[ome-devel] Image/Transform on the OME schema

[Éric Piel]

On 24/06/16 18:20, Sebastien Besson (Staff) wrote:
>
:
> Hi Éric,
>
> Adding a Transform attribute to the Image had been considered for
> inclusion in the 2013-06
> schema but this addition has been reverted late in the development
> process - see [1] [2].
>
> As you rightfully reported, the live oXygen documentation had not been
> updated from a
> development version of this schema and was erroneous documenting this
> element. We have
> now regenerated our set of schema documentations to prevent confusion.
>
>> While trying to update our code to use the newer schema, I've realised
>> that this attribute is gone in 2015-01 (and 2016-06). There is no
>> mention of this in the changelog, nor in the XSLT transformations.
>
> The Image.Transform attribute was not included as part of the 2013-06
> Data Model which is
> why neither the Model documentation nor the Transforms mention it.
> Having published a
>   outdated schema documentation is entirely our mistake and we accept
> full responsibility for it.
> As a consequence the OME-TIFF files generated by your software using
> this attribute might
> be invalid as you can verify using the xmlvalid tool [3].
>
>> There is still 'Shape/Transform', but it's not clear to me how it can
>> be used as replacement.
>
> At the moment, Transforms are only used in the context of Regions of
> Interest although we have
> certainly heard interest in modelling it for images as well.
>
>> Could anyone confirm this attribute was intentionally removed? Is
>> there a suggested way to convey the same information with newer OME
>> schema versions?
>>
> Our best recommendation would be to annotate the Image with a
> MapAnnotation using a custom
> namespace and store the Transform elements as key/value pairs - see [4]
> for an example. These
> annotations are completely supported across our software stack and will
> be maintained over model
> upgrades.
>
> We sincerely apologize for this serious documentation issue. Thanks for
> raising it and please let us
> know if we can assist further in the upgrade of your exporter functionality.
>
Thanks Sebastien for this very precise, documented and helpful answer!

I hadn't realised the XSD files where also on the git repository, that's 
quite handy to follow the history :-)

As the alignment feature of our microscope is pretty unusual, I wasn't 
surprised that generic OME-TIFF viewers weren't using the "Transform" 
attribute... now that explains why it was really unlikely ;-)

We'll see to switch to using the MapAnnotation in the coming future.

Thanks again,
Éric