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

[Grabmayr, Heinrich]

Dear Roger,
> 
> 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.

I am using a PCO.edge 4.2 sCMOS camera, but cropping and binning is common for most CCD, EMCCD, and (s)CMOS cameras. Probably, people don't often need to store this information because the excitation intensity distribution doesn't remain constant from session to session, or they don't care as much about comparing positions with respect to the excitation intensity. So it would be interesting to see whether adding this would be of interest to the larger community.
In general, these are rectangular shapes with edges parallel to the chip, and you are right, it simply specifies which pixels are read out and transmitted to the computer. Another related feature that I don't use but that can be done with most cameras as well, is binning, which means that the camera treats every n pixels as one and adds their charges together. This can have different n for the two detector dimensions and results in an image with pixel size W/nx times H/ny.

> 
> 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.

Great, thanks! I'll try to implement that. As for the namespace, it doesn't have to point to any real server location, right?

> 
> 
> 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
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