http://imagej.273.s1.nabble.com/bioformats-import-nd2-Files-tp5008687p5008732.html
> Hi Curtis, thanks for responding.
>
> showinf shows the same behaviour. Metadata are partially correct and
> partially not. At some places in the metadata the correct number of
> image(planes) appear at others, obviously more important, the reduced
> number. E.g. the list of scanning table coordinates show the existence of
> another image, the list of time stamps shows the reduced number!
>
> I have send the meta data of the two files I have to the ome-users list.
>
> Regards
> Karsten
>
>
> Am 14.07.2014 um 18:09 schrieb Curtis Rueden <
[hidden email]>:
>
> > Hi Karsten,
> >
> >> Bioformats importer : "Open all series" ON and "Concatenate series
> >> when compatible" ON
> >
> > Glad you figured out the "Concatenate series when compatible" option.
> That
> > is indeed the easiest way to solve your specific issue.
> >
> >> Still there is a missing image, the last one.
> >
> > I have seen this bug before... but have not had time to reproduce. Have
> you
> > reported it to the Bio-Formats development team via the OME Users [1]
> > mailing list?
> >
> > Does the problem also happen using the "showinf" Bio-Formats command line
> > tool [2] with the "-nopix" flag? I.e.: what does the metadata say? Is it
> > short one plane? Or is it correct?
> >
> > Regards,
> > Curtis
> >
> > [1]
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users/> > [2]
> >
>
https://www.openmicroscopy.org/site/support/bio-formats5/users/comlinetools/> >
> >
> > On Fri, Jul 11, 2014 at 8:27 AM, Karsten <
[hidden email]> wrote:
> >
> >>
> >> I have found a solution concerning the construction of one hyperstack
> >> instead of a bunch of images.
> >>
> >> Bioformats plugin configuration : Nikon ND2: Switch off windowless
> >> Bioformats importer : "Open all series" ON and "Concatenate series when
> >> compatible" ON
> >>
> >> These settings read in both mentioned nd2 files.
> >>
> >> Still there is a missing image, the last one.
> >>
> >> Thanks for looking into my request.
> >>
> >> Karsten
> >>
> >> Anfang der weitergeleiteten Nachricht:
> >>
> >>> Von: Karsten <
[hidden email]>
> >>> Betreff: bioformats import nd2-Files
> >>> Datum: 11. Juli 2014 14:56:33 MESZ
> >>> An:
[hidden email]
> >>>
> >>>
> >>> Hi I am just trying to read Nikon nd2 Files with Fiji (and pure ImageJ
> >> too).
> >>>
> >>> One results in a hyperstack 1280x960x3x106, which is ok, the other
> >> results in a sequence of 104 images. The latter nd2 contains 105 images
> >> according "NIS Elements Viewer"! One image more or less might be
> >> acceptable, but how can I merge that set of images? Additionally the
> >> metadata of the latter show series alphabethical sorted.
> >>>
> >>> Trying to do "Images to Stack" gives the message "There should be at
> >> least two images open", in fact 104 are open! Seemingly the opened
> images
> >> are 1-dim 3-color hyperstacks!
> >>>
> >>> Perhaps there is some knowledge on the net to configure the bioformats
> >> importer to merge that heap of images?
> >>>
> >>> Thanks in advance
> >>>
> >>> Karsten
> >>>
> >>
> >>
> >> --
> >> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> >>
> >
> > --
> > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
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