[ome-users] trouble opening .nd2 files

[Melissa Linkert]

Hi Pradeep,

Thank you for uploading example files.

> I downloaded the latest version of Fiji (Image J 1.48c). I was able to see
> thumbnails of the various series, but ran out of memory trying to open more
> than 4 (2-channel) slices (4X2) images.
> I also had to manually adjust the brightness and contrast settings for the
> images to be visible. I have attached a powepoint file showing one slice as
> opened by Image J/Fiji and the other z-slice with auto contrast and
> brightness (DAPI and DIC).
> 
> So this is definitely an improvement over the problem I had earlier but now
> I am running into memory and brightness/contrast issues.
> Is there anything you could suggest.

For the brightness/contrast, have you tried selecting the "Autoscale"
option in the "Bio-Formats Import Options" window when you open the
files?  I would expect that to solve the problem.

I was able to open all of the images in both files at once, with 2 GB of
memory allocated to Fiji.  Could you please check how much memory is
allocated ("Edit > Options > Memory & Threads..."), and if it is less
than 512 MB or so try increasing it?

Regards,
-Melissa

On Mon, Sep 16, 2013 at 03:48:21PM -0700, Pradeep Joshi wrote:
> Hi Melissa,
> 
> I downloaded the latest version of Fiji (Image J 1.48c). I was able to see
> thumbnails of the various series, but ran out of memory trying to open more
> than 4 (2-channel) slices (4X2) images.
> I also had to manually adjust the brightness and contrast settings for the
> images to be visible. I have attached a powepoint file showing one slice as
> opened by Image J/Fiji and the other z-slice with auto contrast and
> brightness (DAPI and DIC).
> 
> So this is definitely an improvement over the problem I had earlier but now
> I am running into memory and brightness/contrast issues.
> Is there anything you could suggest.
> 
> I have also uploaded the file and the corresponding deconvolved and cropped
> version
> 
> Thanks for your help
> Pradeep
> 
> "The known is finite, the unknown infinite. Intellectually we stand on an
> islet in the midst of an illimitable ocean of inexplicability. Our business
> every generation is to reclaim a little more land"- T.H. Huxley
> 
> Dr. Pradeep M. Joshi
> Neuroscience Research Institute
> University of California Santa Barbara
> Santa Barbara, CA 93106
> 
> Lab: 805 893 8090
> Cell: 805 680 1369
> 
> 
> 
> 
> 
> On Mon, Sep 16, 2013 at 10:09 AM, Melissa Linkert <
> melissa at glencoesoftware.com> wrote:
> 
> > Hi Pradeep,
> >
> > > I am trying to open .nd2 files in Bisque and am encountering following
> > > problems
> > > My two channel images (DIC and DAPI) are defaulting to green and red
> > false
> > > colors with no option of changing the colors.
> > > My deconvolved images are not displayed correctly. Please see attached
> > > screenshots.
> > >
> > > The images were collected on a Nikon T1 Eclipse running NIS Elements 4.
> > > Versions 4.10.01 Build 834
> >
> > Which version of Bio-Formats are you using?  If you are using something
> > prior to the current stable version (4.4.8), then I would suggest first
> > upgrading to see if that fixes the problem.
> >
> > If upgrading to 4.4.8 does not solve the problem, then it would be very
> > helpful if you could send one of the original .nd2 files.  Files can be
> > uploaded to http://qa.openmicroscopy.org.uk/qa/upload/
> >
> > Regards,
> > -Melissa
> >
> > On Mon, Sep 16, 2013 at 10:00:56AM -0700, Pradeep Joshi wrote:
> > > I am trying to open .nd2 files in Bisque and am encountering following
> > > problems
> > > My two channel images (DIC and DAPI) are defaulting to green and red
> > false
> > > colors with no option of changing the colors.
> > > My deconvolved images are not displayed correctly. Please see attached
> > > screenshots.
> > >
> > > The images were collected on a Nikon T1 Eclipse running NIS Elements 4.
> > > Versions 4.10.01 Build 834
> > >
> > > Please help.
> > >
> > > Best
> > > Pradeep
> > >
> > > "The known is finite, the unknown infinite. Intellectually we stand on an
> > > islet in the midst of an illimitable ocean of inexplicability. Our
> > business
> > > every generation is to reclaim a little more land"- T.H. Huxley
> > >
> > > Dr. Pradeep M. Joshi
> > > Neuroscience Research Institute
> > > University of California Santa Barbara
> > > Santa Barbara, CA 93106
> > >
> > > Lab: 805 893 8090
> > > Cell: 805 680 1369
> >
> >
> > > _______________________________________________
> > > ome-users mailing list
> > > ome-users at lists.openmicroscopy.org.uk
> > > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> >
> >