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.

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

@@ Line 3: / Line 3: @@
 = Motivation =
-Provide better support for lafte datasets, particularly those used in microscopy.
+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