[ome-users] AxioScan.Z1 *.czi fails to open

[Curtis Rueden]

Hi Kai,

You can find out what ImageJ is stuck doing by following these directions:

http://imagej.net/Troubleshooting#If_ImageJ_freezes_or_hangs

The stack trace will help the Bio-Formats developers to understand and fix
the problem. Although in this case, since you uploaded sample data, that is
probably already enough to reproduce.

Thanks,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Thu, Feb 9, 2017 at 10:39 AM, Kai Schleicher <kai.schleicher at unibas.ch>
wrote:

> Hi,
>
> I have a Bright-field *.czi image containing 4 scenes/scopes (upload ID
> 17539) from the Zeiss Axioscan Z1 slidescanner that fails to open without
> error message (FIJI, latest Bio-Formats). FIJI is stuck during
> "Analysing...".
>
> Manuel Stritt(Orbit) has reproduced the problem with some further insight:
>
> tested with Bioformats 5.3.2:
>> IFormatReader reader = new ImageReader();
>> reader.setId("2017_02_03_12wksWTQm3179.czi");
>> reader.close();
>>
>> hangs at reader.setId...
>>
>> it seems that ZeissCZIReader gets stuck at initFile().
>>
>
> Notably, when I split the 4 scenes into 4 individual files they open fine.
>
> Do you have an idea what the problem could be in this case?
>
> Thanks for your help and cheers,
> Kai
>
> --
>
>> Please note my NEW PHONE NUMBERS: +41 61 207 57 31 (direct) +41 61 207
>>> 22 50 (central)<<
>>>
>> Kai Schleicher, PhD | Research Associate in Advanced Light Microscopy |
> Biozentrum, University of Basel | Klingelbergstrasse 50/70 | CH-4056 Basel |
> Phone: +41 61 207 57 31 (direct) +41 61 207 22 50 (central) |
> kai.schleicher at unibas.ch | www.biozentrum.unibas.ch |
> www.microscopynetwork.unibas.ch
>
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