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

[Christophe Leterrier]

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
>
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>
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