[ome-users] Fwd: .ND2 reader in BioFormats

[Melissa Linkert]

Hi Christophe,

> I am using Bio-Formats 5.0.4 indeed. Have tried from a vanilla IJ1 install
> (as suggested on the IJ mailing list) but I see the same memory usage
> pattern : some saw-teeth usage around 100MB, then using ~3 times the stack
> size (still reading the header), then if I don't max out memory at this
> stage it starts reading planes up to ~1x stack size memory usage and
> opening.
> 
> These are 1-channel streamed stacks from an N-STORM acquisition under NIS
> Elements 4.2, with between 50,000 and 120,000 256x256 16-bit images. As
> regards Bio-Formats import options, everything is unchecked and I ask for a
> regular ImageJ stack as output.

Thank you for uploading an example file, and my apologies for not
getting back to you sooner.

The problem was indeed related to the number of images in the file; we
now have a fix under review:

http://github.com/openmicroscopy/bioformats/pull/1351

I would expect this fix to be included in 5.1.0, but if you wish to try
it in advance, then these builds can be used (once the above pull
request shows as being merged):

http://ci.openmicroscopy.org/view/Bio-Formats/job/BIOFORMATS-5.1-latest/lastSuccessfulBuild/artifact/artifacts

Regards,
-Melissa

On Tue, Sep 09, 2014 at 11:48:03AM +0200, Christophe Leterrier wrote:
> Hi Melissa,
> 
> I am using Bio-Formats 5.0.4 indeed. Have tried from a vanilla IJ1 install
> (as suggested on the IJ mailing list) but I see the same memory usage
> pattern : some saw-teeth usage around 100MB, then using ~3 times the stack
> size (still reading the header), then if I don't max out memory at this
> stage it starts reading planes up to ~1x stack size memory usage and
> opening.
> 
> These are 1-channel streamed stacks from an N-STORM acquisition under NIS
> Elements 4.2, with between 50,000 and 120,000 256x256 16-bit images. As
> regards Bio-Formats import options, everything is unchecked and I ask for a
> regular ImageJ stack as output.
> 
> Thanks for your help,
> 
> Christophe
> 
> 2014-09-08 23:44 GMT+02:00 Melissa Linkert <melissa at glencoesoftware.com>:
> 
> > Hi Christophe,
> >
> > > I'm trying to open a big Nikon .nd2 files in Fiji using Bio-Formats (not
> > > the new SciFiIO) in Fiji, Windows 7 64 bits, 64GB RAM. The "Reading file
> > > header part" usually peaks well above the actual file size with 17.6 GB
> > (on
> > > ImageJ memory monitor) for a 6.3 GB nd2 file. For a 15.9 GB file, it
> > maxes
> > > out the 60 GB allocated to Fiji. As it is the header reading part, it
> > does
> > > not make a difference to try to open as a virtual stack or not.
> >
> > Thank you for the bug report.  Could you please confirm which version of
> > Bio-Formats you're using?  Using 5.0.4, we've been able to initialize 8.5
> > GB
> > files with <1GB of RAM, so if you're using an older version then
> > upgrading may solve the problem.
> >
> > If you see the same behavior with 5.0.4, which options are selected in
> > the "Bio-Formats Import Options" window?
> >
> > Regards,
> > -Melissa
> >
> > On Mon, Sep 08, 2014 at 12:00:48PM +0200, Christophe Leterrier wrote:
> > > I have a question regarding Bio-Formats regarding memory use of Nikon
> > .nd2
> > > files, and Curtis Rueden advised me to post it here rather than on the
> > > ImageJ mailing list.
> > >
> > > thanks for your help,
> > >
> > > --
> > > Christophe Leterrier
> > > Chercheur
> > > Equipe Architecture des Domaines Axonaux
> > > CRN2M CNRS UMR 7286 - Aix Marseille Université
> > >
> > > ---------- Forwarded message ----------
> > > From: Christophe Leterrier <christophe.leterrier at gmail.com>
> > > Date: 2014-09-05 16:42 GMT+02:00
> > > Subject: .ND2 reader in BioFormats
> > > To: ImageJ Mailing List <imagej at list.nih.gov>
> > >
> > >
> > > Hi,
> > >
> > > This is primarily a Bio-Formats question.
> > >
> > > I'm trying to open a big Nikon .nd2 files in Fiji using Bio-Formats (not
> > > the new SciFiIO) in Fiji, Windows 7 64 bits, 64GB RAM. The "Reading file
> > > header part" usually peaks well above the actual file size with 17.6 GB
> > (on
> > > ImageJ memory monitor) for a 6.3 GB nd2 file. For a 15.9 GB file, it
> > maxes
> > > out the 60 GB allocated to Fiji. As it is the header reading part, it
> > does
> > > not make a difference to try to open as a virtual stack or not.
> > >
> > > Is this a known situation? What are my options for opening these files?
> > >
> > > Thanks for your help,
> > >
> > > Christophe
> >
> > > _______________________________________________
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> > > ome-users at lists.openmicroscopy.org.uk
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> >
> >