Reading Nd2 files [was: Re: Circle Detection in ImageJ]

[ctrueden]

Hi Papia,


> I have taken pictures on a Nikon, saved as an Nd2 file (with both
> different Z and channel data-sets). Which plugin is best for opening those
> on a Mac?


Download and install Fiji (Fiji Is Just ImageJ, http://fiji.sc/) which
comes with Bio-Formats preinstalled.

If you really want to use plain ImageJ, you can install Bio-Formats by
following the directions at:
    http://loci.wisc.edu/bio-formats/imagej

Also, be aware that ND2 is one of the most convoluted and difficult to
support formats out there. If you are able to save as anything else, it
might make your life easier.

-Curtis

P.S. In the future, it is best not to "hijack" unrelated threads by hitting
Reply, but rather to start a new thread with correct subject line.


On Tue, Jun 19, 2012 at 2:52 PM, Ghosh, Papia
<[hidden email]>wrote:

> Hi,
>
> I have taken pictures on a Nikon, saved as an Nd2 file (with both
> different Z and channel data-sets). Which plugin is best for opening those
> on a Mac? My goal is to merge individual images (say at z1 Gfp and z2
> DAPI). I see one for Windows and the link to the bioformats page for Mac
> http://loci.wisc.edu/software/bio-formats, but I'm not sure what file I
> should be down-loading. If I click on the Nd2 link it takes me to something
> that lists either the native or legacy version.
>
> Thanks in advance for any help.
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Benjamin Grant
> Sent: Friday, June 15, 2012 9:35 PM
> To: [hidden email]
> Subject: Re: Circle Detection in ImageJ
>
> The circular hough transform has been implemented in imagej, which is
> not the algorithm described in the paper so I apologize if this is
> irrelevant.  I can attest to the hough transform finding circles
> pretty reliably though
>
> http://rsbweb.nih.gov/ij/plugins/hough-circles.html
>
> if you're interested
> Ben
>
> On Fri, Jun 15, 2012 at 8:29 PM, David Webster <[hidden email]>
> wrote:
> > I could probably modify some existing ImageJ code that I have. How soon
> do
> > you need something? Hoe close does it need to be to the algorithm in the
> > paper?
> >
> > David Webster
> >
> > On Fri, Jun 15, 2012 at 7:53 AM, Jan Eglinger
> > <[hidden email]>wrote:
> >
> >> Dear all,
> >>
> >> can anyone tell me if the Fast Circle Detection (FCD) described in this
> >> paper:
> >>
> >> Fast circle detection using gradient pair vectors (2003)
> >> by Ali Ajdari Rad , Karim Faez , Navid Qaragozlou
> >> http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.121.9956
> >>
> >> or a similar algorithm has been implemented as an ImageJ plugin yet?
> >>
> >> Thx,
> >> Jan
> >>
> >> --
> >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >>
> >
> > --
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