[ome-users] OMERO pyramid creation

[Kai Schleicher]

Hi Sebastian,

thanks for clarifying! I am happy that the bug is already fixed :)

Have a nice weekend and cheers,
Kai


On 06/16/2017 02:11 PM, Sebastien Besson (Staff) wrote:
> Hi Kai,
>
> thanks for the update. I could also confirm the error while 
> reimporting your image into the
> OMERO server.
>
> The issue is actually a bug associated with the reading of the CZI 
> file. Luckily this bug has
> been  fixed and released in the most recent Bio-Formats version as you 
> could confirm by
> opening the file using Fiji.
>
> This version is not yet included in the latest release of OMERO but 
> the import of the file into
> one of our development server went through without errors. So I expect 
> your problem to be
> fixed with the imminent release of OMERO 5.3.3.
>
> Answering one of your initial questions, if Bio-Formats reads 
> pyramidal subresolutions available
> within the file, OMERO should not recalculate pyramids. In this case, 
> the client message was slightly
> misleading as the issue is rather at the file import level.
>
> Best,
> Sebastien
>
>> On 16 Jun 2017, at 13:02, Kai Schleicher <kai.schleicher at unibas.ch 
>> <mailto:kai.schleicher at unibas.ch>> wrote:
>>
>> Hi,
>>
>> I have an update to this: while there was no error during upload, I 
>> received an error during processing "failed to read pixels" for one 
>> of the images (example image ID 576 
>> <https://demo.openmicroscopy.org/webclient/?show=image-576> , see 
>> attached error log)
>>
>> thanks for your help and cheers,
>> Kai
>>
>>
>>
>> On 06/16/2017 11:45 AM, Kai Schleicher wrote:
>>>
>>> Hi,
>>>
>>> first, even though its already a bit in the past: Thanks for the 
>>> great OME meeting! I was happy to meet everyone and see all the new 
>>> and amazing things to come :)
>>>
>>> second, thanks for the freshly installed 5.3.2 OMERO demo server! 
>>> For testing I have uploaded some jpegXR compressed multi-sceen BF 
>>> and FL images of our AxioScan slidescanner (*czi), which uploaded 
>>> with no issue (dataset ID 17 
>>> <https://demo.openmicroscopy.org/webclient/?show=dataset-17>, 
>>> example image ID 576 
>>> <https://demo.openmicroscopy.org/webclient/?show=image-576> ).
>>>
>>> I noticed however that the OMERO sever spends some time calculating 
>>> a pyramid for my images.
>>>
>>> Since these images already contained pyramids that where calculated 
>>> by Zen after acquisition, do you think it would be possible to skip 
>>> pyramid creation on the OMERO server side and use the ones provided 
>>> in the czi instead?
>>>
>>> While I could confirm that FIJI/Bio-formats recognises the pyramids 
>>> in those images, I don't really know if they are on the same 
>>> zoom-level that OMERO expects/ likes to use.
>>>
>>> Let me know if you wish to have the example images uploaded 
>>> somewhere else other than your demo server :)
>>>
>>> Thanks 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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>>> ome-users at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
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