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Generating an xml metadata screen file

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Generating an xml metadata screen file

Postby etienne.dumoulin » Mon Feb 11, 2019 5:24 pm

Hi everyone,

We have a plate from which the metadata file has been removed, so we only have a bunch of tiff files. In this case, a file per channel with no z-stacks.
Do you know of a tool to generate the simplest xml metadata file, so I can load the plate into omero?

Thanks for your time.

Regards,

Etienne
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Re: Generating an xml metadata screen file

Postby sbesson » Tue Feb 12, 2019 8:20 pm

Hi Etienne,

First of all, I assume there is no way to recover this metadata file from an existing backup. The expectation is that the naming/organization of the files is consistent and self-descriptive in order to be able to recreate the SPW layout.

For an OMERO workflow , there are really two classes of solutions: 1- post-import i.e. importing the images as they are into the system and add the SPW layout using the API e.g. via an OMERO.script 2- pre-import as you suggest, i.e. recreating a metadata file such that the fileset is detected as HCS by Bio-Formats.

For the second option, what kind of file format was the file originally stored under? I assume there is no available tool from the manufacturer to recreate this structure.

In a recent ome-users thread discussing a similar problem, we suggest companion OME-XML files could be a viable option to describe datasets composed of multiple TIFF files with rich metadata such as a Screen/Plate/Well layout.
There is currently no official example but the thread contains some prototype of how this fileset could look like.

If Python is an option, we started prototyping a simple experimental library for generating this type of metadata files. So far this has been applied in production for non-HCS datasets in the context of IDR but some code exists to handle SPW datasets (see e.g this snippet).

Best,
Sebastien
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Re: Generating an xml metadata screen file

Postby etienne.dumoulin » Wed Feb 13, 2019 8:55 pm

Hi Sebastien,

Thanks for the reply.

I have no idea what the original metadata format would look like. I have a folder with a flex file per channel.

I think OMERO.script is the best option for us.

Regards,

Etienne
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Re: Generating an xml metadata screen file

Postby wmoore » Thu Feb 14, 2019 6:54 am

Hi, In case you have multiple fields per well, you might want to read how to handle that at viewtopic.php?f=6&t=8150&p=17593

If you want to assemble several TIFFs into a multi-channel image, you'll need to do something similar to the Combine_Images script or you could even create the multi-channel images directly in OMERO via the API, reading the TIFFs with Pillow instead of importing.
See an example at: https://gist.github.com/will-moore/cea1 ... efc649a25b

Regards,

Will.
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