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

[Melissa Linkert]

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