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

[Sebastien Besson (Staff)]

On 23 Jun 2016, at 14:33, Éric Piel <piel at delmic.com<mailto:piel at delmic.com>> wrote:

Hello,

In our microscope software, we have an exporter to OME-TIFF. Following the OME schema of 2013, we save the image transformation needed of some (fluorescence) images to align them on some other (SEM) images using the Image/Transform attribute:
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2013-06/ome_xsd.html#Image_Transform

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 outdated schema documentation is entirely our mistake and we accept full responsibility for it.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.

Best regards,
Sebastien

Thanks in advance,
Éric
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[1] https://github.com/openmicroscopy/bioformats/pull/559
[2] http://trac.openmicroscopy.org/ome/ticket/3742
[3] http://www.openmicroscopy.org/site/support/bio-formats/users/comlinetools/xml-validation.html
[4] http://www.openmicroscopy.org/site/support/ome-model/developers/structured-annotations.html



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