[ome-users] bug in Bio-Formats Exporter for ImageJ?

[Roger Leigh]

On 13/03/2014 13:01, Peter van Loon wrote:
> Hi,
>
> I have problems when I use the Bio-Formats Exporter in ImageJ. I used
> the latest versions of both ImageJ and Bio-Formats (5.0.0).
> I tried older versions of Bio-Formats (4.4.10) and it seemed to work but
> the next day I got the same exceptions.
> I tried in the latest Fiji but with the same result.
>
> It happens with just ordinary test files like this: RGB file (1 layer):
>
> *This is the ImageJ Exception:*
>
> ****begin*****
> ImageJ 1.48s; Java 1.6.0_21 [32-bit]; Windows 7 6.1; 15MB of 640MB (2%)
>
> java.lang.IllegalArgumentException: ZCT size vs image count mismatch
> (sizeZ=1, sizeC=3, sizeT=1, total=1)
>          at loci.formats.FormatTools.getZCTCoords(FormatTools.java:467)
>          at loci.plugins.out.Exporter.run(Exporter.java:592)
>          at loci.plugins.LociExporter.run(LociExporter.java:77)
>          at

Dear Peter,

Could you possibly provide some more detail about what you did before
this export step?

When you originally loaded the image into ImageJ, did you use the
Bio-Formats importer?  Was the source image an OME-TIFF, or some other
format?

Did you perform any operations in ImageJ which would alter the image
dimensionality?  Examples: Adding or removing channels, z planes and/or
timepoints?  Converting from discrete channels to RGB would also be
included here.

When it comes to exporting as OME-TIFF, the exporter will reuse OME-XML
attached to the image from what I can see, and if the image
dimensionality has been changed, the actual values may mismatch with the
expected (cached) values, and this might be one reason it fails.  This
is not to say this is what's going wrong in your case, just one
possibility to investigate.

We really need to be able to reproduce the failure in order to be able
to further investigate what's going wrong here.  If it would be possible
to upload one of the source images demonstrating the problem here:
https://www.openmicroscopy.org/qa2/qa/upload/ and let us know the steps
you went through to get the error, this would be much appreciated.


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