Proposals:HDF5 ImageIO: Difference between revisions
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* Large datasets ( Size > 4Gb ) | * 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 | * Single experiment images of size 1024 x 1024 x 75 (XYZ), 2 channels, 1000 time-points | ||
* 8bit and 16bit | * 8bit and 16bit | ||
Latest revision as of 17:31, 25 May 2010
Adding support for HDF5
Motivation
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
