ITK/Summer v4 2011 Meeting: Difference between revisions

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== Registration Information ==
== Registration Information ==


* Download [[Media:ITKv4 Summer2011Meeting Registration.pdf |Registration Form]]
* It is a fillable PDF form
* Fill it up please.
** Indicate the number of days that you are attending.
** Registration fee = ( NumberOfDays * $65 );
** Print it as a PDF file
*** since otherwise the form is still modifiable
* Send the processed form back to Kitware
** email it at: admin at kitware dot com


== Meeting Room ==
== Meeting Room ==
Line 30: Line 39:
== Meeting Agenda ==
== Meeting Agenda ==


* '''WARNING : THE AGENDA IS BEING REORGANIZED RIGHT NOW..."
* '''WARNING : THE AGENDA WAS REORGANIZED ON MAY 27th : PLEASE REVIEW'''


=== Must See Topics ===
=== Must See Topics ===
Line 47: Line 56:
* [[ITK_Release_4/The Team/ITKv4 Development Team|ITKv4 Development Team]]
* [[ITK_Release_4/The Team/ITKv4 Development Team|ITKv4 Development Team]]


==== Morning A ====
==== Monday Morning ====


* 8:30 am Welcome: Terry Yoo
* 8:30 am Welcome: Terry Yoo
* 9:00 am State of the Toolkit: Hans Johnson
* 8:50 am State of the Toolkit: Hans Johnson [[http://www.vtk.org/Wiki/File:20110627ITKToolKitStatus.pdf#filelinks]] [[http://www.vtk.org/Wiki/File:20110627ITKToolKitStatus.pptx#filelinks]]
* 9:10 am [[ITK_Release_4/New_Code_Contribution_Process|Procedures for integrating A2D2 contributions]] (Bill/Luis)
* 9:30 am Split in to Focus Groups
* 9:30 am Split in to Focus Groups
** Group1 : Microscopy
** '''Group1''' : Microscopy
** Group2 : Clinical Applications
** '''Group2''' : Clinical Applications
** Group3 : Video
** '''Group3''' : Video
** Group4 : Data and Web-based Applications
** '''Group4''' : Data and Web-based Applications
* 10:00 Break
* 10:00 Break
* 10:30 am Working Groups (continuation)
* 10:30 am Working Groups (continuation)
** Group1 : Microscopy
** '''Group1''' : Microscopy
** Group2 : Clinical Applications
** '''Group2''' : Clinical Applications
** Group3 : Video
** '''Group3''' : Video
** Group4 : Data and Web-based Applications
** '''Group4''' : Data and Web-based Applications
* 12:00 pm Lunch
* 12:00 pm Lunch


