Re: bioformats import nd2-Files

Posted by ctrueden on Jul 14, 2014; 4:09pm
URL: http://imagej.273.s1.nabble.com/bioformats-import-nd2-Files-tp5008687p5008717.html

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
> >
>
>
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>

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