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

[Josh Moore]

On Wed, Feb 18, 2015 at 4:22 PM, Niko Ehrenfeuchter
<nikolaus.ehrenfeuchter at unibas.ch> wrote:
>
> On 17.02.2015 20:55, Josh Moore wrote:

>> On Tue, Feb 17, 2015 at 5:19 PM, Niko Ehrenfeuchter
>> <nikolaus.ehrenfeuchter at unibas.ch> wrote:

>>> 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.


Ah, that works out well, thanks.


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

Nope, I mean the log file which sits beside the fileset under
ManagedRepository. For example, for

# jamoore at joshuas-mbp:/opt/ome6$ dist/bin/omero -q fs sets
 # | Id  | Prefix                          | Images | Files | Transfer
---+-----+---------------------------------+--------+-------+----------
 0 | 301 | root_0/2015-02/18/10-27-33.022/ | 1      | 1     |
 1 | 251 | root_0/2015-02/18/10-20-40.871/ | 1      | 1     |
 2 | 202 | root_0/2015-02/18/10-01-20.181/ | 1      | 1     |
 3 | 201 | root_0/2015-02/18/10-01-02.432/ | 1      | 1     |
(4 rows, starting at 0 of approx. 4)
# jamoore at joshuas-mbp:/opt/ome6$ dist/bin/omero hql "select
f.templatePrefix from Image i join i.fileset as f where i.id = 251" -q
 # | Col1
---+---------------------------------
 0 | root_0/2015-02/18/10-20-40.871/
(1 row)

the log file would be found under

/OMERO/ManagedRepository/root_0/2015-02/18/10-20-40.871.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!

I'll defer to Melissa on that.
Cheers,
~Josh.


> Thanks,
> ~Niko
>