==== Afternoon A ====
==== Monday Afternoon ====


* 1:00 pm  Plenary: Group 1 : 20min presentation + discussion
* 1:00 pm  Plenary: '''Group 1''' : 20min presentation + discussion
* 2:00 pm  Plenary: Group 2 : 20min presentation + discussion
* 2:00 pm  Plenary: '''Group 2''' : 20min presentation + discussion [[Summer_ITKv4_ClinicalGroupMeetingNotes | Group 2 notes]]
* 2:45 pm  Break
* 2:45 pm  Break
* 3:15 pm  Plenary: Group 3 : 20min presentation + discussion
* 3:15 pm  Plenary: '''Group 3''' : 20min presentation + discussion
* 4:00 pm  Plenary: Group 4 : 20min presentation + discussion
* 4:00 pm  Plenary: '''Group 4''' : 20min presentation + discussion
* 4:45 pm  Adjourn
* 4:45 pm  Adjourn
==== Group Details ====
===== Group 1: Microscopy and Histology =====
# '''Ross Whitaker''' (designated speaker), '''Kris Zygmunt''' ''Fast Nonlocal Algorithms for Denoising Microscopy, MRI, and Ultrasound Images Using Nonparametric Neighborhood Statistics.'' [[Summer_ITKv4_2011_Meeting/A2D2/Denoising| Pre-Meeting Document]]
# '''Marc Niethammer''' ''Adding Deconvolution Algorithms to ITK'' [[Summer_ITKv4_2011_Meeting/A2D2/Deconvolution| Pre-Meeting Document]]
# '''Raghu Machiraju''' ''A Comprehensive Workflow for Robust Characterization of Microstructure for Cancer Studies''
# '''Raghu Machiraju''' ''A Comprehensive Workflow for Large Histology Segmentation and Visualization''
===== Group 2: Clinical Applications and CADs =====
# '''Thomas Fletcher''' (designated speaker) ''ITK Algorithms for Analyzing Time-Varying Shape with Application to Longitudinal Heart Modeling''
# '''Ricardo Avila''' ''Fostering Open Science for Lung Cancer Lesion Sizing''
# '''Nikos Chrisochoides''' ''3D Real-Time Physics-Based Non-Rigid Registration for Image Guided Neurosurgery''
===== Group 3: Video =====
# '''Amitha Perera''' and '''Patrick Reynolds''' (designated speakers) ''ITKExtensions for Video Processing'' [[Summer_ITKv4_2011_Meeting/A2D2/VideoExtensions| Pre-Meeting Document]]
# '''Kevin Cleary''' ''Real-Time Image Capture for ITK through a Video Grabber''
# '''John Galeotti''' ''Methods in Medical Image Analysis: An ITK-Based Course with Deliverable Algorithms that extends and evaluates ITK while broadening its developer base''
===== Group 4: Data and Web-based Applications =====
# '''Sean Megason''' (designated speaker) ''SCORE++: Crowd source data, automatic segmentation and ground truth for ITK4''
# '''Marcel Prastawa''' ''SCORE: Systematic Comparison through Objective Rating and Evaluation''
# '''Ziv Yaniv''' ''Framework for automated parameter tuning of ITK registration pipelines''
[http://www.vtk.org/Wiki/images/a/ae/ITK4-Group4.pptx Presentation]
===== Working Groups Tasks =====
* Each PI or representative will share a brief summary (max 5min) of their proposal with the other members of the group.
* Things to Discuss:
*# How the A2D2s will advance the subject under consideration.
*# Find possible overlaps and similarities between the A2D2s - solve them.
*# Decide how the software will be distributed. (e.g. ITK module, ITK classes, independent software, IJ, etc...)
*# List all the new classes/modules that will be contributed to ITK
*# Discuss the design, architecture, and dependencies
*# List ITKv4 features that you might need to use (e.g. GPU? Multi-thread? Streaming?)
*# Discuss how each member of the group can help/assist each other
*# Come-up with a plan of action and '''time-line'''
*# Combine slides into a single presentation showing all the points that were discussed
===== Plenary Sessions =====
* Designated speaker will present
* Each of the other members should be available to anser questions and/or provide additional explanation
* Discuss possible problems and challenges


==== Dinner ====
==== Dinner ====
==== Arrival Group Dinner ====
==== Arrival Group Dinner ====


* Irish Pub
 
* Hackfest at Kitware NC Office (KRS)
 
* Location:
 
  Suite G-4
  101 East Weaver St
  Carrboro, North Carolina
  27510  USA
  518-371-3971 (voice/fax)
 
  http://www.kitware.com/company/NC_mapsdirections.html
 
This is at walking distance from the Franklin Hotel.
 
* Date:  Monday June 27th
* Time: 6pm-10pm
 
* Hands Raised so Far:
 
Terry, Bill, Stephen, Luis, Nick, Hans, Bill(ret), Arnaud, Cory


=== Tuesday June 28th ===
=== Tuesday June 28th ===




==== Morning A ====
==== Tuesday Morning ====


* 8:30 am Welcome: Terry Yoo
* 8:30 am Welcome, Questions, Concerns
* 8:45 am State of the Toolkit : Hans Johnson
* 9:00 am Working Groups
* 9:00 am Registration Refactoring: Brian Avants
** '''Group 1''' ITK Revise / Refactor
* 10:00 am Break
** '''Group 3''' GPU and Multithreading
* 10:30 am Level Sets Refactoring: Arnaud Gelas
* 10:30 am Break
* 11:15 am FEM Refactoring: Vincent Magnotta
* 11:00 am Working Groups
* 12:00 pm Lunch
** '''Group 2''' DICOM
** '''Group 4''' Simplify
* 12:30 pm Lunch


