MICCAI 2016 Medical Image Computing and Computer Assisted

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MICCAI 2016 Medical Image Computing and Computer Assisted Intervention SATELLITE EVENTS Challenges MSSEG +

MICCAI 2016 Medical Image Computing and Computer Assisted Intervention SATELLITE EVENTS Challenges MSSEG + PETSEG Project and technical aspects France Life Imaging (FLI) Information Analysis and Management (IAM) https: //its. aviesan. fr/ 21/10/2016 MICCAI 2016 1

People network 21/10/2016 MICCAI 2016 2

People network 21/10/2016 MICCAI 2016 2

Project timeline • 2015 -05 -12: “Birth” of challenge MSSEG: Assemblée Générale of FLI-IAM

Project timeline • 2015 -05 -12: “Birth” of challenge MSSEG: Assemblée Générale of FLI-IAM in Paris, ICM (heavily discussed) • 2016 -01 -25: Proposal submission • 2016 -03 -11: MICCAI acceptance • 2016 -03 -28: Registration opens on portal of FLI-IAM • 2016 -04 -13: Training data release (15 patients with expert annotations for each) • 2016 -04 -29: Pipeline integration opens (guidelines release) • 2016 -06 -24: Paper submission deadline • 2016 -07 -20: Segmentation pipeline submission deadline • 2016 -07 -27: Papers acceptance • 2016 -08 -01: Final papers submission • 2016 -10 -21: today, workshop day 21/10/2016 MICCAI 2016 3

Major work packages Definition/Planning Recruitment Data Preparation Portal Shanoir/DTM Testing/QC VIP/Boutiques Pipeline Integration Evaluation/SPA

Major work packages Definition/Planning Recruitment Data Preparation Portal Shanoir/DTM Testing/QC VIP/Boutiques Pipeline Integration Evaluation/SPA 21/10/2016 MICCAI 2016 4

Key numbers - 1 15 challengers / 23 pipelines integrated 5 engineers hired for

Key numbers - 1 15 challengers / 23 pipelines integrated 5 engineers hired for the challenges More than 25 task force meetings organized since October 2015 More than 600 emails exchanged between challengers and pipeline integrators • Around 85 man-months of work (45 m-m engineers FLI-IAM) • • – – – – – 21/10/2016 Definition/Planning/Orga Recruitment Data Preparation Portal Shanoir/DTM VIP/Boutiques Pipeline Integration Evaluation/SPA Testing/QC Challengers work 11 m-m 22 m-m (with interns) 6 m-m 15 m-m 3 m-m 10 m-m 4 m-m ? ? ? Much work, but unknown MICCAI 2016 5

Key numbers - 2 Definition/Plann Recruitment; 1 ing/Orga; 11 Testing/QC; 4 Evaluation/SPA; 10 Data

Key numbers - 2 Definition/Plann Recruitment; 1 ing/Orga; 11 Testing/QC; 4 Evaluation/SPA; 10 Data Preparation; 22 Pipeline Integration; 13 VIP/Boutiques; 3 Man-months Shanoir/DTM; 15 Portal; 6 21/10/2016 MICCAI 2016 6

FLI-IAM Engineers, behind the scenes • WG 1 - Engineer CATI/ICM: Jinpeng Li –

FLI-IAM Engineers, behind the scenes • WG 1 - Engineer CATI/ICM: Jinpeng Li – Integrations on Cati. DBv 3 • WG 2 - Engineer VISAGES: Florent Leray – Integration of use cases Rennes and CARMIN • WG 2 - Engineer CREATIS: Axel Bonnet – Integration of CARMIN REST into VIP • WG 3 - Engineer GIN: Simon Loury – Shanoir extensions for little animals • Portal - Engineer VISAGES: Mathieu Simon – Portal development for FLI-IAM • Task Force Challenges Miccai 2016 - Engineer LATIM: Baptiste Laurent – Data preparation for challenges • Task Force Challenges Miccai 2016 - Engineer CREATIS: Pascal Girard – Integration of challenger pipelines into VIP • Task Force Challenges Miccai 2016 - Engineer VISAGES: Julien Louis – Extensions on Shanoir for challenges • Quality Assurance/Testing - Engineer VISAGES: Aneta Morawin – Testing on portal, challenges, common catalog and CARMIN 21/10/2016 MICCAI 2016 7

