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OME-XML files

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OME-XML files

Postby brandon.scott » Mon Oct 25, 2010 9:22 pm

I was wondering if I have to manually update the ome schema, and if so how does one go about doing this. Thanks for any feedback because i am unable to use omero as i cannot upload any ome.tif files via importer.

Thanks
-Brandon
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Re: OME-XML files

Postby ajpatterson » Thu Oct 28, 2010 12:57 pm

Hello Brandon,

Importing of all the ome-xml and ome.tiff files is handled by the version of Bio-Formats build into the importer.

Can you let me have some versions:

The version of OMERO.server
The version of OMERO.importer
And the version of the ome.tiff file - you can find this using the online validator:
http://validator.openmicroscopy.org.uk/

Thanks,

Andrew
--
Andrew Patterson
Software Developer, Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression
University of Dundee
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Re: OME-XML files

Postby brandon.scott » Thu Oct 28, 2010 2:01 pm

Andrew,

The version of OMERO.server and OMERO.importer is Beta-4.2.0

Here is the validation results for my image.

Summary
Validated file: 2010-10-28-13-57-13_SerumAdded_Marker_1__1.ome.tif
File schema: http://www.openmicroscopy.org/Schemas/OME/2008-02 (Standard V2)
The file is valid.
The file is an OME-TIFF.
The file's xml could be parsed.
The file was not checked for internal consistency.
The OME-TIFF data appears consistent with the OME-TIFF metadata.
The file has custom attributes.
Error list
None

Warning list
Line Column Type Message
Info
File also valid under schema: February 2008 V1

Unresolved list
None

Thanks for the feedback.

I have also submitted the error via importer, and here is the link for my ticket if it will add anymore insight.
http://qa.openmicroscopy.org.uk/qa/feedback/2973/?token=73e314ec364a44b5edce58b8b1b3fff1

-Brandon
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Re: OME-XML files

Postby bwzloranger » Thu Nov 04, 2010 12:35 pm

Hi Brandon,

I've replied to your QA message as well, but basically this issue is resolved in the latest 4.2.1 release (due out soon!). Thanks again for your error report!

Cheers,

Brian Loranger, Programmer
OMERO Team
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Re: OME-XML files

Postby brandon.scott » Fri Nov 12, 2010 9:13 pm

Just wanted to thank everyone for the help, and the new update. I'm so excited that we are finally through the deployment stage and onto the usage portion.

-Brandon
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