XML annotations - visualizing & search

[sbesson]

Hi Yuriy,

The issue should be resolved the same way as the one described in
viewtopic.php?f=13&t=7661.

Regarding the annotationRefIndex argument, you can view it as a counter of all the annotation references within a given Image block. See https://github.com/openmicroscopy/biofo ... .java#L650 for an example of code which is creating multiple annotations of multiple types and linking them to an image where annotationRefIndex gets incremented every time.

Best,
Sebastien

[yuriy_alexandrov]

Thanks Sebastien,

Unfortunately the link ( viewtopic.php?f=13&t=7661. ) doesn't work.

I'll try to understand the example You provided, - it looks quite mm.. involved .

Best regards,
Y.

[yuriy_alexandrov]

Good news - adding the last line here makes XMLAnnotations visible as "others".

Code: Select all

          metadata.setXMLAnnotationID(['Annotation:' num2str(index)],index);
          metadata.setXMLAnnotationValue(description,index);
          metadata.setImageAnnotationRef(['Annotation:' num2str(index)],0,index);

small step for a man!!

So, one can discard duplicated Description visualization.. maybe.
However, - these annotations still look like not searchable.
We definitely need something searchable, and tags as well.

Another strange thing - instead of single ModuloalongZ annotation now 2 are displayed (copies - only 1 was specified).

Best regards,
Y.

[yuriy_alexandrov]

...
More good news - the same method worked for fixing tags

Code: Select all

for k=1:numel(tags)
  metadata.setTagAnnotationID(['Annotation:' num2str(n_anno+k)],k-1);
  metadata.setTagAnnotationValue(tags{k},k-1);
  metadata.setImageAnnotationRef(['Annotation:' num2str(n_anno+k)], 0, n_anno+k);
end       


The list of tags was updated for Omero-imported image, which is very encouraging.
It looks like, the only problem remained is searchability for custom XML.

Best,
Y.

[sbesson]

Hi Yuriy,

as per FullTextBridge, the value of all text annotations, including XML annotations, should be indexed. Note however this indexation is not in a structured form like tag annotations or file annotations.

Best,
Sebastien

[yuriy_alexandrov]

Thanks,

As I can see now - XMLAnnotations that I add, aren't included into Omero.Insight/Webclient search scope.
But not sure if that is standard behavior, or it is because I forgot something else.

Another thing - the image description added with the help of

Code: Select all

metadata.setImageDescription(sprintf('first line\nsecondline'), 0);
metadata.setImageDescription(sprintf(description),0);

also looks not searchable.

Unfortunately I have no access to Omero at the moment so I can check tomorrow if any suggestion arises.
Please let me know if sending generated file might help.

Best,
Y.

[sbesson]

Hi Yuriy,

if the image cannot be searched by description then an issue likely lies with at your server level not at the image writing level. Did you check and optionally fix the search indexer after upgrading to 5.0.x? Did you check that images are searchable either by name of descriptions? See https://www.openmicroscopy.org/site/sup ... earch.html for more information.

Sebastien

[yuriy_alexandrov]

Very good, many thanks - will investigate the issue, maybe get some help from server admin.
Will be back when something new appears.

Best,
Y.

PS
I remember importing this generated OME.tiff into Octopus, and it wasn't searchable there as well.
Will re-check tomorrow.