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

[Roger Leigh]

On 14/03/2014 12:07, Roger Leigh wrote:
> 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?

Apologies, I didn't notice that you attached an example image.  I can
reproduce the problem you are seeing exactly.  I have opened a ticket
for this here, and CC'd you on it:

   https://trac.openmicroscopy.org.uk/ome/ticket/12091


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