.ND2 reader in BioFormats
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Hi,
This is primarily a BioFormat question. I'm trying to open a big Nikon .nd2 files in Fiji using BioFormats (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 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Have you tried standard IJ1 plus bioformats? It always seems to work
better than FIJI/IJ2 in my experience. Cheers Rich On 05/09/14 15:42, Christophe Leterrier wrote: > Hi, > > This is primarily a BioFormat question. > > I'm trying to open a big Nikon .nd2 files in Fiji using BioFormats (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 > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- Dr Richard Mort MRC Human Genetics Unit MRC IGMM University of Edinburgh Western General Hospital Crewe Road Edinburgh. EH4 2XU, UK Tel: +44 (0)131 332 2471 Fax: +44 (0)131 467 8456 The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Rich,
> Have you tried standard IJ1 plus bioformats? > It always seems to work better than FIJI/IJ2 > in my experience. Sorry to hear that. The ImageJ2 team would appreciate issue reports regarding any specific behavior of ImageJ2 and/or Fiji that does not work as well as vanilla ImageJ1. Regards, Curtis On Sep 5, 2014 10:03 AM, "Richard Mort" <[hidden email]> wrote: > Have you tried standard IJ1 plus bioformats? It always seems to work > better than FIJI/IJ2 in my experience. > Cheers > Rich > > On 05/09/14 15:42, Christophe Leterrier wrote: > >> Hi, >> >> This is primarily a BioFormat question. >> >> I'm trying to open a big Nikon .nd2 files in Fiji using BioFormats (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 >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> >> > -- > Dr Richard Mort > MRC Human Genetics Unit > MRC IGMM > University of Edinburgh > Western General Hospital > Crewe Road > Edinburgh. > EH4 2XU, UK > > Tel: +44 (0)131 332 2471 > Fax: +44 (0)131 467 8456 > > > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by lechristophe
Hi Christophe,
> This is primarily a BioFormat question. The best place for Bio-Formats questions is the ome-users mailing list. Regards, Curtis On Sep 5, 2014 9:52 AM, "Christophe Leterrier" < [hidden email]> wrote: > Hi, > > This is primarily a BioFormat question. > > I'm trying to open a big Nikon .nd2 files in Fiji using BioFormats (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 > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by Richard Mort-2
Hi Christophe,
You can also go through the Bio-Formats bug reporting process <http://www.openmicroscopy.org/site/support/bio-formats5/about/bug-reporting.html>. If is a previously unknown bug, the Bio-Formats developers might ask you to upload a sample dataset demonstrating this issue for them to analyze. Regards, Mark On Fri, Sep 5, 2014 at 10:01 AM, Richard Mort <[hidden email]> wrote: > Have you tried standard IJ1 plus bioformats? It always seems to work > better than FIJI/IJ2 in my experience. > Cheers > Rich > > > On 05/09/14 15:42, Christophe Leterrier wrote: > >> Hi, >> >> This is primarily a BioFormat question. >> >> I'm trying to open a big Nikon .nd2 files in Fiji using BioFormats (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 >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> >> > -- > Dr Richard Mort > MRC Human Genetics Unit > MRC IGMM > University of Edinburgh > Western General Hospital > Crewe Road > Edinburgh. > EH4 2XU, UK > > Tel: +44 (0)131 332 2471 > Fax: +44 (0)131 467 8456 > > > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by ctrueden
Hi Curtis,
I have forwarded my question to the ome-users list, thanks for the tip. The last part about strategies other than Bio-Formats to open/convert .nd2 files in ImageJ is an ImageJ question though. I have found a mention of this plugin on the .nd2 page of Bio-Formats: http://rsbweb.nih.gov/ij/plugins/nd2-reader.html Best Regards, Christophe 2014-09-05 17:16 GMT+02:00 Curtis Rueden <[hidden email]>: > Hi Christophe, > > > This is primarily a BioFormat question. > > The best place for Bio-Formats questions is the ome-users mailing list. > > Regards, > Curtis > On Sep 5, 2014 9:52 AM, "Christophe Leterrier" < > [hidden email]> wrote: > > > Hi, > > > > This is primarily a BioFormat question. > > > > I'm trying to open a big Nikon .nd2 files in Fiji using BioFormats (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 > > > > -- > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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