[ome-users] Import plate data from the FEI MORE as screen in OMERO

[Mark Carroll (Staff)]

Dear Kai,

 > sorry to open this old discussion again, but it is only now that I
finally came around to look into it again.

I understand completely. (-: Within OME there is still so much we want
to do to improve OMERO but there are enough pieces that often we have to
put tasks aside for a while so as to make progress on others.

 > All references mentioned below are to
"testplate-splitC_noZ_noT_C5_1_C1.xml/.tif" of my new dataset

There doesn't seem to be a *.companion.ome file providing the metadata
for the multiple TIFF files. Though that's fine if you're okay to import
the different files as being many plates with one field on each.

 >> * In the XML files there are multiple channels with the same ID. Channel
 >> IDs are defined by the ome.xsd file as unique keys. (In practice, OMERO
 >> will unify identical ones on import.)
 > in the new xml files, channel IDs are now unique (line 132)

Indeed they are. (-:

 >> * The second XML file has no WellSample tags tying the field images to
 >> plate wells.
 > All xml files now have a unique WellSample tag (eg line 36)

Great. However, they don't contain an ImageRef element tying them to the
image.

 >> The provided XML files do not have a UUID,
 > I found a SA:XMLAnnotation with UUID in line 151, is that it?

I was expecting a UUID attribute on the top-level OME element. However,
that's less important if you're not using a companion file to tie all
the fields into the one plate.

 >> they do not name the image files
 > I found an entry OME:Image with UUID in line132. In this case, does
the UUID serve as the name as well? Otherwise, the filename entry is
really missing.

I'm referring to the FileName attribute that I use with the UUID inside
the TiffData element for my companion file example. However, again,
that's probably not needed if you're not using a companion file to tie
all the fields into the one plate.

 >> nor do the image files reference their XML file by filename or UUID.
 > I am not sure if Ichecked at the right place. I opened the *.tif
image with bio-formats with ome xml metadata checked and then compared
the content of the such opened xml with the xml that was saved beside
the image.

If you look at the XML in the description of my example TIFFs it's the
attributes of the BinaryOnly element I'm referring to here. In those
attributes all my TIFFs provide the name and UUID of the companion file.
Again, only needed if you're using a companion file to tie all the
images together into a plate.

(snip)
 >> * For a multi-file OME-TIFF, as in the example I provided, UUIDs and
filenames tie the XML file and the field image files together.
 >
 > I am not sure exactly how to tie these things together, and I
realised that several fields are missing in my image metadadata.

With luck, comparing with my example should get you much of the way there.

 > Do you think there is a way to make it work with my files the way
they are right now?

Depending what "it" is, all I can think of is that if you want them all
in the one plate then perhaps there is some trick where you import the
many one-field plates then write a script to use OMERO's query and
update services to relink the well samples all into the one plate and
delete the others. As even your separate channels are (I think) in
different TIFFs that's probably not for the faint-hearted though.

 > To reproduce the example that you have, I would need to edit the
metadata stored inside each .tif. Is it necessary to do that, and if yes
- how can it be done?

https://docs.openmicroscopy.org/latest/bio-formats5.9/users/comlinetools/edit.html
can help you there. You /might/ be able to get away with getting the
companion file right and being a lot more minimal about the TIFFs' XML
but I am not sure what you can do without there: my example tried to
adhere to our current suggestions for how things should be but maybe
includes more than is needed to get something working.

 > Thank you very much for your help! I apologise for the vague
questions, but I unfortunately do not really have a clear understanding
of how things are supposed to be in this case.

With luck we can get you there in the end. (-:

-- Mark

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