[ome-users] Bioformats Import problem with .nd2 files recorded with NIS Elements 4.3

[Probst, Christopher]

Hey guys,

did you have any luck in finding the problem?

Best
Christopher
________________________________________
Von: Probst, Christopher
Gesendet: Mittwoch, 16. März 2016 14:45
An: ome-users at lists.openmicroscopy.org.uk
Betreff: AW: [ome-users] Bioformats Import problem with .nd2 files recorded with NIS Elements 4.3

Hi Melissa,

thx for your message I uploaded the file last week hope the upload worked!

Best
Christopher


________________________________________
Von: Melissa Linkert [melissa.linkert at gmail.com]" im Auftrag von "Melissa Linkert [melissa at glencoesoftware.com]
Gesendet: Donnerstag, 10. März 2016 16:14
An: Probst, Christopher
Cc: ome-users at lists.openmicroscopy.org.uk
Betreff: Re: [ome-users] Bioformats Import problem with .nd2 files recorded with NIS Elements 4.3

Hi Christopher,

> thank you for you reply! I did try to open it with the current Bioformats Version 5.1.8 (sorry forgot to mention).

OK, thank you for clarifying.

> The file is around 16 GB so alternative upload would be much appreciated :).

Alternate upload instructions have been sent via private mail; we'll
follow up here once the file has been uploaded.

Regards,
-Melissa

On Thu, Mar 10, 2016 at 09:10:56AM +0000, Probst, Christopher wrote:
> Hi Melissa,
>
> thank you for you reply! I did try to open it with the current Bioformats Version 5.1.8 (sorry forgot to mention). The file is around 16 GB so alternative upload would be much appreciated :).
>
> Best
> Christopher
> ________________________________________
> Von: Melissa Linkert [melissa.linkert at gmail.com]" im Auftrag von "Melissa Linkert [melissa at glencoesoftware.com]
> Gesendet: Mittwoch, 9. März 2016 17:09
> An: Probst, Christopher
> Cc: ome-users at lists.openmicroscopy.org.uk
> Betreff: Re: [ome-users] Bioformats Import problem with .nd2 files recorded with NIS Elements 4.3
>
> Hi Christopher,
>
> Thank you for reporting this problem.
>
> > we recently updated a couple of our microscopy setups to a newer version of the NIS Elements software (4.3) and while importing recorded files in FIJI with Bioformats
> > there is a mix up between series and time points. Meaning that in a file with 100 series and 200 time points after selecting series 1 to be imported, series 1 will result in a stack of images from the first frame of each of the 100 series and 100 blank images.
>
> Could you please clarify which version of Bio-Formats is installed?
> "Help > About Plugins > Bio-Formats Plugins" in Fiji will show the
> version number and date.  If your Fiji is up to date, the version number
> will be 5.1.8; if you see an older version, then please try running the
> Fiji updater first.
>
> > I can provide a file to test of course!
>
> If you're seeing this problem with 5.1.8, then it would be much
> appreciated if you could upload the file to:
>
> https://www.openmicroscopy.org/qa2/qa/upload/
>
> If the file is larger than 2GB, please let us know and we'll send
> alternate upload instructions.
>
> Regards,
> -Melissa
>
> On Wed, Mar 09, 2016 at 09:30:33AM +0000, Probst, Christopher wrote:
> > Hi,
> >
> > we recently updated a couple of our microscopy setups to a newer version of the NIS Elements software (4.3) and while importing recorded files in FIJI with Bioformats
> > there is a mix up between series and time points. Meaning that in a file with 100 series and 200 time points after selecting series 1 to be imported, series 1 will result in a stack of images from the first frame of each of the 100 series and 100 blank images.
> > I can provide a file to test of course!
> >
> > Best
> >
> > Christopher
> > Research Centre Jülich Germany
> > Institute of Bio- and Geosciences (IBG-1)
> > 52428 Jülich, Germany
> >
> >
> > ------------------------------------------------------------------------------------------------
> > ------------------------------------------------------------------------------------------------
> > Forschungszentrum Juelich GmbH
> > 52425 Juelich
> > Sitz der Gesellschaft: Juelich
> > Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
> > Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
> > Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
> > Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
> > Prof. Dr. Sebastian M. Schmidt
> > ------------------------------------------------------------------------------------------------
> > ------------------------------------------------------------------------------------------------
> >
>
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>