OMERO and OMX V4/OMX SR metadata

Dear all,

I have a question regarding OMX-generated data uploaded to OMERO. I thought all the log info from the companion file should be included in the metadata of the image files. However, I could not find the complete info for it. For instance, I cannot find the Wiener filter setup or the amplitude after reconstruction for reconstructed SI files.

Is the information is hidden somewhere? Or do we have to save the log files in other ways so that they are not lost after import in OMERO?

Thanks a lot for your help,
Alexia

@OMETeam

Hi Alexia,

Under which proprietary file format is the OMX storing data? Typically in the case of file formats like .dv, a few companion log file formats are detected and included as part of the fileset and the content of these files is parsed so that the metadata appears either in the Original Metadata tab or even in the Acquisition tab where appropriate.

Could you check whether the log files are available as part of the files associated with the image? If the log files are uploaded but the metadata is not available from the UI, it is possible that it was stored in a variant of the log format that the reader does not know how to parse. In both cases, a (public) sample fileset might be useful to help understanding the underlying problem.

Best,
Sebastien

Dear Sebastien,

Many thanks for your reply.

Yes, OMX files are .dv files, and some of the information are available in the Acquisition tab. The companion files are imported. We have been using this functionality a lot in the past, but a user pointed out that some of the information is missing (Wiener filter value and amplitude for instance). I checked in older files, and it was already the case. I also checked Insight and the webclient.

I will make a dataset available in our server and send you a link to get the data (or is there a place to do so in this forum?). I also added the original log files.
I also wanted to mention that we still use version 5.4.10.

Many thanks,
Alexia

The last file is still uploading. There should be 7 files in the end.

Best regards,
Alexia

Yes, seven files, and they all import into OMERO fine, it recognizes the associated logfiles. The missing metadata: could you provide us the expected values, e.g., pick one of the files, like 170831-InvitrogenSlide_1516_SI_01_SIR.dv, and give us a screenshot from the microscope vendor’s software, showing the correct metadata? I do find with that image I can re-download the companion logfile from OMERO and see the “-wiener 0.00500” therein.

Dear all,

So that means that the log file needs to be re-downloaded, and that “all” metadata (Wiener, amplitude) cannot be visualised directly in OMERO, do I understand properly?

Many thanks,
Alexia

Hi Alexia,

as a general rule, the Original Metadata tab in OMERO will only display what has been detected as either global or image-specific key/value pairs by the Bio-Formats reader. Unfortunately, this approach suffers from the same pitfalls as the ones discussed in OME’s position regarding file formats i.e. any original metadata stored in a breaking variant of the file format is likely to be ignored.

As the companion files are preserved during import, downloading them and parsing the reconstruction metadata is your best short-term option. In the mid-term, it might be possible to update the reader to recognize and parse this extra metadata. In the case of the DeltavisionReader, there have already been similar efforts in the past - see https://github.com/ome/bioformats/pull/2974 for an example.

As Mark mentioned above, it might be useful to have an authoritative definition of the extra key/values that should be read either using the manufacturer’s software or some other reference tool.

Best,
Sebastien

Thanks for the answer, I will forward that to the user.
Next time I go to the OMX, I will send you screenshots of the values in SoftWorx, in case that could be implemented in the future.
Best regards,
Alexia

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