[ome-devel] camera crop region into ome-xml

[Roger Leigh]

On 24/09/15 20:23, Grabmayr, Heinrich wrote:
> I would like to write the ROI I read out from the camera into the metadata. I had thought there might be an attribute for that in OME\Instrument\Detector, but I didn't find anything of the sort there in the 2015-01 schema. Does anyone save their ROI in the metadata? What is the best way? Should I add a Structured Annotation for it?

Dear Heinrich,

We don't currently have any formal attribute for this in the data model,
however we can consider adding such an attribute if there will be
general need for such a feature.

For modelling purposes, it would be useful to know some more details
about how this works and what it's used for.  What is the make and model
of the CCD?  Are the regions rectangular or can they be other shapes, or
are there restrictions on sizes and placement?  Is this simply limiting
the CCD readout to the specified region?  Is this feature common to
other models of CCD; for the model we need to be able to generalise this
to support other types.

You certainly can use a Structured Annotation to attach the metadata to
the Detector object.  You can use any annotation type you see fit here.
  One possibility would be to use the MapAnnotation to store the region
data.  An example:

        <SA:MapAnnotation ID="Annotation:1"
Namespace="uk.ac.dundee.lifesci:ccd-roi">
                <SA:Description>CCD Region</SA:Description>
                <SA:Value>
                        <M K="X">64</M>
                        <M K="Y">64</M>
                        <M K="W">256</M>
                        <M K="H">256</M>
                </SA:Value>
        </SA:MapAnnotation>

You can then reference this in the Detector:

        <Detector Gain="nn" Voltage="mm" Offset="oo" Zoom="0"
AmplificationGain="0" ID="Detector:1" Type="CCD">
                <SA:AnnotationRef ID="Annotation:1"/>
        </Detector>

This currently needs setting directly on the Detector element; it's not
possible to annotate DetectorSettings--this is something which we can
review for the next model revision.


Kind regards,
Roger

--
Dr Roger Leigh -- Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364

The University of Dundee is a registered Scottish Charity, No: SC015096