FLI-IAM Engineers, behind the scenes Engineers with finished contracts: • • • WG 1

FLI-IAM Engineers, behind the scenes Engineers with finished contracts: • • • WG 1 - Engineer CICIT: – Integration of Archi. Med WG 2 - Engineer CREATIS: – Integration of VIP WG 2 - Engineer CATI/ICM: – Integration of pipeline into CATI WG 2 - Engineer GIN - Bordeaux: – integration of pipeline into VIP WG 3 - Engineer ICUBE: – Dicomifier, extensions on Medi. Base/Medi. Py Laëtitia Tin Nouha Boujelben Mamadou Diallo Solveig Badillo Romain Lahaxe Contracts started recently / starting soon: • • WG 1 - Engineer CICIT: 01. 10. 2016 – Integration of Archi. Med WG 1 - Engineer VISAGES: 01. 11. 2016 – Integration of Shanoir WG 3 - Engineer LBI: 01. 10. 2016 – Integration of pipelines WG 3 - Engineer ICUBE: 01. 10. 2016 – Dicomifier, extensions on Medi. Base/Medi. Py 21/10/2016 MICCAI 2016 Mohamed Eissa Yao Mathieu Bonnet Farid Ouhmich 8

MSSEG: data preparation 21/10/2016 MICCAI 2016 9

MSSEG: data preparation 21/10/2016 MICCAI 2016 9

Architecture FLI-IAM FLIWS 21/10/2016 MICCAI 2016 10

Architecture FLI-IAM FLIWS 21/10/2016 MICCAI 2016 10

Architecture for challenges VIP/Boutiques Portal FLI-IAM Processing platform SFTP Shanoir DTM Database for medical

Architecture for challenges VIP/Boutiques Portal FLI-IAM Processing platform SFTP Shanoir DTM Database for medical images 21/10/2016 MICCAI 2016 11

VIP/Boutiques: tool integration Your tool ? VIP Niak / PSOM Tool description (JSON) Virtual

VIP/Boutiques: tool integration Your tool ? VIP Niak / PSOM Tool description (JSON) Virtual Imaging Platform http: //vip. creatis. insa-lyon. fr http: //cbrain. mcgill. ca Tool implementation http: //boutiques. github. io http: //pegasus. isi. edu Workflow Management System for Science Automation

Shanoir data access, customized for different roles 21/10/2016 MICCAI 2016 13

Shanoir data access, customized for different roles 21/10/2016 MICCAI 2016 13

Shanoir data access, customized for different roles 21/10/2016 MICCAI 2016 14

Shanoir data access, customized for different roles 21/10/2016 MICCAI 2016 14

Seg. Perf. Analyzer (SPA) • • Evaluates the precision of a segmentation by comparing,

Seg. Perf. Analyzer (SPA) • • Evaluates the precision of a segmentation by comparing, according to various metrics, the reference image (ground-truth) and the result image of a segmentation Segmentation • Dice score • Sensitivity • Specificity • Relative total lesion load error • Positive predictive value Distance • Average symmetric surface distance Detection • Lesion sensitivity • Lesion positive predictive value • F 1 score 21/10/2016 MICCAI 2016 15

Data Transfer Module (DTM) 21/10/2016 MICCAI 2016 16

Data Transfer Module (DTM) 21/10/2016 MICCAI 2016 16

Take home • VIP enables worldwide visibility and collaboration • Access your data today,

Take home • VIP enables worldwide visibility and collaboration • Access your data today, open since 08: 30 (how-to video on starting page of portal) – Connect to portal: https: //portal. fli-iam. irisa. fr/services – Login to Shanoir and browse your data • Video of services platform IAM? 21/10/2016 MICCAI 2016 17