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

[Manuel Stritt]

Hi Curtis,

it seems that the ZeissCZIReader gets stuck in the initFile() method in the
for (int i=0; i<planes.size(); i++) { ... loop.
For this file plane.size() is 681...

Regards,
Manuel




On Thu, Feb 9, 2017 at 6:01 PM, Curtis Rueden <ctrueden at wisc.edu> wrote:

> 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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>
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