Difference between revisions of "Agenda&Status 081010"

From KitwarePublic
Jump to navigationJump to search
 
(12 intermediate revisions by 4 users not shown)
Line 1: Line 1:
= 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 =
= Project Management =


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


= Technical Topics =
= Technical Topics =


== Microscopy ==
== Stable ITK 3.20 ==
 
=== Management of Large Datasets ===


* Sean Megason & Arnaud Gelas
* How to get it.
** How to deal with multiple channels ?
* Maintenance rules (gate keeper ?)
** and multiple time points ?
** Managing very large datasets (>10Gb to Terabytes)
** Having a multi-resolution representation for images ? ( ala JPEG2000, or wavelets ?)


== Refactoring Optimization Framework ==
== DICOM ==
 
Dan and Mathieu to report
* Is the [http://www.itk.org/Wiki/Proposals:Refactoring_of_optimization_framework | refactoring of the optimization framework] going to be considered for itkv4?
* [[ITKv4_DICOM_Communications_Discussion | Beginnings of a requirements document]].  Comments welcome.
** Brian Avants to lead discussion on registration refactoring.
* Updating openjpeg
* Introducing JPEG2000
* Updating to GDCM 2.0
* Release Saturday 14th ?


== Simple ITK ==
== Simple ITK ==
Line 29: Line 39:
* Sandbox in Github
* Sandbox in Github
* [[ITK_Release_4/SimpleITK|Simple ITK Layer]]
* [[ITK_Release_4/SimpleITK|Simple ITK Layer]]
* Gathering Feedback from the attendees to the [[ITK_Release_4/Microscopy/Related Events#Hackathon_at_HHMI:_V3D-ITK_Plugins|Hackathon in Janelia Farm (HHMI)]]
** Luis to report
** [[ITK_Release_4/Microscopy|Microscopy community]].
*** Pixel types used
*** Image Dimensions (2,3,4,5)
*** Channels as dimension ?
*** Time as dimension ?
*** Memory organization ?
**** [http://insight-journal.org/browse/publication/646 Alternative Memory Models for ITK Images] ?
*** Multi-scale datasets
*** Needs for Object representation data structures


== Wrapping ==
== Wrapping ==
Line 48: Line 47:
* [[ITK_Release_4/Wrapping|Wrapping]]
* [[ITK_Release_4/Wrapping|Wrapping]]
* update from brad on wrapitk test (new swig usage that addresses existing concerns)?
* update from brad on wrapitk test (new swig usage that addresses existing concerns)?
== Refactoring Optimization Framework ==
* Is the [http://www.itk.org/Wiki/Proposals:Refactoring_of_optimization_framework | refactoring of the optimization framework] going to be considered for itkv4?
** Brian Avants to lead discussion on registration refactoring.


== Modularization ==
== Modularization ==
Line 56: Line 60:
** Brad King & Dave Cole Report
** Brad King & Dave Cole Report


== DICOM ==
== Microscopy ==
Dan and Mathieu to report
 
* [[ITKv4_DICOM_Communications_Discussion | Beginnings of a requirements document]]. Comments welcome.
* Scheduling a dedicated tcon for this topic.
 
=== Gathering Feedback from the attendees to the [[ITK_Release_4/Microscopy/Related Events#Hackathon_at_HHMI:_V3D-ITK_Plugins|Hackathon in Janelia Farm (HHMI)]] ===
* Luis to report
* [[ITK_Release_4/Microscopy|Microscopy community]].
** Pixel types used
** Image Dimensions (2,3,4,5)
** Channels as dimension ?
** Time as dimension ?
** Memory organization ?
*** [http://insight-journal.org/browse/publication/646 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 ()
* [http://www.loci.wisc.edu/software/bio-formats BioFormats] has readers and example files for these. It is Java with C++ bindings for ITK, BUT it's GPL.


= Software Process =
= Software Process =

Latest revision as of 16:38, 10 August 2010

How to Join the Tcon

Number to Call

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

Webex

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

Simple ITK

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

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)

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

  • 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


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

ITKv4-TransitionPlanProposal.png


  • 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