[ome-users] Exception when loading czi image with bfGetReader (matlab)

[Roger Leigh]

On 12/03/2013 07:56, Matthias Pospiech wrote:
> Hello,
> I am am using the matlab extension with loci_tools.jar for a while now
> and it works
> very well with Zeiss images (zvi, czi).
>
> However currently I have some images that fail to load with this exception:
>
> Error using bfGetReader (line 54)
> Java exception occurred:
> java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
>
>          at java.util.ArrayList.RangeCheck(Unknown Source)
>          at java.util.ArrayList.get(Unknown Source)
>          at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:489)
>          at loci.formats.FormatReader.setId(FormatReader.java:1105)
>          at loci.formats.ImageReader.setId(ImageReader.java:695)
>          at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:505)
>          at loci.formats.ChannelFiller.setId(ChannelFiller.java:263)
>          at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:505)
>          at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274)
>
> Can you tell me anything about what is going wrong by these error messages?

Dear Matthias,

The CZI format reader is failing to read your file, probably because
your file contains information we have not seen before, so we are not
properly handling it.

Please could you provide one or more example CZI files which fail to
import, so that we can investigate this further and fix the problem with
the reader for your files?  You can upload them here:
   http://qa.openmicroscopy.org.uk/qa/upload/


Many thanks,
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