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

Thu Apr 14 17:02:18 BST 2016

Hi,

Thank you for submitting your files.

Testing the same locally, we were able to reproduce the issue and I have
filed a ticket on this regard,
https://trac.openmicroscopy.org/ome/ticket/13204

And you have been added to the cc list.
Notifications will be sent to your email id, when there is a status change
on the ticket.

Best,
Balaji

__________________
Mr Balaji Ramalingam
Software Developer

OME Team
College of Life Sciences
University of Dundee

On 11/04/2016 11:48, "Probst, Christopher" <c.probst at fz-juelich.de> wrote:

>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
>> >
>> >
>> >
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>> > Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
>> > Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
>> > Prof. Dr. Sebastian M. Schmidt
>> >
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