ITK/Summer v4 2011 Meeting

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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


Must See Topics

  • BETA Release
  • GPU
  • Modularization
  • SimpleITK
  • 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
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


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)

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
    • 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

  • 1:30 pm Plenary Session: Revise
    • 20min presentations and the discussion about Registration, FEM, LevelSets.
  • 3:00 pm Break
  • 3:30 pm Plenary Session: Simplify
    • 20min presentations and the discussion about SimpleITK, WrapITK, Doxygen for SimpleITK
  • 4:30 pm Plenary Session: GPU & Multithreading
    • 20min presentations and discussion
  • 5:30 pm Adjourn


Wednesday June 29th

Wednesday Morning

  • 8:30 am Welcome, Questions, Concerns
  • 9:00 am Plenary Session: DICOM
    • 20min presentation and discussion DCMTK, GDCM
  • 9:30 am Modularization (Bill Hoffman)
  • 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

Wednesday Afternoon

  • 1:00 pm Testing Data (Patric Reynolds / Bill Hoffman)
  • 1:30 pm Integration (Slicer/Wiki Examples/OTB/ImageJ/ICY/OME/V3D) (Bill Lorensen / Luis Ibanez)
  • 2:00 pm Code Revisions (Jim Miller)
  • 2:30 pm Break
  • 3:00 pm New Process for New Incoming Code (Bill Lorensen)
  • 3:30 pm Doxygen Documentation (Arnaud Gelas)
  • 4:00 pm Adjourn


  • GROUP DINNER for Survivors
    • Carolina Brewery.


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


  • 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)


  • 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


  • Bill Lorensen


  • 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