[ome-users] missing images reading Nikon nd2 files

[Melissa Linkert]

Hi Karsten,

> each file is about 410 MB, that would last some time! I don't have access to the microscope (and the Nikon software) to produce a smaller one.

Before uploading a file then, could you please try the "Latest build"
from http://downloads.openmicroscopy.org/bio-formats/5.0.2 and see if
that fixes the problem?  It's not clear to me which version you are
currently using, but there have been significant changes to .nd2 support
in the last few weeks which may fix this.

If updating does not work, then an example file would be appreciated; I
will send FTP instructions as requested in a private mail.

Regards,
-Melissa

On Tue, Jul 15, 2014 at 01:10:45PM +0200, Karsten wrote:
> 
> Hi Roger,
> 
> each file is about 410 MB, that would last some time! I don't have access to the microscope (and the Nikon software) to produce a smaller one.
> 
> Regards
> Karsten
> 
> Am 15.07.2014 um 13:00 schrieb ome-users-request at lists.openmicroscopy.org.uk:
> 
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> > 
> >   1. Re: missing images reading Nikon nd2 files (Curtis Rueden)
> >   2. Re: missing images reading Nikon nd2 files (Roger Leigh)
> > 
> > Von: Curtis Rueden <ctrueden at wisc.edu>
> > Betreff: Aw: [ome-users] missing images reading Nikon nd2 files
> > Datum: 14. Juli 2014 23:06:08 MESZ
> > An: Karsten <karo13de at googlemail.com>
> > Kopie: OME-users mailing list <ome-users at lists.openmicroscopy.org.uk>
> > 
> > 
> > Hi everyone,
> > 
> > > Importing nd2 files (two) delivers one (3-channel) image less than the
> > > NIS Elements Viewer.
> > 
> > For the archives: this report emerged from a related thread on the ImageJ mailing list, which you can find at:
> > https://list.nih.gov/cgi-bin/wa.exe?A2=IMAGEJ;cc9bcbc2.1407
> > 
> > Regards,
> > Curtis
> > 
> > 
> > On Mon, Jul 14, 2014 at 3:25 PM, Karsten <karo13de at googlemail.com> wrote:
> > 
> > Importing nd2 files (two) delivers one (3-channel) image less than the NIS Elements Viewer.
> > 
> > This happens under ImageJ, Fiji and the commandline tool showinf.
> > 
> > The meta data show the reduced number of images, still the list of the scanning table coordinates show the full number of images extended by a constant dummy coordinate to the number of (1-channel) images found from bioformats software.
> > 
> > I attache the output of showinf.
> > 
> > The second file delivers also one image less than the Nikon Viewer. Additionally the metadata show a different structure by dividing the list of images in a large number of series. According the microscope users, they did not change anything saving the second data file.
> > 
> > One image less is possibly not so important. However for the sake of correctness it could be improved.
> > 
> > Thanks in advance for any help
> > 
> > Karsten
> > karo13de at googlemail.com
> > 
> > 
> > 
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> > 
> > 
> > 
> > 
> > 
> > Von: Roger Leigh <rleigh at dundee.ac.uk>
> > Betreff: Aw: [ome-users] missing images reading Nikon nd2 files
> > Datum: 15. Juli 2014 11:54:54 MESZ
> > An: <ome-users at lists.openmicroscopy.org.uk>
> > 
> > 
> > On 14/07/14 21:25, Karsten wrote:
> >> 
> >> Importing nd2 files (two) delivers one (3-channel) image less than the NIS Elements Viewer.
> >> 
> >> This happens under ImageJ, Fiji and the commandline tool showinf.
> >> 
> >> The meta data show the reduced number of images, still the list of the scanning table coordinates show the full number of images extended by a constant dummy coordinate to the number of (1-channel) images found from bioformats software.
> >> 
> >> I attache the output of showinf.
> >> 
> >> The second file delivers also one image less than the Nikon Viewer. Additionally the metadata show a different structure by dividing the list of images in a large number of series. According the microscope users, they did not change anything saving the second data file.
> >> 
> >> One image less is possibly not so important. However for the sake of correctness it could be improved.
> >> 
> >> Thanks in advance for any help
> > 
> > Dear Karsten,
> > 
> > Would it be possible for you to upload this image (or any sample image
> > demonstrating this problem) using
> > http://qa.openmicroscopy.org.uk/qa/upload/ so that we can investigate
> > the problem further?
> > 
> > 
> > Many thanks,
> > Roger Leigh
> > 
> > --
> > Dr Roger Leigh -- Open Microscopy Environment
> > Wellcome Trust Centre for Gene Regulation and Expression,
> > College of Life Sciences, University of Dundee, Dow Street,
> > Dundee DD1 5EH Scotland UK   Tel: (01382) 386364
> > 
> > The University of Dundee is a registered Scottish Charity, No: SC015096
> > 
> > 
> > 
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> > ome-users at lists.openmicroscopy.org.uk
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> 
> Karsten
> karo13de at googlemail.com
> 
> 
> 

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