[ome-users] Bug report for version 2012-06 OME-XML in Fiji, seen in grid/collection stitching

[Roger Leigh]

On 08/11/16 19:50, Michael Pinkert wrote:
> Hi Mark,
>
> I just uploaded 9 files, from a much smaller sample image set.  I tried using the ImageJ/Fiji stitching algorithm again with this smaller sample size and it ran into the same problem, with the same warning.  It seems not to be reading the metadata correctly, because it was interpreting different Z-slices as different T-time points.
>
> This problem occurred after a recent Fiji/ImageJ update and applies to older sets of images that I've already stitched; I don't think there's anything wrong with the formatting of the images.

Dear Michael,

I've taken a look at your files, and the problem is that the XML schema
is invalid.  Using bftools' xmlvalid program:

% ./tools/xmlvalid ~/images/17416/FijiTester.ome.xml
Parsing schema path
https://raw.github.com/openmicroscopy/openmicroscopy/schema-2012-06/components/specification/InProgress/ome.xsd
Validating /home/rleigh/images/17416/FijiTester.ome.xml
Error parsing schema at
https://raw.github.com/openmicroscopy/openmicroscopy/schema-2012-06/components/specification/InProgress/ome.xsd
org.xml.sax.SAXParseException: schema_reference.4: Failed to read schema
document
'https://raw.github.com/openmicroscopy/openmicroscopy/schema-2012-06/components/specification/InProgress/ome.xsd',
because 1) could not find the document; 2) the document could not be
read; 3) the root element of the document is not <xsd:schema>.

% ./tools/xmlvalid ~/images/17416/FijiTester_C0_TP0_SP0_FW0.ome.tiff
Parsing schema path
https://raw.github.com/openmicroscopy/openmicroscopy/schema-2012-06/components/specification/InProgress/ome.xsd
Validating /home/rleigh/images/17416/FijiTester_C0_TP0_SP0_FW0.ome.tiff
Error parsing schema at
https://raw.github.com/openmicroscopy/openmicroscopy/schema-2012-06/components/specification/InProgress/ome.xsd
org.xml.sax.SAXParseException: schema_reference.4: Failed to read schema
document
'https://raw.github.com/openmicroscopy/openmicroscopy/schema-2012-06/components/specification/InProgress/ome.xsd',
because 1) could not find the document; 2) the document could not be
read; 3) the root element of the document is not <xsd:schema>.


The schema which is being used here is an invalid URL, and was never a
released schema.  I'm not sure why any software would be using that.

You can find sample files using the old 2012-06 schema here:
http://downloads.openmicroscopy.org/images/OME-TIFF/2012-06/
They are using a root element like this:

<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2012-06"
      xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
      xmlns:ROI="http://www.openmicroscopy.org/Schemas/ROI/2012-06"
      xmlns:SA="http://www.openmicroscopy.org/Schemas/SA/2012-06"
      xmlns:SPW="http://www.openmicroscopy.org/Schemas/SPW/2012-06"
      xmlns:Bin="http://www.openmicroscopy.org/Schemas/BinaryFile/2012-06"

xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2012-06
  http://www.openmicroscopy.org/Schemas/OME/2012-06/ome.xsd">

while your samples do this:

<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2012-06"
      xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"

xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2012-06
https://raw.github.com/openmicroscopy/openmicroscopy/schema-2012-06/components/specification/InProgress/ome.xsd">

It's the schemaLocation which is wrong, making the file invalid.  If you
fix that up, and the rest of the file is valid for the 2012-06 schema,
it should then work correctly.


Kind regards,
Roger

--
Dr Roger Leigh -- Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364

The University of Dundee is a registered Scottish Charity, No: SC015096