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

[Kai Schleicher]

Hi Mark,

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

I collected a new dataset and checked it with respect to the issues you 
mentioned.

Please find it for download alongside the working example you provided 
some time ago:
https://drive.switch.ch/index.php/s/JzKkw3iiDpluvi2

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

> * 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)

> * 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)

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

> 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.

> 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.

They appear almost identical. regarding your points:
The XMLAnnotation ID seems to match, but the Image ID does not. In the 
image metadata the image ID is "Image:0" , while in the separate xml it 
is "Image:807cf434-d32f-4016-983b-1a15bbc5e486". For all subsequent 
images the OME-xml metdata read by imagej the image ID is always 
Image:0, so that could be a problem I assume...

> * 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.

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

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.

Cheers,
Kai

On 7/31/18 11:26 AM, Mark Carroll wrote:
> Dear Kai,
>
>> Both the image metadata and the xml file is supposedly compatible with
>> the ome data model, but I did not yet find a configuration in which
>> these images can be imported into OMERO as a plate/screen.
>
> My previous response demonstrated a way to have the various field TIFFs
> import together as a single plate test-plate.companion.ome. I figured I
> should also more explicitly address the files you helpfully provided.
>
> They do look like a good try at compliant OME-TIFF. I think the separate
> image files are fine standalone. The most obvious issues we see are:
>
> * 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.)
>
> * The second XML file has no WellSample tags tying the field images to
> plate wells.
>
> * 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. The
> provided XML files do not have a UUID, they do not name the image files,
> nor do the image files reference their XML file by filename or UUID.
>
> I suggest these as the first things to fix to make the plates more
> compatible with Bio-Formats. You may have already noticed these issues
> in comparing my working example with the ones from your acquisition
> system. Good luck!
>
> -- Mark
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
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