ITK/Summer v4 2011 Meeting

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.

• http://franklinhotelnc-px.trvlclick.com/index.html

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 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

• A2D2 Development Team
• ITKv4 Development Team

Monday Morning

• 8:30 am Welcome: Terry Yoo
• 8:50 am State of the Toolkit: Hans Johnson
• 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
• 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) Fast Nonlocal Algorithms for Denoising Microscopy, MRI, and Ultrasound Images Using Nonparametric Neighborhood Statistics.
2. Marc Niethammer Adding Deconvoltion Algorithms to ITK
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
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

• Irish Pub

Tuesday June 28th

Tuesday Morning

• 8:30 am Welcome, Questions, Concerns
• 9:00 am Working Groups
  • Group 1 ITK Revise
  • Group 2 DICOM
• 10:30 am Break
• 11:00 am Working Groups
  • Group 3 GPU and Multithreading
  • 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

Dinner

• GROUP DINNER
  • Mama Dip's
    • http://www.mamadips.com/

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

Dinner

• GROUP DINNER for Survivors
  • Carolina Brewery.

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)

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

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
Xiaoxiao Liu
Andinet Enquobahrie
Michel Audette
Amitha Perera
Gabe Hart
Patrick Reynolds
Brad Davis
Vincent Magnotta
Hans Johnson
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