Where is the specimen information stored?

[Anne]

Looking at the suitability of the OME Data Model: where is specimen/sample information stored in this model?

[ajpatterson]

Hello Anne,

In the OME model there is mainly information about the acquisition system used, who used it, and how. There are some values related to the sample.

Each Image has an ImagingEnvironment which can store:
- AirPressure is in millibars[mbar]
- Carbon Dioxide concentration around the sample [%]
- Humidity around the sample [%]
- The Temperature is in Celsius[C]

The Experiment structure contains storage for any Microbeam Manipulation (e.g. photobleaching of a region) that happened on the sample, including a reference to any Light Source used for this operation.

If you are using the High Content Screening(HCS) part of our model (Screen, Plate & Well) you also have the list of Reagents used in a Screen and references from each Well to the Reagent used in it. The Reagent structure in OME provides a short name and an identifier value for use with an external reagent database.

Does this store what you need?

If not, please reply back with the detail of what you would like to store. We are in the process of revising the model to expand it for new use cases and I am always happy to have more requests to add to our user stories.

Thanks,

Andrew

[wmoore]

Hi,

Just to add another approach:

There are various ways you can add sample data as "Annotations" of some type.

E.g. Use the OMERO.editor to define and add your own parameters.
Short demo movie:
http://cvs.openmicroscopy.org.uk/snapsh ... riment.mov
Older (more complete) movie here:
http://cvs.openmicroscopy.org.uk/snapsh ... -Beta4.mov

This is the approach taken by the PSLID project (Bob Murphy's Lab)
http://www.openmicroscopy.org.uk/site/c ... l.pdf/view


The ASCB image library (which uses OMERO) is an example of using custom annotations on images to store sample data. E.g. see http://cellimages.ascb.org/images/26533

[Anne]

Thanks to you both for your responses. With the annotations approach, is that only possible if OMERO is implemented? (I believe the team is looking at BioFormats, at this stage)

[wmoore]

You can add annotations into the data model outside of OMERO, using OME-XML (or OME-TIFF, which contains OME-XML in the header).

For example, this is an XML annotation on an Image (Image element is mostly not shown) taken from our SPIM examples page, used to add StagePosition info to an image.

Code: Select all

<Image>
...
    <SA:AnnotationRef ID="Annotation:ExtraStageLabel:1:0"/>
</Image>

<SA:XMLAnnotation ID="Annotation:ExtraStageLabel:1:0" Namespace="ome-xml.org:additions:post2010-06:spim:positions">
    <SA:Value>
        <OME-Extra:SpimPositions xmlns:OME-Extra="http://www.openmicroscopy.org/Schemas/Additions/2010-10">
            <StagePosition TheZ="0" TheT="0" TheC="0" Name="objective_stage" PositionX="-4.345366" PositionY="11.947302" PositionZ="11.94645"/>
            <StagePosition TheZ="0" TheT="0" TheC="1" Name="objective_stage" PositionX="-4.345366" PositionY="11.947302" PositionZ="11.94645"/>
            <StagePosition TheZ="0" TheT="0" TheC="0" Name="cylinder_stage" PositionX="23.745692"/>
            <StagePosition TheZ="0" TheT="0" TheC="1" Name="cylinder_stage" PositionX="23.745692"/>
        </OME-Extra:SpimPositions>
    </SA:Value>
</SA:XMLAnnotation>


You could use XML annotations to store your particular metadata in your own XML (using different Namespace, ID etc). If the data you want to store is much simpler, E.g. a name or value, you could use "Comment Annotation" etc.

However, I'm afraid the OMERO.editor doesn't help you with this - you would have to generate the XML yourself, and combine it with the image data, either as OME-XML or OME-TIFF.

[ajpatterson]

Hello,

At the very bottom of page:
http://www.ome-xml.org/wiki/ModelOverview/2010-04
the last diagram shows every point in the model where you can attach an annotation.

This diagram is also valid for the current 2011-06 version of the OME model.

Hope this helps,

Andrew