[ome-users] Problem with CZI image file

Roger Leigh rleigh at dundee.ac.uk
Wed Feb 19 12:38:12 GMT 2014

On 17/02/14 15:41, Stéphane Dallongeville wrote:
> Just wanted to report you an issue meet by a Icy user. He obtain the
> following error while trying to load a CZI file with LOCI:
> java.lang.IllegalArgumentException: Invalid T index: 1/1
>      at loci.formats.FormatTools.getIndex(FormatTools.java:383)
>      at loci.formats.FormatTools.getIndex(FormatTools.java:328)
>      at loci.formats.FormatReader.getIndex(FormatReader.java:1071)
>      at
> loci.formats.in.ZeissCZIReader.assignPlaneIndices(ZeissCZIReader.java:1017)
>      at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:612)
>      at loci.formats.FormatReader.setId(FormatReader.java:1360)
> Tested on 5.0.0 RC1 and the last daily RC2.
> As the image file is large i'm uploading it on the LOCI FTP test server:
> AO5.czi
> Should be done in 10 minutes :)

Dear Stéphane,

Thanks for uploading the image.  I can also reproduce the problem, and
I've opened a ticket for this.  It looks like the CZI reader might not
be coping with the timeseries in two separate blocks, but that will need
further investigation.  I added you as a CC on the ticket, but if you'd
like your user adding in addition (or instead) of you, please let me
know their email address privately and I'll update the ticket.

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

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