range   of   imaging   technologies   (150   imaging   systems)   and   integrated   services;   in   addi:on,   the   infrastructure   will   be   open  to  collabora:ons  with  industrial  partners   •  This   project   was   selected   in   2012   by   the   call   “Inves:ssements   d’Avenir   -­‐   Infrastructure  en  Biologie  et  Santé”   •  37  million  Euros  for  8  years   •  Nodes  (see  next  slide)  and  work  packages:   –  Molecular  Imaging  Agents   –  Instrumenta:ons  &  Innova:ons  Technologiques   –  Imagerie  Interven:onnelle   –  Traitement  et  Analyse  en  Imagerie  Mul:modale   –  Forma:on   •  hdp://francelifeimaging.fr   France  Life  Imaging  (FLI)  -­‐  1   2017-­‐12-­‐07   PIV  2017:  Ges:on  des  données   scien:fiques  en  imagerie  in  vivo   3  
  • 4. 2017-­‐12-­‐07   PIV  2017:  Ges:on  des  données   scien:fiques  en  imagerie  in  vivo   4   France  Life  Imaging  (FLI)  -­‐  2  
  • 5. •  Objec:ves  of  the  Node:  “Build  an  in-­‐vivo  image  management  infrastructure”  for   –  Clinician:  to  conduct  clinical  and  preclinical  research  studies  involving  new  innova:ve  in-­‐vivo  medical   imaging  and  therapeu:c  procedures   –  Pharma:  to  provide  pharma  and  CRO  companies  high   technological  computa:onal  solu:ons  in  medical  imaging   –  Companies  and  startups:   –  Medical  imaging  community:  to  allow  experimenta:on  and   valida:on  of  new  innova:ve  medical  imaging  solu:ons   •  Strengths:  based  on  exis?ng  high  technological  exper:se  and  experience   –  From  data  management  solu:ons:  ArchiMed,  CATI,  SHANOIR,  …   –  From  medical  image  processing  solu:ons:  BrainVisa,  medInria,  VIP  +  Bou:ques,  …   –  From  large  na:onal  clinical  Cohorts:  CATI,  OFSEP,  …   •  Mul:ple  research  labs  involved,  around  10     •  3  Work  groups:  "Interoperability  and  data  management",  "Processing  and   workflow"  and  "Preclinical  imaging"     •  hdps://portal.fli-­‐iam.irisa.fr/services   Informa:on  Analysis   and  Management  (IAM)  -­‐  1   2017-­‐12-­‐07   PIV  2017:  Ges:on  des  données   scien:fiques  en  imagerie  in  vivo   5  
  • 6. Phases  of  FLI-­‐IAM   2017-­‐12-­‐07   PIV  2017:  Ges:on  des  données   scien:fiques  en  imagerie  in  vivo   6   Today   Goal   Publicly  funded   Self-­‐financing  Par:ally  publicly  funded   Phase  1   Phase  2  (2-­‐3  years)   Phase  3?   Beginning   of  2018   Beginning   of  2020/21   2  Mio.  €   for  research  ins:tutes   1,2  Mio.  €   for  sub-­‐contrac:ng   ?   Business  model   Prototype  development  
  • 7.     FLI@Interoperability   Shanoir   Archi   Med   CATI-­‐ DB   Retrieve   Query   Registra:on   Register   Standalone   Compute/Display       CARMIN-­‐API   Server   Download   VIP + Boutiques OAK Open App Catalog HPC   FLI-­‐IAM   Compu?ng   Components   FLI-IAM image processing clients and viewers     Execute   Information System and Search Engine Metadata Catalogs SingleSignOn Auth.service FLI-­‐IAM   Web   Portal   FLI-­‐IAM   Distributed   Archive   Black Board FLI-­‐IAM  Architecture   2017-­‐12-­‐07   PIV  2017:  Ges:on  des  données   scien:fiques  en  imagerie  in  vivo   7   CARMIN-­‐API  Client   FLIWS medInria DTM  
  • 8. •  Image  Databases:   –  ArchiMed   –  CATIDB   –  Dopamin   –  Shanoir  (Shanoir  Classic,   Shanoir  Small  Animal,   Shanoir-­‐NG)   –  (XNAT)   •  Image  importers/ uploaders:   –  ArchiMed  Desktop  Client   –  ShanoirUploader   •  Processing  plaMorms:   –  CATI   –  FLIWS   –  VIP  +  Bou:ques   Products   2017-­‐12-­‐07   PIV  2017:  Ges:on  des  données   scien:fiques  en  imagerie  in  vivo   8   •  Viewers/local  processings:   –  BrainVisa   –  medInria   •  Pipelines/processings:   –  Preclinical   –  Bordeaux  -­‐  Func:onal   connec:vity   –  Marseilles/Paris  -­‐  Sulcal   Morphometry   –  24  MICCAI  2016  Challenger   Pipelines   •  Others:   –  Open  App  Catalog  (OAK)   –  CARMIN  API,  +  clients  below:   •  carmin-­‐widget.js  (browser)   •  Janicule  (desktop)   •  Portal  client  (backend)   –  Dicomifier   –  SegPerfAnalyzer  (SPA)   –  Data  Trans  Module  (DTM)   –  Portal,  based  on  LifeRay   •  Single-­‐Sign-­‐On  module   –  Common  catalog   –  Automated  test  cases    
