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

[David Gault (Staff)]

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<mailto: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<http://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<mailto:ome-users at lists.openmicroscopy.org.uk>
Cc: kaustav0bera at gmail.com<mailto: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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