[ome-users] metadata in Nikon nd2 files

[Melissa Linkert]

Hi Christian,

> I've noticed that upon importing Nikon nd2 image files into Fiji
> using the LOCI BioFormats importer the metadate are not correctly
> read. If you open for example a nd2 file of a z-stack and go to
> Image -> Properties... the numbers for Slices (z) and Frames (t) are
> exchanged. Meaning for a stack of 100 slices at one timepoint it
> shows 1 slice and 100 frames. In addition the voxel depth is always
> 1.0 regardless of the true value. The pixel width and height are
> imported correctly. Are you aware of this problem or will there be a
> solution soon?

This was a known problem, which was recently fixed and so should be
working with the upcoming 4.4.3 release of Bio-Formats.  You can also
try the "trunk" build (from http://loci.wisc.edu/bio-formats/downloads),
but note that if you have recently updated Fiji you will need to
download all of the files in the "Trunk build" column under the
"Bio-Formats component builds" section.

Regards,
-Melissa

On Wed, Aug 22, 2012 at 04:22:41PM +0200, Christian Wenzl wrote:
> Hi,
> 
> I've noticed that upon importing Nikon nd2 image files into Fiji
> using the LOCI BioFormats importer the metadate are not correctly
> read. If you open for example a nd2 file of a z-stack and go to
> Image -> Properties... the numbers for Slices (z) and Frames (t) are
> exchanged. Meaning for a stack of 100 slices at one timepoint it
> shows 1 slice and 100 frames. In addition the voxel depth is always
> 1.0 regardless of the true value. The pixel width and height are
> imported correctly. Are you aware of this problem or will there be a
> solution soon?
> 
> Best,
> Christian
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