[ome-users] .nd2 files bug

[Melissa Linkert]

Hi Michael,

Apologies for not following up sooner.

> I can check the version on the computer.
> 
> I upgraded both IJ and LOCI to daily builds last Thurs or Friday.

If you could please send the exact versions (from "Help > About Plugins > Bio-Formats Plugins"),
that would be very helpful.  Both of the formats you've mentioned have
been the target of several bug fixes over the last several weeks, so
it's important to know which of these fixes would have been present.

> No error messages.  Simply stops as though the whole thing worked fine.
> 
> I was opening as a standard hyperstack.  IJ has 48GB allocated to it on a computer with 192GB.  When we export to TIF from the Nikon software, we can open the entire 17GB  dataset and do everything we want.
> 
> I can put the dataset on your ftp server.
> 
> We also have similar problems with big CZI files.  For instance, tiling 3 X2 opens fine, but 100+ tiles pops up a message asking us for a range of tiles we want opened and then displays nothing useful.

I've sent FTP information via private email, as you won't be able to
upload these large files via our QA system.

Regards,
-Melissa

On Tue, Sep 22, 2015 at 09:03:00PM +0000, Cammer, Michael wrote:
> I can check the version on the computer.
> 
> I upgraded both IJ and LOCI to daily builds last Thurs or Friday.
> 
> No error messages.  Simply stops as though the whole thing worked fine.
> 
> I was opening as a standard hyperstack.  IJ has 48GB allocated to it on a computer with 192GB.  When we export to TIF from the Nikon software, we can open the entire 17GB  dataset and do everything we want.
> 
> I can put the dataset on your ftp server.
> 
> We also have similar problems with big CZI files.  For instance, tiling 3 X2 opens fine, but 100+ tiles pops up a message asking us for a range of tiles we want opened and then displays nothing useful.
> 
> =========================================================================
> Michael Cammer, Microscopy Core & Skirball Institute, NYU Langone Medical Center
>                       Cell:  914-309-3270     ** MY OFFICE HAS MOVED TO SKIRBALL 2nd FLOOR, Back right **
>           http://ocs.med.nyu.edu/microscopy & http://microscopynotes.com/
> 
> From: ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of Sebastien Besson (Staff)
> Sent: Tuesday, September 22, 2015 4:01 PM
> To: users OME
> Subject: Re: [ome-users] .nd2 files bug
> 
> Hi Michael,
> 
> thanks for your feedback.
> 
> Reading through your email, I suppose you are opening your nd2 files
> using ImageJ. Which version of Bio-Formats did you download and use
> for opening the files?
> Also when  the file opening stops, do you receive a warning or an
> error message or does the application exit?
> 
> Assuming the dataset started to load correctly, there might be a memory
> issue. This page of the Bio-Formats user documentation [1] provides
> some suggestions for dealing with large datasets. Is the dataset loaded
> using the virtual stack for instance?
> 
> Best regards,
> Sebastien
> 
> [1] https://www.openmicroscopy.org/site/support/bio-formats5.1/users/imagej/managing-memory.html
> 
> 
> On 22 Sep 2015, at 17:39, Cammer, Michael <Michael.Cammer at med.nyu.edu<mailto:Michael.Cammer at med.nyu.edu>> wrote:
> 
> We are having a problem opening  .nd2 files.
> We have this problem is an older version of LOCI and a daily build we downloaded late last week.
> 
> Each file is 17.8 GB with 55 timepoints of 2 channels of 15 Z positions.
> 
> LOCI opens the first 27 timepoints, 2 channels, and 7 Z of the 28th timepoint and then just stops.
> 
> If we export the file from Nikon Elements to OME TIFF, the whole thing can be operated on fine, but it would be preferable to be able to open directly into ImageJ.
> 
> Thank you.
> 
> =========================================================================
> Michael Cammer, Microscopy Core & Skirball Institute, NYU Langone Medical Center
>                       Cell:  914-309-3270     ** MY OFFICE HAS MOVED TO SKIRBALL 2nd FLOOR, Back right **
>           http://ocs.med.nyu.edu/microscopy & http://microscopynotes.com/
> 
> 
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