[ome-users] Problem displaying OME.Tiff exports from zeiss Zen blue

[Damir Sudar]

Hi Kai,

As Sebastien mentions, I have the exact same problem. Sebastien provided 
guidance how to write a script to delete the broken pyramid files that 
block new ones from being generated and as soon as my current grant is 
out the door, I'll look at writing such a script. But in case you do it 
sooner than me, please let us all know. No doubt there are others with 
the same issue.

Note that pyramid generation for those very large Axioscan/ZEN-generated 
OME-TIFFs takes a fairly long time, even on a powerful server. But I can 
attest that it does work on 5.2.2.

Cheers,
- Damir

On 3/8/2016 3:00 AM, Sebastien Besson (Staff) wrote:
> Hi Kai,
>
> thanks for reporting this issue. Looking at the images, they were 
> imported back into February
> using OMERO 5.2.1 / Bio-Formats 5.1.6. The pyramid generation was 
> broken with exactly the
> same stack trace than the one reported by Damir in a forum thread [1] 
> and fixed in Bio-Formats
> 5.1.8.
>
> There are a different answers to your email:
>
> - re-importing the same image into an OMERO 5.2.2 instance e.g. the 
> demo server should work
>   out-of-the-box and the pyramid should be properly generated
> - in a production environment, deleting the stale pyramid files using 
> the command suggested
>   in the thread linked above should also work without forcing a new import
> - from our side, we have created a card to improve the behavior 
> illustrated by this use case both
>   server-side during pyramid generation and client-side e.g. via 
> scripts [2]
>
> Best,
> Sebastien
>
> [1] https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=7907
> [2] https://trello.com/c/TM1Si3UN/38-pyramids
>
>> On 7 Mar 2016, at 14:01, Kai Schleicher <kai.schleicher at unibas.ch 
>> <mailto:kai.schleicher at unibas.ch>> wrote:
>>
>> Hi,
>>
>> I recorded images in the czi format on the Zeiss Axioscan 
>> Slidescanner and exported them via Zen Blue to OME-TIFFs.
>>
>> These OME-Tiffs open correctly in FIJI using the latest Bioformats.
>>
>> However, they fail to open after being imported into OMERO.
>>
>> Import to is handled without error but the images cannot be displayed 
>> in the viewer. The also do not have a preview, instead the 
>> “watch”-icon is shown.
>>
>> I am using the latest version of OMERO (your demo server) and this 
>> client: OMERO.insight-5.2.2-ice35-b17-win.
>>
>> The images in question have the ID 203547 and 203548.
>>
>> Thanks for your help and cheers,
>>
>> Kai
>>
>> --
>>
>> Kai Schleicher, PhD | Research Associate in Advanced Light Microscopy 
>> | Biozentrum, University of Basel | Klingelbergstrasse 50/70 | 
>> CH-4056 Basel
>>
>> Phone: +41 61 267 22 50 | kai.schleicher at unibas.ch 
>> <mailto:kai.schleicher at unibas.ch> | www.biozentrum.unibas.ch 
>> <http://www.biozentrum.unibas.ch/> | www.microscopynetwork.unibas.ch 
>> <http://www.microscopynetwork.unibas.ch/>
>>
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>
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-- 
Damir Sudar - Staff Scientist
Lawrence Berkeley Natl Laboratory / MBIB
One Cyclotron Road, MS 977, Berkeley, CA 94720, USA
T: 510/486-5346 - F: 510/486-5586 - E: DSudar at lbl.gov

Visiting Scientist, Oregon Health & Science University

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