[ome-users] Append "original metadata" to already imported images

[Sebastien Besson (Staff)]

For reference (and to minimize the number of concurrent threads),

part of this discussion might be covered in the ongoing Bio-Formats
issues:

https://github.com/openmicroscopy/bioformats/issues/2308
https://github.com/openmicroscopy/bioformats/issues/2309

Best,
Sebastien

On 1 Apr 2016, at 16:54, Thomas Julou <thomas.julou at unibas.ch<mailto:thomas.julou at unibas.ch>> wrote:

Hi Josh,

Sorry, I overlooked your answer in the digest… Luckily Seb Besson drew my attention on it recently in a github thread!

Because I?m not familiar with omero scripts, I would like to know first
whether appending ?original metadata? to an already imported image is doable
through the script API.

The original metadata section is parsed on the fly from the fileset by
Bio-Formats. So, it might be doable, but tricky, since it will
potentially require adding to and re-ordering the fileset. And due to
the various issues discussed recently, I'm not completely sure that it
will do what you need. If it *would* work, then I would also thinking
upgrading to a later version of Bio-Formats (on the server-side) would
show you the results anyway.

Other options I can think of:

* re-import the files (never a great thing to suggest, I know, but
often the most practical)
* store the parsed json data in an annotation (which also appears in
the right hand panel) rather than trying to get it into the original
metadata. The primary downside of this is that for newer imported
files the metadata you're looking for (I think!) will be in original
metadata, while in older filesets, it will be in an annotation.

As I understand, what I aimed at is too complicated to be worth doing (because, as their name suggests, it’s not easy to append original metadata). I’ll keep hassling the bio-formats people until the MM reader does what it should and reimport important datasets by then.

Best,
Thomas

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