[ome-users] OME TIFF from Andor Fusion software produces errors

[Roger Leigh]

On 13/03/18 16:03, James Wainwright wrote:
> Hi Bio-formats team!
>
> I'm pretty sure that I was previously able to open OME TIFFs that our
> latest microscopy software, Fusion, generates.
>
> I just tried opening both a recent (today in the latest version of
> Fusion) and older (late 2016) file and they both fail to fully open in
> FIJI using the Bio-formats plugin.
>
> Both generate the following error:
>
> Warning:  org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser: Property
> 'http://www.oracle.com/xml/jaxp/properties/entityExpansionLimit' is not
> recognized.

Which version of Java are you using?  I think this might be Java
9-related.  The current release of Bio-Formats should work correctly
with Java 9, but if you're using an older release, you could try
updating to the latest version to see if this quells these warnings.

It might also be worth trying with the Bio-Formats tools (showinf) to
see if you get the same warnings.  Fiji might also be part of the
problem, though current versions should also run with Java 9 without
warnings.

> [WARN] SamplesPerPixel mismatch: OME=-1, TIFF=1

> I have uploaded a test file for you using the OMERO upload tool. The
> file is called:
>
> "2018-03-13_15.51.33_Sample Prefix_WAINWRIGHT James_Protocol_F0.tif"
>
> Please let me know if the problem with our generation of the file or the
> Bio-formats import?

I have looked at the file, and I have attached a fixed copy of the
OME-XML plus a diff of the changes.  There are a few problems, from
minor to more critical, which I'll list below:

1) Outdated comment pointing to the OME-TIFF specification.  This could
    be updated to:

<!-- Warning: this comment is an OME-XML metadata block, which contains
crucial dimensional parameters and other important metadata. Please edit
cautiously (if at all), and back up the original data before doing so.
For more information, see the OME-TIFF documentation:
https://docs.openmicroscopy.org/latest/ome-model/ome-tiff/ -->

2) Old schema version.  Can be changed from 2015-01 to 2016-06, with
    no other changes other than dropping the old BIN and ROI namespaces,
    which are now included in the main OME namespace

3) No UUID attribute on the OME element.  Used in TiffData (but less
    important for single-file OME-TIFFs).

4) Absolute filename (Name attribute on Image).  Can be made relative to
    make the file portable if moved elsewhere.  Otherwise, it will try to
    look in this location when reading the file, and if there's another
    file by the same name it will cause confusion.

5) Use of LSIDs.  All cases of urn:lsid:ome.bitplane.com:<Element>:
    {UUID}[:<n>] can be replaced with <Element>:n.  Unless you have a
    specific need for LSIDs, in which case they could be retained.

6) Channel elements are missing the SamplesPerPixel attribute.  The sum
    of the SamplesPerPixel values for each channel must equal the SizeC
    value on Pixels.  If they are unspecified it uses a heuristic to
    determine the sizes, which it's got wrong.  This one is the cause of
    the "SamplesPerPixel mismatch" warning.

7) No TiffData elements.  Might be intentional given this is an example
    file?

8) The TIFF plane count (22) doesn't equal the number of planes
    described by the Pixels element (8z × 2c × 10t = 160 planes).  May
    also be because it's a sample file.


I hope these suggestions help you generate a valid OME-TIFF.  If you
want any of the above points clarifying further or you would like any
future OME-TIFF files or OME-XML metadata looking over for correctness,
please get back in touch.


Kind regards,
Roger Leigh

--
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
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