[ome-users] FEI MORE tf8 files sorted to Orphaned Images

[Kai Schleicher]

Hi Dominik,

Thanks once again for your help!

I was wondering if you could specify at which exact position in the 
metadata the incorrect entry is found?

I would then forward this information to the FEI support to ask them if 
this is due to a "bug" in their software in general or simply due to the 
way we set/acquired the image here on our side.

Thanks and cheers,
Kai

On 07/20/2016 10:51 AM, Niko Ehrenfeuchter wrote:
> Hi Domink,
>
> thanks a lot for investigating this!
>
> We'll try to contact FEI to see whether they can change this in the 
> software (or whether we are doing something wrong in the acquisition).
>
> Thanks again,
> ~Niko
>
> On 20.07.2016 10:42, Dominik Lindner (Staff) wrote:
>> Hi Niko and Kai,
>>
>> I did some more investigation, and I think the main problem simply is
>> that the metadata contains a plate definition although the file is not
>> supposed to be a plate. There was some discussion going on here as well
>> https://github.com/openmicroscopy/openmicroscopy/pull/4751 (I closed it
>> again, because the PR would introduce other problems). Basically in
>> Insight I have to rely on the metadata, I couldn't find a way to
>> determine that the file is not plate other then checking the metadata.
>> And if it's reported as plate, Insight ignores the Project/Dataset
>> setting, which is reasonable.
>>
>> Regards,
>> Dominik
>>
>>
>>> On 14 Jul 2016, at 13:17, Nikolaus Ehrenfeuchter
>>> <nikolaus.ehrenfeuchter at unibas.ch
>>> <mailto:nikolaus.ehrenfeuchter at unibas.ch>> wrote:
>>>
>>> Hi Dominik,
>>>
>>> Kai and me did some more investigation on this and figured out that
>>> the tf8 files will be  placed in the correct location when using the
>>> command-line importer instead of insight. Does this give any
>>> additional hint?
>>>
>>> Cheers
>>> Niko
>>>
>>>
>>> Am 14.07.2016 2:11 nachm. schrieb "Dominik Lindner (Staff)"
>>> <d.lindner at dundee.ac.uk <mailto:d.lindner at dundee.ac.uk>>:
>>>
>>>     Hi Kai,
>>>
>>>     sorry, that issue slipped a bit from my attention. Up to now I
>>>     traced it back to the
>>>     OMETiffReader. For these files it reports "High-Content Screening
>>>     (HCS)", that causes
>>>     the Insight importer to ignore the Dataset/Project settings. I'm
>>>     not sure if that's an
>>>     Importer problem, or more a Bioformats issue. I'll have to involve
>>>     some Bioformats people
>>>     into this. Sorry for the late reply.
>>>
>>>     Cheers,
>>>     Dominik
>>>
>>>
>>>     > On 13 Jul 2016, at 13:45, Kai Schleicher
>>>     <kai.schleicher at unibas.ch <mailto:kai.schleicher at unibas.ch>> wrote:
>>>     >
>>>     > Hi Dominik,
>>>     >
>>>     > I was just wondering whether you'd already have some news
>>>     regarding this issue.
>>>     >
>>>     > I have just tested this problem again with OMERO 5.2.4, but it
>>>     still persists.
>>>     >
>>>     > As Niko wrote this is indeed the case for both "regular" TIFFs
>>>     and tf8 files recorded with the LA software on the FEI MORE.
>>>     >
>>>     > Thanks and cheers,
>>>     > Kai
>>>
>>>
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