Proposals:HDF5 ImageIO

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