[ome-devel] OME-tif & original_metadata.xml Now you see it...

[Melissa Linkert]

Hi Ian,

Just taking this discussion back to the list now that I have one of the files.

The issue is that all of the useful metadata in these files is stored as
CustomAttributes (now called StructuredAnnotations, but these files
still use the 2008-02 schema).  CustomAttributes aren't reliably parsed
out as "original metadata", which is why you don't see the
original_metadata.txt annotation.  I have filed a ticket for this here:

http://trac.openmicroscopy.org.uk/ome/ticket/9905

Once that ticket is resolved, you would be able to check for the
"ImspectorVersion" tag in original_metadata.txt, as mentioned in a
private email.

Regards,
-Melissa

On Tue, Nov 06, 2012 at 05:46:56PM +0000, Munro, Ian wrote:
> Thanks Melissa. 
> 
> I'm happy to send the files as you suggest.
> Should they go to you & if so what's your preferred method?
> 
> Ian
> 
> 
> 
> 
> On 6 Nov 2012, at 17:23, Melissa Linkert wrote:
> 
> > Hi Ian,
> > 
> >> I''ve been sent a batch of OME-tif files from another group.
> >> These have been generated using an instrument manufacturers own software.
> >> 
> >> I have imported the files into OMERO via the insight client & am now trying to work with them from there.
> >> 
> >> Some of the imported images have an annotation called original metdadata.txt which contains a very minimal amount of information.
> >> 
> >> Others don't seem to have any annotation at all.!
> >> 
> >> Frustratingly,when I open the original OME-tifs, using a text-editor, the ones that import with no annotation seem to have a readable xml looking  header.
> >> The ones that import with an annotation aren't readable in a text editor.
> > 
> > That sounds very much like you have a set of OME-TIFFs (XML header, no
> > "original metadata.txt") and a set of some other sort of TIFFs from the
> > same software (no XML header, with "original metadata.txt").
> > 
> >> I ned some way of determining whether a given image comes from this particular instrument.
> >> For those images  with original_metadata.txr annotation I can look in there.
> > 
> > If the XML in the OME-TIFFs is fully and properly populated, then I would expect
> > that you could find what you need in the 'Model' and 'Manufacturer'
> > attributes of 'Microscope'.  Probably the best thing to do though would
> > be to send an example from each of the two sets, and we can investigate
> > from there.
> > 
> > Regards,
> > -Melissa
> > 
> > On Tue, Nov 06, 2012 at 02:37:54PM +0000, Munro, Ian wrote:
> >> Hi All 
> >> 
> >> I''ve been sent a batch of OME-tif files from another group.
> >> These have been generated using an instrument manufacturers own software.
> >> 
> >> I have imported the files into OMERO via the insight client & am now trying to work with them from there.
> >> 
> >> Some of the imported images have an annotation called original metdadata.txt which contains a very minimal amount of information.
> >> 
> >> Others don't seem to have any annotation at all.!
> >> 
> >> Frustratingly,when I open the original OME-tifs, using a text-editor, the ones that import with no annotation seem to have a readable xml looking  header.
> >> The ones that import with an annotation aren't readable in a text editor.
> >> 
> >> I ned some way of determining whether a given image comes from this particular instrument.
> >> For those images  with original_metadata.txr annotation I can look in there.
> >> 
> >> For the other files, however, I'm baffled.  Any suggestions welcome.
> >> 
> >> 
> >> Thanks
> >> 
> >> ian
> >> _______________________________________________
> >> ome-devel mailing list
> >> ome-devel at lists.openmicroscopy.org.uk
> >> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>