  • 9. Installa:ons  of  ShanoirUploader  in  France   within  the  OFSEP  project   2017-­‐12-­‐07   PIV  2017:  Ges:on  des  données   scien:fiques  en  imagerie  in  vivo   9  
  • 10. •  Our  main  goal:  interoperability   •  We  believe  that  the  long-­‐:me  life:me  of  today  sovware  systems  are  defined   by  the  interoperability  between  the  systems  and  their  environment   •  Plays  between  the  following  standards/formats  (and  more):   –  DICOM  (Digital  Imaging  and  Communica:ons  in  Medicine)  and  PACS  (Picture   Archiving  and  Communica:on  System)   –  DICOM  De-­‐iden:fica:on,  Pseudonymiza:on  and  Anonymiza:on   –  DICOMWeb:  WADO-­‐URI,  -­‐WS  or  -­‐RS,  QIDO-­‐RS,  STOW-­‐RS   –  NIfTI  (Neuroimaging  Informa:cs  Technology  Ini:a:ve)   –  NRRD  (Nearly  Raw  Raster  Data)   –  XDS  (Cross-­‐Enterprise  Document  Sharing)   –  HL7  CDA  (Clinical  Document  Architecture)   –  HL7  FHIR  (Fast  Healthcare  Interoperability  Resources)   –  BIDS  (Brain  Imaging  Data  Structure)   –  NIDM  (The  Neuroimaging  Data  Model)   –  Medical  Health  Record  (DMP,  EHR,  PHR,  openEHR)   Interoperability  -­‐  1   2017-­‐12-­‐07   PIV  2017:  Ges:on  des  données   scien:fiques  en  imagerie  in  vivo   10  
  • 11. •  Within  the  following  legal  environments:   –  France:   •  CNIL,  e.g.  Agrément  d’hébergement  de  données  de  santé  (ou  «  agrément  HDS  »)   •  ANSM   –  Europe:   •  GDPR  (General  Data  Protec:on  Regula:on),  applies  on  25.  May  2018   –  USA:   •  HIPAA  (Health  Insurance  Portability  and  Accountability  Act)   •  Title  21  CFR  Part  11  by  FDA   •  Work  started  on  that  road:   –  Common  catalog,  unified  meta-­‐data  search  index  over  all  image  databases   –  Unified  access  to  processing  playorms:  CARMIN-­‐API   –  OAK:  open  app  catalog  for  processing  applica:ons  of  medical  images   –  VIP  +  Bou:ques:  exchange/execute  pipelines  encapsulated  in  Docker  images  (local/cluster)   •  S:ll  a  very  long  way  to  go:   –  Traceability  of  access  to  data  and  systems   –  Assure  security  on  the  most  high  level   –  Open  and  unified  access  for  (commercial)  viewers,  e.g.  Osirix,  to  databases  in  FLI-­‐IAM   –  Integrate  all  databases  compa:ble  with  ShanoirUploader  and  name  to  FLI-­‐IAM  Uploader   –  Unified  data  exchange  between  research  databases   Interoperability  -­‐  2   2017-­‐12-­‐07   PIV  2017:  Ges:on  des  données   scien:fiques  en  imagerie  in  vivo   11  
  • 12. •  CARMIN:  a  Common  web  API  for  ReMote  pipeline  Invoca:on   •  Unifies  the  remote  access  to  pipeline  hos:ng  playorms   •  Core  API  features:   –  Authen:ca:on  (username+password  or  API-­‐Key)   –  Playorm  informa:on   –  List  of  available  pipelines  and  pipeline  informa:on:  e.g.  Params   –  Input  data  upload   –  Pipeline  execu:on   –  Output  data  download   •  Implemented  in:   –  FLIWS   –  CATI   –  VIP   –  Coming  soon:  CBRAIN?   Interface  to  processing  playorms   2017-­‐12-­‐07   PIV  2017:  Ges:on  des  données   scien:fiques  en  imagerie  in  vivo   12  
  • 13. •  Centralized,  open  app  catalog  for   processing  applica:ons  of  medical  images   •  Based  on  CARMIN,  /pipelines  (1  method)   OAK  –  the  open  app  catalog   2017-­‐12-­‐07   PIV  2017:  Ges:on  des  données   scien:fiques  en  imagerie  in  vivo   13  
