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

[Probst, Christopher]

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 we recently updated a couple of our microscopy setups to a newer version of the NIS Elements software (4.3) and while importing recorded files in FIJI with Bioformats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 we recently updated a couple of our microscopy setups to a newer version of the NIS Elements software (4.3) and while importing recorded files in FIJI with Bioformats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
>
>
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