[ome-users] bug in Bio-Formats with LEI file

[Balaji Ramalingam]

Hi,

Could you please let us know the version of bio-formats/Loci-tools you are
using?
I couldn¹t get access to the files that you had uploaded (More details of
the FTP site?).

But I tested a few Œ.lei' uploads via insight(latest release version,
which uses bio-formats 5) and opened them as well.
If your version of bio-formats/loci-tools is outdated, I suggest
downloading the latest version from our downloads page,

For Bio-formats,
http://downloads.openmicroscopy.org/bio-formats/5.0.0/

And for OMERO clients,
http://downloads.openmicroscopy.org/omero/5.0.0/

This should hopefully solve the problem.
If you still see the issue in the latest version as well (highly
unlikely), please do let us know.

Best,
Balaji

On 18/03/2014 08:47, "Stéphane Dallongeville"
<stephane.dallongeville at pasteur.fr> wrote:

>Hi,
>
>Just wanted to report this problem : trying to opening a multi serie LEI
>file with LOCI i obtained the following error message :
>
>java.lang.IndexOutOfBoundsException: Index: 1, Size: 1
>     at java.util.ArrayList.RangeCheck(ArrayList.java:547)
>     at java.util.ArrayList.get(ArrayList.java:322)
>     at ome.xml.model.Pixels.getChannel(Pixels.java:573)
>     at
>loci.formats.ome.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMe
>tadataImpl.java:9731)
>     at
>loci.formats.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetad
>ata.java:1686)
>     at
>loci.formats.in.LeicaReader.parseInstrumentData(LeicaReader.java:1410)
>     at loci.formats.in.LeicaReader.initFile(LeicaReader.java:695)
>     at loci.formats.FormatReader.setId(FormatReader.java:1360)
>
>The same dataset converted to LIF does open correctly so i guess it is
>just a problem with metadata retrieving from the LEI reader.
>I uploaded the sample to the FTP, it's named "3c x40 correct.zip", it's
>an archive containing both the LEI and LIF file.
>Thanks.
>
>--
>Stephane Dallongeville
>Unité d'Analyse d'Images Biologiques
>CNRS URA 2582
>Institut Pasteur
>25 rue du Dr Roux - 75015 Paris - France
>
>Tel: +33 (0)1 45 68 86 90
>Fax: +33 (0)1 40 61 33 30
>
>http://www.bioimageanalysis.org/
>
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