==== Afternoon A ====
==== Tuesday Afternoon ====


* 1:00 pm SimpleITK : Dan Blezek / Brad Lowekamp
* 1:30 pm Plenary Session: '''Revise'''
* 2:00 pm DICOM : Drew Wasem / Dan Blezek
** 20min presentations and the discussion about Registration, FEM, LevelSets.
* 2:45 pm Break
**[[File:ITKv4–Refactoring-June-2011.odp]]
* 3:00 pm Wrapping : Ashish Sharma
**[[File:ITKv4–Refactoring-June-2011.pptx]]
* 4:00 pm GPU : Won Ki / Jim Miller
* 2:30 pm Plenary Session: '''Simplify'''
* 4:30 pm Changing txx extensions: Hans Johnson
** 20min presentations and the discussion about SimpleITK, WrapITK, Doxygen for SimpleITK
* 5:00 pm Adjourn
** WrapITK [[File:WrapITK.pptx]]
** SimpleITK [[Media:SimpleITK_Status.pptx|SimpleITK Status Presentation(pptx)]]
* 3:00 pm Break
* 3:30 pm Plenary Session: '''GPU & Multithreading'''
** 20min presentations and discussion
** [[File:GPU-ITKv4-Summer-2011-final.pptx]]
* 4:30 pm DICOM
** 20min presentation and discussion
** [[File:ITKv4_DICOM-GDCM_Summer_Presentation.pptx]]
* 5:30 pm Adjourn


==== Dinner ====
==== Dinner ====
Line 109: Line 198:
=== Wednesday June 29th ===
=== Wednesday June 29th ===


==== Wednesday Morning ====


==== Morning B ====
* 8:30 am Welcome, Questions, Concerns
* 8:35 am Integration (Slicer/Wiki Examples/OTB/ImageJ/ICY/OME/V3D) (Bill Lorensen / Luis Ibanez)
** [http://www.cdash.org/CDash/index.php?project=Slicer4 Slicer4 Dashboard]
** [http://slicer-devel.65872.n3.nabble.com/ITK-Modular-Slicer4-updates-td2776514.html Slicer4 Modular ITKv4 updates]
*** [http://www.na-mic.org/Wiki/index.php/2011_Winter_Project_Week:_Slicer4-ITK4_Continuous_Integration Slicer4/ITKv4 Continuous Integration]
** [http://www.cdash.org/CDash/index.php?project=Insight&filtercount=1&showfilters=1&field1=site/string&compare1=63&value1=BillsBasement ITKApps]
** [http://www.cdash.org/CDash/index.php?project=ITKWikiExamples ITK Wiki Examples]
** Integration Efforts
*** [[File:ITK_Developers_Meeting_June_2011_IntegrationWithApplications.odp]]
*** [[File:ITK_Developers_Meeting_June_2011_IntegrationWithApplications.pdf]]
* 9:00 am Who is doing What ? - Action Items (Hans Johnson)
** https://itk.icts.uiowa.edu/jira/secure/Dashboard.jspa
* 9:30 am [[Media:Code Reviews 2011-06-29.ppt|Code Revisions (Jim Miller)]]
* 10:00 am Break
* 10:30 am Migration Guide (Gabe Hart / Dave Cole)
* 11:00 am Road Ahead (What's Next ?) (Terry Yoo)


* 12:00 pm Lunch
* 12:00 pm Lunch


==== Afternoon B ====
==== Wednesday Afternoon ====


* 1:00 pm Migration Guide - Gabe Hart
* 1:00 pm Testing Data (Patric Reynolds / Bill Hoffman)
* 1:30 pm Testing Data - Patrick Reynolds / Bill Hoffman
* 1:30 pm Modularization (Bill Hoffman)
* 2:00 pm Integration (Slicer/WikiExamples/OTB/ImageJ/ICY/V3D) - Bill Lorensen / Luis Ibanez
* 2:00 pm Doxygen Documentation (Arnaud Gelas) [[File:ITKv4-Doxygen.ppt]]
* 2:30 pm Break
* 2:30 pm Break
* 3:00 pm Modularization : Bill Hoffman
* 3:00 pm Hack / Work / Hack More
* 3:30 pm Code Revisions : Jim Miller
* 5:00 pm Adjourn
* 4:00 pm New Process for New Incoming code : Bill Lorensen
* 4:30 pm Doxygen Documentation : Arnaud Gelas
* 5:00 pm Adjourn


