Open Microscopy Environment

Hi

I am a beginner wrt. the OMERO system and I would like to learn from you how to store additional (unique) identifier for an image in OMERO.

Lets say that the image that I want to store in OMERO is based on an experiment with a specific compound. I want to store the identifier for the compounds that was registered in another system together with the image.

What is the best way to do that? Are tag or attachments the best way? Is it possible to store such identifier to the OME-TIFF metadata? How can I do this?

Can you help me by providing some ideas, keywords, links, etc.?

Best Reagards,
Frank

Hi Frank,

If you want to store such information either in OMERO or in the OME-TIFF, your best solution is certainly to use the Structured Annotations defined by the OME model. For what you want to achieve, either a text annotation or a numeric annotation looks like a good starting point.

Exporting an OMERO image with annotations should also embed these annotations in the OME-XML metadata block of the OME-TIFF file. Note a current limitation when importing OME-TIFF files with annotations is that new annotations will be created even if an annotation with the same name exists on the database.

Sebastien

Thank you. Your idea with the tag works. But I will also try the solution with "structured annotations".


Frank

In the screen-plate-well (SPW) model for HCS data, there's also a Reagent type. You can find out more about it on the model documentation page. It would be interesting to know how close this would get you to being able to store what you want, and what changes might be needed.

Cheers,
~Josh

Hi,

just for test reasons I want to use the command line tool "tiffcomment -set". This is my XML comment at the moment. See below.

Did I understand correctly that I can add the following in within the <Image> tag:
<AnnotationRef>
Compound1234
</AnnotationRef>

Or within the <OME> tag (plus a new name space?):
<StructuredAnnotations>
<Annotation>
Compound1234
</Annotation>
</StructuredAnnotations>

Greetings, Frank


<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!-- Warning: this comment is an OME-XML metadata block, which contains crucial dimensional parameters and other important metadata. Please edit cautiously (if at all), and back up the original data before doing so. For more information, see the OME-TIFF web site: http://ome-xml.org/wiki/OmeTiff. -->
<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2013-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" UUID="urn:uuid:ce84aab7-bbf8-402c-b2a4-9d26ae0fe910" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2013-06 http://www.openmicroscopy.org/Schemas/O ... 06/ome.xsd">
<Image ID="Image:0" Name="single-channel">
<AcquisitionDate>
2013-06-19T13:02:10
</AcquisitionDate>
<Pixels DimensionOrder="XYZCT" ID="Pixels:0" SizeC="1" SizeT="1" SizeX="439" SizeY="167" SizeZ="1" Type="int8">
<Channel ID="Channel:0:0" SamplesPerPixel="1">
<LightPath/>
</Channel>
<TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1">
<UUID FileName="single-channel.ome.tif">
urn:uuid:ce84aab7-bbf8-402c-b2a4-9d26ae0fe910
</UUID>
</TiffData>
</Pixels>
</Image>
</OME>

Hi,

I just pasted a large OME.xml file here https://gist.github.com/will-moore/9507510
This has a load of Structured Annotations (XML annotations) which I hope will provide a good example of how these work.

Hope that helps,

Will.