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

Melissa Linkert melissa at glencoesoftware.com
Thu Nov 15 14:38:43 GMT 2012


Hi Ian,

> So from what you are saying the software they're using to do the conversion to OME-tiff needs updating?
> If you think this would give a solution then I can get back to the lab in question  & ask them to check for updates from LaVision?

It might be nice if the software in question wrote OME-TIFFs with a more
recent schema version, but that won't solve the immediate problem of
CustomAttributes/StructuredAnnotations not being preserved.

Regards,
-Melissa

On Wed, Nov 14, 2012 at 12:14:31PM +0000, Munro, Ian wrote:
> Thanks Melissa that's really helpful.
> 
> So from what you are saying the software they're using to do the conversion to OME-tiff needs updating?
> If you think this would give a solution then I can get back to the lab in question  & ask them to check for updates from LaVision?
> 
> Regards 
> 
> ian
> 
>  
> On 13 Nov 2012, at 20:19, Melissa Linkert wrote:
> 
> > 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
> >> 
> 


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