[ome-users] Swap dimensions in OMERO (time vs. z)

[Niko Ehrenfeuchter]

Hi Josh,

On 17.02.2015 20:55, Josh Moore wrote:
> Hi Niko,
>
>
> On Tue, Feb 17, 2015 at 5:19 PM, Niko Ehrenfeuchter
> <nikolaus.ehrenfeuchter at unibas.ch> wrote:
>> Dear all,
>>
>> we're having a couple of datasets where OMERO mistakes time steps for Z
>> slices - is there an easy way to swap them?
>
>
> what type of dataset is it? Could you send us the import log?

it's a .nd/.stk dataset produced by a Visitron system (which uses 
Metamorph as far as I understood it). If you want to try yourself, the 
full dataset is available in QA tickets 10440 (the .nd file), 10442 and 
10512 (the three corresponding .stk files). They were initially uploaded 
for a different problem, that is solved with 5.0.8.

Otherwise I can also dig through the logs here, I guess you're asking 
for the Blitz-0.log?

On top of that we have some more (non-Visitron) Metamorph TIFFs which 
have their T interpreted as Z and their C as T. I can upload one of 
these, although the smallest one that I have is ~850 MB. Inspecting the 
metadata with Fiji shows the expected odd inconsistency on those, 
stating the images should have 2 timepoints (instead of the real 165), 
but then giving T x C "timepoints" further down.

Don't know if this is a related issue though. Let me know if I should 
upload it!

Thanks,
~Niko