[ome-users] OMERO Image archival (Leica)

Woodbridge, Mark R m.woodbridge at imperial.ac.uk
Thu Jan 14 10:50:39 GMT 2010

Hello Josh,

Thanks for your quick reply.

> There's currently no collapsing/merging of original files into a
> single container (like a .tar or .zip). We've discussed various ways
> of doing this (do it on import so there's only one attachment, etc.)

A zip file would be best. I guess this could be generated when requested, or saved on upload. The latter would be safest. This issue has arisen because users assume that if archival is enabled then they can throw away data once uploaded, but that is obviously dangerous if they can't get back exactly what they uploaded. This is complicated by the fact there is a file in the raw dataset (a .txt file corresponding to the .lei file) which I don't think is imported by OMERO but which might be expected by the Leica software, so this would need to be present in the zip file even if the Importer doesn't read it (and it's not explicitly referenced by the .lei).

I think it would make most sense to attach the zip to the OMERO dataset but there are issues with this - we previously discussed the fact that there isn't a direct correspondence between the Leica dataset and the OMERO dataset (e.g. you can subsequently add images to the OMERO dataset that weren't part of the original .lei file). For that reason it might be better to have one copy of the zip but link it to each image in the dataset.

>  > On a related issue, when I actually click the download arrow for an
>  > individual image Insight crashes with the attached stacktrace -
>  > does this happen for anyone else? Everything else seems to be
>  > working fine...
> This is a known server-side problem:
>   https://trac.openmicroscopy.org.uk/omero/ticket/1614
> which we thought we had worked around in the client. What version are
> you using?

4.1.1 for both server and client. (though the image was probably uploaded using 4.1.0).


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