ITK/Tcons/Agendas/2010 12 14

How to Join the Tcon

Number to Call

• 1-800-728-9607 (in the US) or
• +1 9139049873 (international)
• access code 6815251

Webex

• Meeting link
• https://emeetings.webex.com/emeetings/j.php?ED=138191182&UID=482060457&PW=NNzJiNDk1ZGU3

Project Management

February Meeting in Boston

• Set for February 2-3, 2011 in Boston at Harvard Medical School.

• • http://www.events.harvard.edu/web/2281
  • http://www.itk.org/Wiki/Winter_ITKv4_2011_Meeting

Please register for the meeting ASAP. Here is the link for the registration:

• http://www.events.harvard.edu/30325

Technical Topics

Dashboard

• Dashboard Status - Today's Dashboard

Lingering Failing Tests ( Feet + Heat )

• JPEG2000 on BigEndian
  • Kitware/Harvard/Malaterre status update
  • Able to reproduce problem?
  • Anticipated resolution?

• DICOM Tests tkGDCMSeriesStreamReadImageWrite3 and tkGDCMSeriesStreamReadImageWrite4
  • Malaterre/Roden status update
  • Able to reproduce the problem?
  • resolution?

• VXL vcl-test_atomic_count
  • Kitware status update?

• KWStyle failing
  • FFT related failure

ITKv4-A04

• Fixing Windows 64bits problem with "long"...

Outreach

• MICCAI 2011 Call for Workshops and Tutorials
  • Suggested Tutorials for MICCAI 2011
• Note that we already have an accepted tutorial for CVPR 2011 on the use of ITK+OpenCV

Redmine demo

• Project management software
• SimpleITK Redmine instance on EC2

Gerrit Reviews

• http://review.source.kitware.com/#q,status:open,n,z

Doxygen Nightly

• • http://www.itk.org/Wiki/ITK_Documentation

ITK Data

Three levels of data :

1. Testing - a select set of data sets that are used for regression testing - exists in MIDAS.
2. Examples - datasets that are part of the itk examples - exists but didn't see on MIDAS
3. Development - a large collection of various image data sets and segmentations used by the ITK developers and the community to tune algorithm parameters and select optimal combinations of components in pipelines.

A data set will include:

1. image(s)
2. additional data file(s) - optional
3. segmentation(s) - optional
4. detailed description of the data

Questions

1. Should this be hosted via MIDAS? NCI has a large, open, repository of various images (DICOM) with a very nice front end [1], perhaps possible to leverage this?
2. Will kitware be willing to host such a large repository (I suspect this will be many Terabytes of data)?
3. What should we use as the file format for image(s), segmentation(s)? [smallest possible set of file formats that support the desired functionality].

Migration Guide Process

• Users Migration Guide (Gabe Hart)
  • What Developers Must Do To Contribute to the Users Migration Guide
  • Developer Tutorial
• Example XML
  • http://review.source.kitware.com/#patch,sidebyside,224,2,Migration/DecoupleNumericTraitsFromContainers.xml

Simple ITK

• Code generations
  • Using Lua and JSON

• Interfacing to
  • ImageJ / Fiji
  • CellProfiler

GPU

• Summary of tcon with NVIDIA from Monday Nov 22 at 1pm EST (Won Ki)
• GPU Acceleration - V4
  • Tcon 2010-11-22

DICOM

Dan and Mathieu to report

• Beginnings of a requirements document. Comments welcome.
• Proposed TConf

Image Registration Revision

• Start sending patches to Gerrit
  • New CompositeTransform class is underway
  • New DeformationFieldTransform class is underway
  • Transform IO will be adjusted accordingly

Level Set

• Refactoring page
  • Refactoring Level-Set framework - V4

Time Stamp Proposal

• Time Stamp

Modularization

• Had a Tcon about modularization on Dec 3 [2].

The initial partition seems to be good to start with.

• Brad King worked on cmake packaging prototypes
• Xiaoxiao Liu (Kitware) is working on scripts to migrate monolithic ITK to modular ITK

TIFF Update

• Brad King addressed the int issues
• Currently at

 git fetch git://kwsource.kitwarein.com/~bradking/itk/bradkings-itk.git +libtiff4beta6:libtiff4beta6

Sequestered Reference Applications

We have already made significant changes, and they are not being recorded yet. It is time to setup these reference applications.

Ongoing

• V3D Plugins
• Slicer
• VV
• Insight Applications now submitting
  • Broken: need to use it as an example for the Migration Guide.

Development Versions following ITKv4

• OTB
  • http://dash.orfeo-toolbox.org/buildSummary.php?buildid=29602
• GoFigure2
  • Nightly build use the current ITKv4.
  • http://my.cdash.org/index.php?project=GoFigure2

Pending

• IGSTK, after SPIE'11 (IGSTK5.0)
• Insight Applications (ITKApps from v3.20)
• ITK tests from v3.20

Wrapping

• Status (Alex)
• Wrapping

ITK Readers for Microscopy formats

• There's a need for readers in the microscopy community in order to be able to use ITK
  • Zeiss (LSM and ZVI)
  • Leica (LIF)
  • Olympus (OIB)
  • Nikon ()
• BioFormats has readers and example files for these. It is Java with C++ bindings for ITK, BUT it's GPL.