Open Microscopy Environment

Hi Team,

I am using Matlab to call java obj/functions to add MapAnnotation into ometiff file. But in the result ometiff xml, AnnotationRef is not in the Image tag but instead in StructuredAnnotations tag:

Code: Select all

  <StructuredAnnotations>
      <MapAnnotation Annotator="test_Annotator" ID="Annotation:1" Namespace="test_Namespace">
         <Description>
            test_Description
         </Description>
         <AnnotationRef ID="Annotation:1"/>
         <Value>
            <M K="test1">
               value1
            </M>
            <M K="test2">
               value2
            </M>
         </Value>
      </MapAnnotation>
   </StructuredAnnotations>

This is part of the code I am using to add the MapAnnotation:

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OMEXMLService = javaObject('loci.formats.services.OMEXMLServiceImpl');
metadata = OMEXMLService.createOMEXMLMetadata();
...
pairList=java.util.ArrayList;
pairList.add(ome.xml.model.MapPair('test1','value1'));
pairList.add(ome.xml.model.MapPair('test2','value2));
metadata.setMapAnnotationID('Annotation:1',0);
metadata.setMapAnnotationDescription('test_Description',0);
metadata.setMapAnnotationNamespace('test_Namespace',0)
metadata.setMapAnnotationValue(pairList,0);
metadata.setMapAnnotationAnnotator('test_Annotator',0)
metadata.setMapAnnotationAnnotationRef('Annotation:1',0,0);
...
bfsave( omeimg, test.ome.tif, 'metadata', metadata, 'Compression', 'LZW' );


Could anyone give me a solution to place AnnotationRef into Image tag but not in StructuredAnnotations tag using matlab calling java way ?

Hi,

Looking at your code

Code: Select all

metadata.setMapAnnotationAnnotationRef('Annotation:1',0,0);
...


is probably the source of the issue. With this call, you are annotating a map annotation with another annotation.
To annotate the image instead, could you update this line to use setImageAnnotationRef instead and see if this generates the expected OME metadata?

Best,
Sebastien

sbesson wrote:Hi,

Looking at your code

Code: Select all

metadata.setMapAnnotationAnnotationRef('Annotation:1',0,0);
...


is probably the source of the issue. With this cal, you are annotating a map annotation with another annotation.
To annotate the image instead, could you update this line to use setImageAnnotationRef instead and see if this generates the expected OME metadata?

Best,
Sebastien

That works thank you so much !