==== Dinner ====
==== Dinner ====


* GROUP DINNER
* GROUP DINNER for Survivors
** Carolina Brewery.
** Carolina Brewery.
** Register in the haptic pad with mechanical stylus


== Attendees ==
== Attendees ==
Line 149: Line 252:
* Patrick Reynolds (A2D2 Video/SCORE/SCORE++)
* Patrick Reynolds (A2D2 Video/SCORE/SCORE++)
* Brad Davis
* Brad Davis
* Mike Grauer (SCORE/SCORE++/A2D2 Registration)
* Jean-Christophe Fillion-Robin


=== University of Iowa ===
=== University of Iowa ===
Line 179: Line 284:


* Ross Whitaker
* Ross Whitaker
* Marcel Prastawa
* Josh Cates
* Kris Zygmunt


=== Cosmo Software===
=== Cosmo Software===
Line 226: Line 334:
| David Cole  ||  ||  ||   
| David Cole  ||  ||  ||   
|-
|-
| Marcus Hanwell ||   ||   ||  
| Marcus Hanwell || X  || X  || X 
|-
|-
| Xiaoxiao Liu  ||  ||  ||   
| Xiaoxiao Liu  ||  ||  ||   
Line 242: Line 350:
| Brad Davis ||  ||  ||   
| Brad Davis ||  ||  ||   
|-
|-
| Vincent Magnotta ||  ||   ||  
| Vincent Magnotta ||  || x  || X
|-
|-
| Hans Johnson ||   ||   ||  
| Hans Johnson || x  || X  || X
|-
|-
| Brian Avants ||  ||  ||   
| Brian Avants ||  ||  ||   
Line 250: Line 358:
| James C. Gee ||  ||  ||   
| James C. Gee ||  ||  ||   
|-
|-
| Nick Tustison ||   ||   ||  
| Nick Tustison || x  || x  || x 
|-
|-
| Sean Megason ||   ||   ||  
| Sean Megason || x || x || x 
|-
|-
| Arnaud Gelas ||   ||   ||  
| Arnaud Gelas || x || x || x 
|-
|-
| Won-Ki Jeong (SEAS) ||   ||   ||   
| Won-Ki Jeong || X || X || X    
|-
|-
| Raghu Machiraju ||   ||   ||  
| Raghu Machiraju || x || x || x
|-
|-
| Kun Huang ||  ||  ||   
| Kun Huang ||  ||  ||   
Line 282: Line 390:
| Dirk Padfield || X  || X  ||  X  
| Dirk Padfield || X  || X  ||  X  
|-
|-
| Dan Blezek ||   ||   ||  
| Dan Blezek || X  || X || X
|-
|-
| Cory Quammen ||  ||  ||   
| Cory Quammen ||  ||  ||   
Line 298: Line 406:
| Bill Lorensen || X  || X  || X   
| Bill Lorensen || X  || X  || X   
|-
|-
| Marcel Prastawa || X  ||  || 
|-
| Josh Cates || X  || X || 
|-
| Kris Zygmunt || X || X || X
|-
| Jean-Christophe Fillion-Robin || X ||  ||
|-
|}
|}

Latest revision as of 01:18, 11 February 2012

ITKv4 Summer Meeting

  • Dates: June 27-29, 2011
  • City: Chapel Hill, NC
  • Location: Franklin Hotel

Travel / Hotel Information

The Meeting will take place at the Franklin Hotel.

Since the meeting starts at

  • 8 am on June 27th,

we recommend people to arrange their hotel accommodation for the previous night!

  • Use the room group 'ITKV4'
    • Reservation line: 866.831.5999
    • Ask for the "room block" reserved under 'ITKV4'
  • The rate is $129 / Night

Registration Information

  • Download Registration Form
  • It is a fillable PDF form
  • Fill it up please.
    • Indicate the number of days that you are attending.
    • Registration fee = ( NumberOfDays * $65 );
    • Print it as a PDF file
      • since otherwise the form is still modifiable
  • Send the processed form back to Kitware
    • email it at: admin at kitware dot com

Meeting Room

Meeting Agenda

  • WARNING : THE AGENDA WAS REORGANIZED ON MAY 27th : PLEASE REVIEW

Must See Topics

  • BETA Release
  • GPU
  • Modularization
  • SimpleITK
  • DICOM
  • Registration Refactoring
  • LevelSet Refactoring

