[ome-devel] Is OME-TIF file with 2 image series of different pixel types supported?

[Michael Ellis]

Dear Roger,

File uploaded https://www.openmicroscopy.org/qa2/qa2/qa/feedback/17455/?token=0d0ad37c09cfdd73ca5c28df3d42e1b0

I am currently just using Metadata methods to populate my metadata. Can you point me in the right direction for adding this TiffData that you refer to?

— Michael Ellis

> On 1 Dec 2016, at 14:17, Roger Leigh <rleigh at dundee.ac.uk> wrote:
> 
> On 01/12/16 10:48, Michael Ellis wrote:
>> BioFormats does not seem to cope with a single OME.TIF file that contains 2 image series one with pixel type uint16 and one with pixel type uint8.
>> 
>> I can create the file with no problem but both the bftools showinfo command line tool and the ImageJ BioFormats importer crash when trying to load the file.
>> 
>> I realise mixing two images of different pixel types in a single OME.TIF file is somewhat bizarre. I have no actual need to do this but stumbled upon the situation whilst designing unit tests for my code.
>> 
>> My questions are:
>> 
>> - Is there anything else apparent from the output that points to anything wrong that I am doing?
>> - Is this a bug or a feature?
>> - If it is a feature, then where is it documented?
> 
> Dear Michael,
> 
> This should work, and is certainly supported by the specification.
> There are two possibilities:
> 
> 1) An outright bug in the OME-TIFF reader
> 2) A bug in the metadata which triggers the behaviour
> 
> Looking at the metadata you pasted, I think a potential culprit is the
> lack of "TiffData" elements in your second Image element.  This likely
> triggers fallback behaviour in the reader which makes it fall back to
> attempting to use IFD0 as Plane0 in the image, which is of the wrong
> pixel type.  It's likely the case that adding TiffData elements to the
> Pixels element in this image will resolve the problem.
> 
> If the above suggestion doesn't help, if you would like to upload the
> file using https://www.openmicroscopy.org/qa2/qa/upload/ I'll be happy
> to look over the metadata and TIFF structure in more detail.
> 
> 
> 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
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Michael Ellis (Managing Director)
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