[ome-users] missing images reading Nikon nd2 files

[Karsten]

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
> 
> 
> 
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> 
> 
> 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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Karsten
karo13de at googlemail.com



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