[ome-devel] Fwd: HDF-based image file formats

[Jason Swedlow]

Dear All-

Another comment forwarded from Michael held (ETH Zurich):

"Despite the use of the OMERO database the points of storing data in a  
more convenient/performant/flexible HDF5/netCDF4 format is very  
pressing. This could also include the raw image data, since storage of  
millions single TIFF is problematic in many ways. Josh mentioned  
something like a OME-HDF4/netCDF4 format. At least for the raw data we  
should make sure that tools like ImageJ will support this format. "

We've discussed using HDF as an image file format for some time.  We  
already use HDF5 for storing tabular data in OMERO (http://trac.openmicroscopy.org.uk/omero/wiki/OmeroTables 
).  There are many obvious advantages to using an HDF5 data store,  
namely flexible in data structures that can be stored.   These have  
been summarised recently (http://queue.acm.org/detail.cfm?id=1628215).

However, the limited case mentioned above-- too many single TIFFs-  
doesn't seem to be a good argument for creating yet another image file  
format.  There are many ways to alleviate the problem of millions of  
TIFFs.  the easiest one is to use multi-page TIFFs (as in, for  
example, OME-TIFF).  The optimization and stability of TIFF readers  
shouldn't be forgotten.  Obviously, other data types, especially  
analysis data etc. won't fit into this data format, at least not  
easily.  Are they strong arguments for choosing HDF etc. purely as a  
multi-plane store over TIFF-based formats?

As is hinted above, putting other data types into image files will  
require adaptation of the various applications to actually use this  
data.  Again, not a small effort.

My two cents-- any other thoughts?  We would love to hear strong  
arguments to invest in and HDF-based image file format.

Cheers,

Jason


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