Proposals:HDF5 ImageIO

From KitwarePublic
Revision as of 17:31, 25 May 2010 by Kishoreraom (talk | contribs) (→‎Use Cases)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to navigationJump to search

Adding support for HDF5


Provide better support for large datasets, particularly those used in microscopy.

Historical Note

  • ITK provides support for MINC2, which in turn is based on HDF5.

Use Cases

  • Chunking (streaming)
  • Multi-Resolution
  • Multi-Channel images
  • Large datasets ( Size > 4Gb )

Use Case: Megason Lab, Harvard University

  • Single experiment images of size 1024 x 1024 x 75 (XYZ), 2 channels, 1000 time-points
  • 8bit and 16bit
  • Images stored as 2D PNGs with filenames giving location
  • Need to support optimized reading (image streaming) of a sub-volume
  • Eg: Box filtering using a kernel of size 5x5x1x1x3
  • Cyclic buffer optimization in the ITK reader that keeps overlapping data and only reads new data
  • Multi-resolution images for heirarchical registration of multiple experimental sets
  • Compression is not as important in the short term but will be needed in the long term