[ome-users] Problems opening Nikon nd2 files with Bioformats

[Melissa Linkert]

Hi Matt,

> We're having some issues opening multidimensional Nikon nd2 data
> sets in FIJI.  The data is multi xy position, lambda, time lapse.
> When i try to open the file using hyperstack it opens as a single
> window.  Instead of containing the time points, moving the Z scroll
> bar moves between different xy stage positions and through time but
> not in order, so somehow the data is all jumbled.  Its been a while
> since i've used nd2 files in fiji but i thought previously the
> initial window you see when opening files is a thumbnail preview of
> each xy position with a checkbox next to each so you can decide
> which xy positions you open.  What has happened to this?  And are
> you aware of issues opening this file type?

Thank you for the bug report.  A few other people have mentioned similar
problems with multiposition .nd2 files; we're actively working on a
solution (see https://trac.openmicroscopy.org.uk/ome/ticket/10773).

Would you be willing to send one of the problematic files, so that we
can verify that any fixes will work for your data as well?  If so,
please upload the file to the OME QA system:

http://qa.openmicroscopy.org.uk/qa/upload/

Regards,
-Melissa

On Wed, Jul 17, 2013 at 10:16:05AM +0100, Matthew Pearson wrote:
> Hi all,
> 
> We're having some issues opening multidimensional Nikon nd2 data
> sets in FIJI.  The data is multi xy position, lambda, time lapse.
> When i try to open the file using hyperstack it opens as a single
> window.  Instead of containing the time points, moving the Z scroll
> bar moves between different xy stage positions and through time but
> not in order, so somehow the data is all jumbled.  Its been a while
> since i've used nd2 files in fiji but i thought previously the
> initial window you see when opening files is a thumbnail preview of
> each xy position with a checkbox next to each so you can decide
> which xy positions you open.  What has happened to this?  And are
> you aware of issues opening this file type?
> 
> Thanks for the help,
> 
> Matt
> 
> 
> 
> --
> Matt Pearson
> Microscopy and Imaging Facility
> MRC Human Genetics Unit
> IGMM
> University of Edinburgh
> Crewe Road
> Edinburgh
> EH4 2XU
> 
> Tel: 0131 467 8425
> 
> 
> 
> 
> 
> 

> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.

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