Counting nuclear foci - getting strange results

Posted by Dimiter Prodanov-3 on Aug 10, 2015; 7:33am
URL: http://imagej.273.s1.nabble.com/Counting-nuclear-foci-getting-strange-results-tp5013962.html

Hello,

It looks like an screen resolution problem.

Try dilating the output mask and see if you really miss nuclei.

best regards,

Dimiter Prodanov

On Mon, Aug 10, 2015 at 6:00 AM, IMAGEJ automatic digest system <
[hidden email]> wrote:

>
> ------------------------------
>
> Date:    Sun, 9 Aug 2015 14:17:41 -0700
> From:    jswalker <[hidden email]>
> Subject: Counting nuclear foci - getting strange results
>
> Hi all,
>
> I'm following the protocol outlined here:
> http://microscopy.duke.edu/HOWTO/countfoci.html
>
> And the commands I'm using are enclosed below.
>
> My problem is that I'm working on massive images (25k x 17k pixels) and
> sometimes I get accurate values but sometimes I get what I see below. Going
> by results table (and by RawIntDen/255 to get the actual number of nuclear
> foci), the cluster highlighted has around 60,000 nuclei! ...which is not
> the
> case as you can see by a quick visual examination.
>
> <http://imagej.1557.x6.nabble.com/file/n5013961/nuclear_foci.jpg>
>
> Any idea why this is or what I can do about it?
>
> I've tried re-binarizing the image in the step immediately before
> measuring.
> That didn't work. I get this problem whether I do the commands manually or
> whether I do it via the macro. Any other ideas?
>
> Thanks in advance.
>
>
>
>
>
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