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

[Jason Swedlow]

Hi All-

Thanks for the follow-up, Guneter.

On 6 Jun 2010, at 14:16, Guenter Giese wrote:

> Hi Guillaume,
> hi Jason and Andrew,
>
> this is a major issue for us too.
>
> My home-built light sheet microscope generates a lot of data, and  
> the microscope configuration as well as the imaging parameters are  
> quite complex, and changed frequently. And a proper storage and  
> retrieval of our metadata is obviously quite important.
>
> I talked about this with Jason Swedlow and Andrew Patterson at the  
> ELMI Meeting 2009 in Glasgow. They were very interested.  
> Unfortunately, we had not enough time until now to check thoroughly  
> and to decide which parameters are represented by or lacking in the  
> OME schemas. And, since the details of our metadata are not fully  
> settled yet (they may never be!), we did not ask for implementation  
> in the OME schema until now.

We're happy to do some of the hard work, if you (and Guillaume, and  
anyone else) just give us a list of what you need, and MOST  
IMPORTANTLY, example data that you have.  That will tell us alot about  
what you are recording and how you use it.
>
>
> In the meantime, we decided to export the metadata into an XML  
> logfile (trying to foresee possible future implementations in the  
> OME schemas, and actually spend a lot of time on this).

OK, great-- we would certainly be interested in driving this forward  
with your help.

>
> Currently a student is working on this (he may be back in the lab in  
> a week). He tries to work around the problem by implementing  
> "Structured Annotations". He is in contact with the OME team too.
>
> We would also like to discuss this SPIM / OME issue with any other  
> users interested.

As would we.  I expect your log file would be a great start--  
something we can see and work with.  In general, we can't add support  
for domains we don't know, but if we can get some access to domain  
expertise, and certainly, great example datasets, that is what we need  
to do real work.

Thanks for pushing this and for your help.

Cheers,

Jason


>
>
> ----- Ursprüngliche Nachricht -----
> Von: gay at cict.fr
> Datum: Freitag, 4. Juni 2010, 18:32
> Betreff: [Spim-lsfm-info] Ome-tiff and light sheet fluorescence  
> microscopy
> An: ome-users at lists.openmicroscopy.org.uk, spim-lsfm-info at lists.sourceforge.net
>
> > 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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> >
> >
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