[ome-users] Ome-tiff and light sheet fluorescence microscopy

gay at cict.fr gay at cict.fr
Fri Jun 4 16:37:35 BST 2010

Hi lists,

-- This is posted in parallel to the ome-users an spim mailing lists --

Our team in Toulouse is developing a SPIM (Selective Plane Imaging  
Microscope). We whish to use OME TIFF format for our data, as it seems  
the more convenient.

But the OME-XML schemata lacks some tags that would be useful in Light  
Sheet Microscopy:
     - The sample can rotate around an axis, so we would need a to  
specify this angle as a SizeA attribute, as well as change a little  
the DimensionOrder spec, etc.
     - We use TWO objectives at a time, one for illumination and one  
for collection, so there should be room for this also.
Plus some other specific stuff I can't see right now.

So my questions are the following:
What's the best way to do this? Should we add the tags as we wish, and  
create our own shemata and xsd file?
Is there a way to keep our files valid ome-tiff ?
For spim users, has anyone given it a thought already?

Eventualy, how should we proceed to get those changes somehow included  
in the ome schemata?

Thank you

Guillaume Gay, Phd.

ITAV - Toulouse

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