[ome-users] Exporting OME/XML data

[Ilya Goldberg]

On Aug 4, 2005, at 6:52 AM, Graham Klyne wrote:

> I've been playing with the OME/XML export feature.
>
> So far, I've been able to export a combination of metadata and pixel
> data in a single large file.  What I'd really like to be able to do is
> export the metadata without the pixel data, but instead with a 
> reference
> URI that can be used subsequently to retrieve the pixel data from 
> OMEIS.
> E.g. replacing the <BinData> elements in the current OME/XML file 
> format.
>
> Is something like this feature present?

Not exactly, but its possible.
What happens during export is this:
1.  Collect list of OME objects
2.  Convert them to XML using the CA.xsd schema (only Project, Dataset, 
Image, Feature and CustomAttributes elements).
	In this schema, <Pixels> uses a reference to an OMEIS Repository - 
they are not encoded in XML.
	The Pixels element/ST has an ImageServerID attribute/field which is 
used in combination with the Repository reference to resolve the pixels 
remotely.
	A Repository element/ST has a URL for an OMEIS server
3.  Apply a style sheet (OME-CA2OME.xslt) to the XML, converting the 
CA.xsd document to an ome.xsd document.
	At this point you have basically what you want.  The Pixels are still 
using a reference
4.  Call the ExportOMEfile method on OMEIS, sending it the XML document 
we have so far:
	http://www.openmicroscopy.org/api/omeis/files.html#ExportOMEfile
5.  The result of the ExportOMEfile is the final OME-XML document with 
the encoded pixels.

There are some attractive features to this type of variant, though it 
would require specification how exactly the pixels would be resolved 
from this Repository reference.  If you use OMEIS, it should "just 
work" (possibly with some massaging).  What if you don't though?
There are libraries to access OMEIS from C and Java (even MATLAB), and 
its always possible to degrade down to plain old HTTP.
Also, this would require changes to the ome.xsd schema to allow for 
this type of Pixels.

-Ilya


>
> #g
>
> -- 
> Graham Klyne
> Image Bioinformatics Research Group (http://www.bioimage.org/)
> Department of Zoology, University of Oxford
> South Parks Road, Oxford OX1 3PS, UK
> E-mail: <Graham.Klyne at zoo.ox.ac.uk>
> Direct phone: +44-(0)1865-281991
> Departmental fax: +44-(0)1865-310447
>
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