[ome-devel] Some OME-HDF questions

[Edwin Bennink]

Dear ome-devel members,


We are planning to create a HDF5 based file format as a replacement for 
ICS/IDS, which is the current default format in our Huygens software. We 
need to start storing parameters and data related to spherical 
aberration together with the images, and we do not think it is a good 
idea to extend ICS/IDS or the current OME for this purpose.

As we would like our HDF format to be compatible with (the future) 
OME-HDF, I've some questions to the OME developers:

 - How are we going to store multi-dimensional data;
   * as a native HDF multi-dimensional array (in a single dataset, like 
OME-XML), or;
   * as lower dimensional datasets within the HDF archive (like the 2D 
image planes in OME-TIFF)?

 - How are we going to store the meta-data;
   * as an HDF-clone of the OME-XML standard (using native HDF elements 
and attributes; no namespaces), or;
   * as a complete OME-XML meta-data block describing the dataset (like 
OME-TIFF)?

To gain some experience with HDF, we'll do a 'general HDF5 reader' with 
limited functionality in the coming month.


Regarding the OME files that we export; these have following custom 
attributes in ome:Image:
    CA:CustomAttributes
          svi:RefrIndexMed
          svi:PinholeSpacing
          svi:ChannelData
                LogicalChannel
                MicroscopeSpec
                ExPhotonCnt


Best regards,

Edwin Bennink
Developer for Scientific Volume Imaging BV
www.svi.nl