  • 14. •  Connect  to  the  OAK:   –  Open  for  all  partners  to  work  on  the  app  catalog   –  Playorm  owners:   •  Implement  one  interface  in  REST:  /pipelines,  that  gives  back  a  list  of   your  public  available  pipelines  (you  keep  control  of  all  your  code)   •  1  week  of  integra:on  work  (maximum)   •  Add  your  playorm  to  the  website  and  your  pipelines  come  into  the  catalog   –  Pipeline  developers/developing  companies:   •  Contact  us  and  we  integrate  your  pipelines   •  Send  us  a  GitHub  link  to  your  private  docker  image   •  We  never  access  to  any  source  code,  we  do  not  even  have   to  see  inside  the  docker  image   •  Implement  your  CARMIN  interface   •  What  we  provide:  hdps://github.com/fli-­‐iam/CARMIN   –  Swagger  defini:on  of  the  REST  interface:  to  create  your  code   –  carmin-­‐client.js  in  JavaScript  for  web  portals   –  Janicule,  C++  desktop  client  to  connect  to  CARMIN   OAK  –  the  open  app  catalog   2017-­‐12-­‐07   PIV  2017:  Ges:on  des  données   scien:fiques  en  imagerie  in  vivo   14  
  • 15. •  3 usage scenarios identified for FLI-IAM –  Software as a Service (SaaS) •  1.a: turn-key service •  1.b: resource service –  Platform as a Service (PaaS) •  Show case: organization of two scientific challenges –  Storage + Computing as a Service (SCaaS) •  MICCAI 2016 –  Medical Image Computing and Computer Assisted Intervention –  SATELLITE EVENTS: Challenges MSSEG + PETSEG –  15  challengers  /  23  pipelines  integrated   –  5  engineers  hired  for  the  challenges   –  More  than  25  task  force  mee:ngs  organized  since  October  2015   –  More  than  600  emails  exchanged  between   challengers  and  pipeline  integrators   (1-­‐2  weeks  average  :me  of  pipeline  integra:on)   –  Around  85  man-­‐months  of  work   Example:  Challenges  MICCAI  2016   15   PIV  2017:  Ges:on  des  données   scien:fiques  en  imagerie  in  vivo   2017-­‐12-­‐07  
  • 16. People network for MSSEG   16   PIV  2017:  Ges:on  des  données   scien:fiques  en  imagerie  in  vivo   2017-­‐12-­‐07  
  • 17. Key numbers - 2   17   Defini:on/ Planning/Orga,   11   Recruitment,  1   Data   Prepara:on,  22   Portal,  6   Shanoir/DTM,   15   VIP/Bou:ques,  3   Pipeline   Integra:on,  13   Evalua:on/ SPA,  10   Tes:ng/QC,  4   Man-­‐months   PIV  2017:  Ges:on  des  données   scien:fiques  en  imagerie  in  vivo   2017-­‐12-­‐07  
  • 18. Architecture for challenges     18   Portal  FLI-­‐IAM   Shanoir   VIP/Bou?ques   Database  for   medical  images   Processing   plaMorm   DTM   SFTP   PIV  2017:  Ges:on  des  données   scien:fiques  en  imagerie  in  vivo   2017-­‐12-­‐07  
  • 19. VIP/Boutiques: tool integration Tool description (JSON) Tool implementation Workflow Management System for Science Automation http://pegasus.isi.edu Virtual Imaging Platform VIP http://vip.creatis.insa-lyon.fr Your tool ? Niak / PSOM http://boutiques.github.io http://cbrain.mcgill.ca 2017-­‐12-­‐07  
  • 20. •  We  did  a  market  study  (TMTG)  at  the  beginning  of  2017   •  Organiza:on  of  phase  2   –  How  will  FLI-­‐IAM  be  structured?   •  As  structure  itself,  and  in  rela:on  to  FLI,  phase  2  (in  valida:on)   •  Partners,  research  and  industrial  (ongoing  exchanges)   •  Poten:al  service  customers  (ongoing  presenta:ons)   –  Order  of  services  to  propose?   •  First  service  offer  to  start:  Shanoir  Small  Animal   •  What  else  aver?   •  Some  of  the  next  steps  to  prepare:   –  More  interoperability!!!   –  Agrément  d’hébergement  de  données  de  santé  (ou  «  agrément  HDS  »)   –  Service  for  clinical  research  studies:  hos:ng  of  electronic  health  records   –  Project  OpenAIRE:  integrate  open  science  directly:   •  DOI  (digital  object  iden:fier)  managment  within  databases  and  processing  playorms   within  FLI-­‐IAM   •  Any  ideas  or  proposals:  please  contact  me  J   Future   PIV  2017:  Ges:on  des  données   scien:fiques  en  imagerie  in  vivo   20  2017-­‐12-­‐07  
  • 21. Thank  you  for  your  aVen?on!   2017-­‐12-­‐07   PIV  2017:  Ges:on  des  données   scien:fiques  en  imagerie  in  vivo   21