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

[Roger Leigh]

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