Fwd: bioformats import nd2-Files

Posted by karo03 on Jul 11, 2014; 1:27pm
URL: http://imagej.273.s1.nabble.com/bioformats-import-nd2-Files-tp5008687p5008688.html


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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