Difference between revisions of "Agenda&Status 081010"

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* Sean Megason & Arnaud Gelas
 
* Sean Megason & Arnaud Gelas
** How to deal with multiple channels ?
+
** Needs
** and multiple time points ?
+
*** Large data sets (greater than RAM) - 100GB to 1TB per experiment
** Managing very large datasets (>10Gb to Terabytes)
+
*** How to deal with multiple channels and time points (e.g. dimensions, vector)
** Having a multi-resolution representation for images ? ( ala JPEG2000, or wavelets ?)
+
*** PixelType may be scalar, vector, or tensor
 +
*** Subset/crop/resample n dimensional image into m dimensional image (m<n)
 +
*** ordering dimensions for iteration (tracking nuclei need time before channel whereas segmentation might want channel first)
 +
*** 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.
  
 
== Refactoring Optimization Framework ==
 
== Refactoring Optimization Framework ==

Revision as of 17:43, 4 August 2010

Project Management

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


Technical Topics

Microscopy

Management of Large Datasets

  • Sean Megason & Arnaud Gelas
    • Needs
      • Large data sets (greater than RAM) - 100GB to 1TB per experiment
      • How to deal with multiple channels and time points (e.g. dimensions, vector)
      • PixelType may be scalar, vector, or tensor
      • Subset/crop/resample n dimensional image into m dimensional image (m<n)
      • ordering dimensions for iteration (tracking nuclei need time before channel whereas segmentation might want channel first)
      • 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.

Refactoring Optimization Framework

Simple ITK

Wrapping

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

Modularization

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

DICOM

Dan and Mathieu to report

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