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

[Jason Swedlow]

Hi Guillaume-

Thanks very much for this.  We'd be very interested in taking this  
forward.  We are currently working on an update to our modeling and  
specification, that will allow us to more easily support the range of  
new imaging modalities that have appeared recently.

However, we'd like to get you a solution you can use now, and a clear  
sense of an upgrade path, as we develop our tools.  We'll discuss this  
at our next meeting, on Tuesday, and get back to soon after that.

Cheers,

Jason

On 4 Jun 2010, at 16:37, gay at cict.fr wrote:

> 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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