Monday June 27th - A2D2 Summit

Monday Morning

  • 8:30 am Welcome: Terry Yoo
  • 8:50 am State of the Toolkit: Hans Johnson [[1]] [[2]]
  • 9:10 am Procedures for integrating A2D2 contributions (Bill/Luis)
  • 9:30 am Split in to Focus Groups
    • Group1 : Microscopy
    • Group2 : Clinical Applications
    • Group3 : Video
    • Group4 : Data and Web-based Applications
  • 10:00 Break
  • 10:30 am Working Groups (continuation)
    • Group1 : Microscopy
    • Group2 : Clinical Applications
    • Group3 : Video
    • Group4 : Data and Web-based Applications
  • 12:00 pm Lunch

Monday Afternoon

  • 1:00 pm Plenary: Group 1 : 20min presentation + discussion
  • 2:00 pm Plenary: Group 2 : 20min presentation + discussion Group 2 notes
  • 2:45 pm Break
  • 3:15 pm Plenary: Group 3 : 20min presentation + discussion
  • 4:00 pm Plenary: Group 4 : 20min presentation + discussion
  • 4:45 pm Adjourn

Group Details

Group 1: Microscopy and Histology
  1. Ross Whitaker (designated speaker), Kris Zygmunt Fast Nonlocal Algorithms for Denoising Microscopy, MRI, and Ultrasound Images Using Nonparametric Neighborhood Statistics. Pre-Meeting Document
  2. Marc Niethammer Adding Deconvolution Algorithms to ITK Pre-Meeting Document
  3. Raghu Machiraju A Comprehensive Workflow for Robust Characterization of Microstructure for Cancer Studies
  4. Raghu Machiraju A Comprehensive Workflow for Large Histology Segmentation and Visualization
Group 2: Clinical Applications and CADs
  1. Thomas Fletcher (designated speaker) ITK Algorithms for Analyzing Time-Varying Shape with Application to Longitudinal Heart Modeling
  2. Ricardo Avila Fostering Open Science for Lung Cancer Lesion Sizing
  3. Nikos Chrisochoides 3D Real-Time Physics-Based Non-Rigid Registration for Image Guided Neurosurgery
Group 3: Video
  1. Amitha Perera and Patrick Reynolds (designated speakers) ITKExtensions for Video Processing Pre-Meeting Document
  2. Kevin Cleary Real-Time Image Capture for ITK through a Video Grabber
  3. John Galeotti Methods in Medical Image Analysis: An ITK-Based Course with Deliverable Algorithms that extends and evaluates ITK while broadening its developer base
Group 4: Data and Web-based Applications
  1. Sean Megason (designated speaker) SCORE++: Crowd source data, automatic segmentation and ground truth for ITK4
  2. Marcel Prastawa SCORE: Systematic Comparison through Objective Rating and Evaluation
  3. Ziv Yaniv Framework for automated parameter tuning of ITK registration pipelines

Presentation

Working Groups Tasks
  • Each PI or representative will share a brief summary (max 5min) of their proposal with the other members of the group.
  • Things to Discuss:
    1. How the A2D2s will advance the subject under consideration.
    2. Find possible overlaps and similarities between the A2D2s - solve them.
    3. Decide how the software will be distributed. (e.g. ITK module, ITK classes, independent software, IJ, etc...)
    4. List all the new classes/modules that will be contributed to ITK
    5. Discuss the design, architecture, and dependencies
    6. List ITKv4 features that you might need to use (e.g. GPU? Multi-thread? Streaming?)
    7. Discuss how each member of the group can help/assist each other
    8. Come-up with a plan of action and time-line
    9. Combine slides into a single presentation showing all the points that were discussed
Plenary Sessions
  • Designated speaker will present
  • Each of the other members should be available to anser questions and/or provide additional explanation
  • Discuss possible problems and challenges

Dinner

Arrival Group Dinner

  • Hackfest at Kitware NC Office (KRS)
  • Location:
  Suite G-4
  101 East Weaver St
  Carrboro, North Carolina
  27510  USA
  518-371-3971 (voice/fax)

  http://www.kitware.com/company/NC_mapsdirections.html

This is at walking distance from the Franklin Hotel.

