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

[Melissa Linkert]

Hi Niko,

> I just re-imported it, the log file is attached.

According to the metadata in the original .nd file, there should be 3
channels and 5 Z sections.  That is what I see when importing either the
.nd or one or the .stk files into a 5.0.8 server.  If you open the .nd
file in a text editor, it should show that "NZSteps" is set to 5 and
"DoTimelapse" is set to false.

Does the acquisition software show 5 timepoints?  That would definitely
worry me; probably the easiest thing for us to do in that case is to
update the reader to change dimensions based upon the recorded acquisition software.

> >>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.

http://trac.openmicroscopy.org/ome/ticket/12503 is likely related if an
.nd file is not present.  It would help to have the file if you don't
mind, and we'll certainly do our best - reliably determining the
dimensions for Metamorph TIFFs (especially distinguishing between Z and
T) is notoriously tricky though, so it may not be 100%.

Regards,
-Melissa

On Thu, Feb 19, 2015 at 12:36:53PM +0100, Niko Ehrenfeuchter wrote:
> Hi Josh,
> 
> On 18.02.2015 20:40, Josh Moore wrote:
> >>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
> 
> I just re-imported it, the log file is attached.
> 
> 
> >>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.
> 
> Alright, I'll happily wait then :-)
> 
> Cheers,
> ~Niko


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