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

[Damir Sudar]

Hi Eric and Sebastien,

Thanks Eric for bringing this topic up. I believe it is quite an 
important concept and with good use cases and discussion, maybe it could 
again be a candidate for a future version of the model. I had a posted 
on the forum over a year ago mentioning how such functionality would 
help EM/LM correlative microscopy (see: 
https://www.openmicroscopy.org/community/viewtopic.php?f=15&t=7756) and 
I was happy to see how the OME team is already implementing this concept 
for ROIs in 5.3 (see: 
http://blog.openmicroscopy.org/data-model/future-plans/2016/06/20/shape-transforms/).

So how about expanding on the ROI Shape.Transform concept with an 
Image/Transform attribute in the form of an 4x4 AffineTransform to 
encode transformations in XYZ? This could indeed be encoded in a 
MapAnnotation but it would then be good if that were codified to avoid 
multiple different implementations.

Cheers,
- Damir

On 6/28/2016 5:40 AM, Éric Piel wrote:
> 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   outdated schema documentation is entirely our mistake and we accept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
>
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-- 
Damir Sudar - Affiliate Scientist
Lawrence Berkeley Natl Laboratory / MBIB
One Cyclotron Road, MS 977, Berkeley, CA 94720, USA
T: 510/486-5346 - F: 510/486-5586 - E: DSudar at lbl.gov
http://biosciences.lbl.gov/profiles/damir-sudar-2/

Visiting Scientist, Oregon Health & Science University