Open Microscopy Environment

Hi -
I have successfully exported our data to OME-TIFF and imported it into OMERO, and now am learning how the MATLAB OMERO client retrieves the data.

Is there a way that I can retrieve the full XML metadata (as DOM/DocumentImpl or as String) for a fileset? I have already written code to convert the OME XML metadata to a MATLAB structure, and I would prefer to reuse this code rather than to retrieve all of the individual annotations and metadata values using the client calls.

Thanks - gary

Hi Gary,

retrieving the full OME-XML Metadata from an Image is not something that is achievable via the OMERO API at the moment. In order to do so, you will need to have access to the original files and then use Bio-Formats to retrieve the OME-XML metadata from it. This implies:
- either downloading the image from OMERO into a local client,
- or, if possible, setting up an in-place import strategy for your OME-TIFF files so that you can access the raw data for images imported into OMERO via the filesystem. This option will require coordination with the administrator of your OMERO system but may scale better depending on how many times you will need to access this metadata.

Best,
Sebastien

Hi Sebastien,
I don't think the import in place is an option (if I understand it correctly), as the local files are not present on the server machine outside of OMERO.

So for now, I would like to ask:
1) How can I programmatically (in MATLAB) retrieve the original file for a given image/fileset from the OMERO server?

2) Could you please add a feature request for the ability to retrieve the DOM of the whole metadata via the OMERO.api?

Thanks! - gary

Hi Gary,

regarding your second point, the ability to retrieve the OME-XML via the API is already listed in our feature request. Hopefully this feature will be implemented as part of 5.1.0.

We are working and testing a small script showing how to download an original file of an image/dataset and will keep you posted on this front as soon as possible.

Best,
Sebastien

Hi Gary,

sorry, but in discussing with Sebastien there was some confusion. The OME-XML Download idea is certainly on the list of things we'd like to work into the download/export API, but it is highly unlikely that that it will make it into 5.1.0. In the meantime, the best server-side workaround I can propose is to use a script which parses out the XML without the need to download the files.

Cheers,
~Josh