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

[Niko Ehrenfeuchter]

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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-- 
Niko Ehrenfeuchter | Image Analysis Specialist | Biozentrum, University 
of Basel | Klingelbergstr. 50/70 | CH-4056 Basel
Phone: +41 (61) 26 72673 | nikolaus.ehrenfeuchter at unibas.ch | 
www.biozentrum.unibas.ch | www.microscopynetwork.unibas.ch