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

[Andrew Patterson]

Hello Guillaume and Guenter,

We had a talk about placing you data into OME-TIFF today and of course have more questions!

You asked two main questions:

== How to store the 2nd objective used for illumination.

This should be simple to do. Within instrument you can already store multiple Objectives. We suggest as a first step you store both Objectives into Instrument but only link the Objective that was used to capture the Image using the ObjectiveSettings element. This would allow you to store most of the values for the second Objective. Of course you just need to know why the second objective is listed to fully understand what it means.

== How to store the SizeA on the Pixels.

This would fall into the work we are doing on N-dimensional data. We have a draft proposal for this here:

http://www.ome-xml.org/ticket/112

You might like to review this proposal to see if it would allow you to store your data in a suitable way. This is obviously a longer term solution as it would only be built into a future release (towards the end of this year). Any comments on this would be most welcome.

In the short term the way to insert the data depends on a few of questions:
Do you use Z? (Z-stacks)
Do you use T? (Time Series)
Do you use C? (Channels)
If the answer to any of these is No then you can use the same type of hack we currently use internally for FLIM data. This involves misusing one of the other dimensions to store your extra one. e.g. putting your SizeA value into the SizeT if you do not use multiple timepoints. This will allow the file to be processed as a standard OME-TIFF but requires a bit of special casing when the image is displayed.

Does this sound workable to you?

If you could outline what is missing then I can look at what might be easy to insert into the schema for the release later this month. I will look at adding SPIM to the list of Experiment Types.

Thanks,

Andrew

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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