[ome-users] MetaMorph nd file metadata

[Melissa Linkert]

Hi Ben,

> I cannot locate detector gain in any of the OME metadata imported from my MetaMorph "MultiDimensional Acquisition" experiment .nd files. None of the various "gain" attributes seem to have any value. In fact, I can get exposure time for each plane and the "channelName" for each channel, very little else. dumpXML seems to show that very few values mapped into the OME metadata. Checking in Metamorph, I can locate the appropriate metadata in "Image Info>Annotations".
> 
> Problem is the same if I open the underlying .stk files individually, instead of the .nd file.

Thank you for reporting this, and for providing an example dataset.
Your absolutely right that the gain value isn't being mapped into OME
metadata, and it looks like a few other things aren't being mapped as
well (e.g. stage position).

I have filed a ticket on our issue tracking system to improve the
metadata mappings for Metamorph datasets:

http://trac.openmicroscopy.org.uk/ome/ticket/9679

You have been CC'd on the ticket, and so will receive an automated email
each time we update the status of the ticket.  If you prefer not to
receive these emails, just let me know.

Regards,
-Melissa

On Wed, Sep 26, 2012 at 12:47:59PM -0400, Ben Timney wrote:
> Hi, 
> 
> I cannot locate detector gain in any of the OME metadata imported from my MetaMorph "MultiDimensional Acquisition" experiment .nd files. None of the various "gain" attributes seem to have any value. In fact, I can get exposure time for each plane and the "channelName" for each channel, very little else. dumpXML seems to show that very few values mapped into the OME metadata. Checking in Metamorph, I can locate the appropriate metadata in "Image Info>Annotations".
> 
> Problem is the same if I open the underlying .stk files individually, instead of the .nd file.
> 
> The problem was observed using bfopen in MatLab using the latest 4.4.4 BioFormats library. Shame, because I see the latest update addressed some .nd file functionality.
> 
> Not sure if this is a general issue with mapping MetaMorph multi-dimensional acquisition data into the OME metadata scheme. Could also be a problem of the replace-user-and-press-any-key variety, since I am newish at trying to peruse the OME metadata structure.
> 
> DropBox link to zipped example data
> 
> Ben Timney
> 
> ________________
> Ben Timney, PhD
> Research Associate
> Rout Laboratory,
> 1230 York Ave, #213
> New York, NY 10065
> 

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