ITK Release 4/Microscopy: Difference between revisions

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=== Attendees ===
=== Attendees ===


* Alex Gouaillard
* Alex Gouaillard - Cosmo
* Sean Megason
* Sean Megason - Harvard
* Marc Niethammer
* Marc Niethammer -UNC
* Cory Quanmenn
* Cory Quanmenn -UNC
* Russ Taylor
* Russ Taylor - UNC
* Marcus Hanwell
* Marcus Hanwell - Kitware
* Brad Lowekamp
* Brad Lowekamp - NLM
* Luis Ibanez
* Luis Ibanez - Kitware
* Dominik Spinczyk
* Dominik Spinczyk - Silesian University
* Dhanannjay Deo - Kitware


=== Topics ===
=== Topics ===

Revision as of 17:10, 12 August 2010

Microscopy

Overview

Microscopy applications bring new challenges to ITK at many different levels

  • Very Large datasets (TeraBytes)
    • Examples:
      • Brainbow dataset = 11000x15000x1000 x (RGB) = 500 Gigabytes for one 3D image.
      • In-toto imaging dataset = 1000x1000x200x1000x5 ~ 500 GB for one imaging session (one organ)
      • Data acquisition
        • Today 100Gb / day
        • Tomorrow 1 Tb / day
        • 3D Stacks of 250Mb (8 seconds to acquire, 900 to deconvolve)
        • J.J. Field Optics Express 2010.
  • Temporal data (2D+t, 3D+t)
  • Multiple Components
  • Very large number of objects of interest per image

Technical Details

The toolkit needs

  • More explicit representation of time and channels
  • Management of multi-resolution datasets
  • Management of multi-gigabyte datasets (TeraBytes being the standard to look for in 5 years)
  • Richer set of classes for object representations

Reference Applications

Related Events


Tcons

August 12th 2010

Attendees

  • Alex Gouaillard - Cosmo
  • Sean Megason - Harvard
  • Marc Niethammer -UNC
  • Cory Quanmenn -UNC
  • Russ Taylor - UNC
  • Marcus Hanwell - Kitware
  • Brad Lowekamp - NLM
  • Luis Ibanez - Kitware
  • Dominik Spinczyk - Silesian University
  • Dhanannjay Deo - Kitware

Topics

  • Large Images: Larger than local RAM
  • Pixel Types:
    • Scalar, Vector, Tensor,
  • Time
  • Many channels