ITK Release 4/Microscopy

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

• Collaborating Groups
• Reference Applications

Related Events

• Related Events

Tcons

August 12th 2010

Attendees

• Alex Gouaillard
• Sean Megason
• Marc Niethammer
• Cory Quanmenn
• Russ Taylor
• Marcus Hanwell
• Brad Lowekamp
• Luis Ibanez
• Dominik Spinczyk

Topics

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