  • Date: Monday June 27th
  • Time: 6pm-10pm
  • Hands Raised so Far:

Terry, Bill, Stephen, Luis, Nick, Hans, Bill(ret), Arnaud, Cory

Tuesday June 28th

Tuesday Morning

  • 8:30 am Welcome, Questions, Concerns
  • 9:00 am Working Groups
    • Group 1 ITK Revise / Refactor
    • Group 3 GPU and Multithreading
  • 10:30 am Break
  • 11:00 am Working Groups
    • Group 2 DICOM
    • Group 4 Simplify
  • 12:30 pm Lunch

Tuesday Afternoon

Dinner

Wednesday June 29th

Wednesday Morning

  • 12:00 pm Lunch

Wednesday Afternoon

  • 1:00 pm Testing Data (Patric Reynolds / Bill Hoffman)
  • 1:30 pm Modularization (Bill Hoffman)
  • 2:00 pm Doxygen Documentation (Arnaud Gelas) File:ITKv4-Doxygen.ppt
  • 2:30 pm Break
  • 3:00 pm Hack / Work / Hack More
  • 5:00 pm Adjourn

Dinner

  • GROUP DINNER for Survivors
    • Carolina Brewery.
    • Register in the haptic pad with mechanical stylus

Attendees

Please add your name to the list below if you are planning to attend.

Kitware

  • Luis Ibanez
  • Bill Hoffman
  • Stephen Aylward
  • David Cole
  • Marcus Hanwell
  • Xiaoxiao Liu (Lesion Sizing Toolkit)
  • Andinet Enquobahrie (A2D2 Registration)
  • Michel Audette (A2D2 Meshes)
  • Amitha Perera (A2D2 Video)
  • Gabe Hart (A2D2 Video / Simple ITK)
  • Patrick Reynolds (A2D2 Video/SCORE/SCORE++)
  • Brad Davis
  • Mike Grauer (SCORE/SCORE++/A2D2 Registration)
  • Jean-Christophe Fillion-Robin

University of Iowa

  • Vincent Magnotta
  • Hans Johnson

University of Pennsylvania

  • Brian Avants
  • James C. Gee
  • Nick Tustison

Harvard University

  • Sean Megason
  • Arnaud Gelas
  • Won-Ki Jeong (SEAS)

The Ohio State University

  • Raghu Machiraju
  • Kun Huang
  • Zhi Han

College of William and Mary

  • Nikos Chrisochoides
  • Dr. Kot
  • Dr. Liu

University of Utah

  • Ross Whitaker
  • Marcel Prastawa
  • Josh Cates
  • Kris Zygmunt

Cosmo Software

  • Drew Wasem
  • Ashish Sharma
  • Alex Gouaillard [A*STAR] (over the phone / internet)

GE

  • Jim Miller
  • Dirk Padfield

Mayo Clinic

  • Dan Blezek

University of North Carolina

  • Cory Quammen
  • Marc Niethammer

National Library of Medicine

  • Terry Yoo
  • Bradley Lowekamp
  • Jesus Caban

Georgetown University / CNMC

  • Ziv Yaniv

Noware

  • Bill Lorensen

Bioscan

  • John McInerney

Attendance Matrix

Name Monday June 27 Tuesday June 28 Wednesday June 29
Luis Ibanez X X X
Bill Hoffman
Stephen Aylward
David Cole
Marcus Hanwell X X X
Xiaoxiao Liu
Andinet Enquobahrie
Michel Audette
Amitha Perera
Gabe Hart
Patrick Reynolds
Brad Davis
Vincent Magnotta x X
Hans Johnson x X X
Brian Avants
James C. Gee
Nick Tustison x x x
Sean Megason x x x
Arnaud Gelas x x x
Won-Ki Jeong X X X
Raghu Machiraju x x x
Kun Huang
Zhi Han
Nikos Chrisochoides
Dr. Kot
Dr. Liu
Ross Whitaker
Drew Wasem X X X
Ashish sharma X X X
Alex Gouaillard (remote)
Jim Miller X X X
Dirk Padfield X X X
Dan Blezek X X X
Cory Quammen
Marc Niethammer
Terry Yoo
Bradley Lowekamp
Jesus Caban
Ziv Yaniv X X
Bill Lorensen X X X
Marcel Prastawa X
Josh Cates X X
Kris Zygmunt X X X
Jean-Christophe Fillion-Robin X
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