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

[Roger Leigh]

On 25/09/15 15:06, Grabmayr, Heinrich wrote:
> 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.

OK, that all makes sense.  We already have support for binning in the
model, though it's currently an enumeration rather than allowing
arbitrary values.  The only minor detail I can see is whether the region
is using the real pixels or binned pixels when describing the size and
position.  What does your CCD do here?

>> 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?

No, this is completely arbitrary, it just needs to be unique for your
purposes; we typically use a java-style namespace to make it unique for
the person or organisation, but it's entirely up to you!


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