[ome-users] Problem opening <dot>nd2 file using FIJI

[Melissa Linkert]

Hi Kaustav,

As David mentions, it would be helpful if you could send the .nd2 file
to the OME team.  In case the file is larger than 2GB, alternate
instructions for sending the file via FTP have just been sent in a
private email.

Regards,
-Melissa

On Fri, Feb 23, 2018 at 7:12 AM, David Gault (Staff)
<d.gault at dundee.ac.uk> wrote:
> Hi Kaustav,
>
> Thank you for reporting this issue, I have created a Trello card on the
> Bio-Formats inbox to track the issue
> https://trello.com/c/IpwZ4EGO/224-nd2-merged-z-and-t.
> To help us troubleshoot the problem it would be great if you could upload
> the file to https://www.openmicroscopy.org/qa2/qa/upload/
>
> With Thanks,
> David Gault
>
> On 23 Feb 2018, at 10:00, Straatman, Kees (Dr.) <krs5 at LEICESTER.AC.UK>
> wrote:
>
> Dear Kaustav,
>
> One option that might work is go to Image > Hyperstack > Stack to Hyperstack
> and see if you can find a setting that will organize the images in the
> correct order. Another option might be to export the files to a different
> format in the ND viewer like ICS/IDS and see if these open correctly in
> Fiji.
>
> Also, occasionally images open differently when opened directly in the
> Bio-Formats plugin (Plugins > Bio-Formats > Bio-Formats Importer) compared
> to File > Open.
>
> Best wishes
>
> Kees
>
>
> Dr Ir K.R. Straatman
> Senior Experimental Officer
> Advanced Imaging Facility
> Centre for Core Biotechnology Services
> University of Leicester
> www.le.ac.uk/advanced-imaging-facility
>
>
>
>
> From: ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On
> Behalf Of Kaustav Bera
> Sent: 22 February 2018 20:09
> To: ome-users at lists.openmicroscopy.org.uk
> Cc: kaustav0bera at gmail.com
> Subject: [ome-users] Problem opening <dot>nd2 file using FIJI
>
> Hi!
>
> I am trying to open a file acquired by Nikon A1 confocal system using FIJI.
> I have updated both the FIJI and the bioformats plugin before opening the
> file. Its a z stack at 8 different time points and two different channels.
> When I open it using FIJI the file opens with the two channels as expected
> but the z stacks and the time points are all merged as a time sequence.
> However when I open the file using NIS Viewer, both the metadata and the
> image are displayed properly. Please find attached some screen-shots for
> your kind referral.
> Any suggestions to curtail this problem will be highly appreciated. I can
> also forward the particular file if required.
>
> System info:
> Operating System: Windows 7 Professional edition
>
> Thanks and regards,
> Kaustav Bera
> Johns Hopkins University
> Baltimore, MD
> USA
>
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