Agenda&Status 081010

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

• Number of Work Assignments?
• Deadline for sending the Draft of T.O 2?
• Minutes of Washington meeting from NIH?
• date of next meeting?

Technical Topics

Stable ITK 3.20

• How to get it.
• Maintenance rules (gate keeper ?)

DICOM

Dan and Mathieu to report

• Beginnings of a requirements document. Comments welcome.
• Updating openjpeg
• Introducing JPEG2000
• Updating to GDCM 2.0
• Release Saturday 14th ?

Simple ITK

• Design Discussions
• Sandbox in Github
• Simple ITK Layer

Wrapping

• Plans for wrapping
• Tools
  • Pros and Cons
• Wrapping
• update from brad on wrapitk test (new swig usage that addresses existing concerns)?

Refactoring Optimization Framework

• Is the | refactoring of the optimization framework going to be considered for itkv4?
  • Brian Avants to lead discussion on registration refactoring.

Modularization

• Gabe Hart to report of initial Modularization efforts
• Exploration of Ryppl
  • Interaction with Boost
  • Brad King & Dave Cole Report

Microscopy

• Scheduling a dedicated tcon for this topic.

Gathering Feedback from the attendees to the Hackathon in Janelia Farm (HHMI)

• Luis to report
• Microscopy community.
  • Pixel types used
  • Image Dimensions (2,3,4,5)
  • Channels as dimension ?
  • Time as dimension ?
  • Memory organization ?
    • Alternative Memory Models for ITK Images ?
  • Multi-scale datasets
  • Needs for Object representation data structures

Management of Large Datasets

• Sean Megason & Arnaud Gelas
  • Needs
    • Large data sets (greater than RAM) - 100GB to 1TB per experiment
    • PixelType may be scalar, vector, or tensor
    • How to deal with multiple channels and time points (e.g. dimensions, vector)
    • ordering dimensions for iteration (e.g. tracking nuclei needs time before channel whereas segmentation might want channel before time)
    • Crop and resample n dimensional image into m dimensional image (m<n)
    • Having a multi-resolution representation for images ? ( ala JPEG2000, or wavelets ?)

• • Partial solutions
    • meta reader - n-dimensional image set stored on disk (or database) as series of 2-d images. Reader can grab any subset of dimensions and stream. Needs an n-dimensional container (hashtable) that can be sorted.

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.

Software Process

Migration to Git

• Migration Completed
  • Workflow
    • The Pro Git book has examples of distributed workflows
    • Master & Next ? See here.
    • Topic Branches: See the ITK Topic Stage, and an example topic merge.
    • Dashboard Branches
      • Master Nightly: so all nightly builds use same source
    • Hooks
      • Come to agreement on which hooks to use for ITK4 (Lorensen)
      • KWStyle?

• Updating Dashboard Machines to Git

• Contractors to send information to Kitware about the developers who should receive Git write access.
  • (include email and public SSH key)

Before Giving Git Write Access

• Changing LICENSE to Apache 2.0

Clean up Releases

Release Tag	Date	Major Changes
Alpha-01	August 7	VS6,BCC55, SunCC (5.7?), Metrowerks Removal (based on compiler features), Remove large Images
Alpha-02	August 14	CMake Variables configuration cleanup
Alpha-03	August 21	GDCM 2.0, OpenJpeg-v2, +JPEG2000
Alpha-04	August 28	Third party libraries update: TIFF, JPEG, PNG

• Phases

• Hans Johnson to report on compilers cleanup.
  • and experiences with Git workflow.

Tools

Coding Style

ITKv4_StyleChangeProposal

• Fixing KWStyle/CDash/CTest for Git : Brad Davis report