Counting nuclear foci - getting strange results

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Counting nuclear foci - getting strange results

Dimiter Prodanov-3
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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Re: Counting nuclear foci - getting strange results

jswalker
This post was updated on .
Hi Dmitri,

Thanks for your reply but I'm not sure I get what you mean about screen resolution. I have the image in question zoomed in as you can see, but that shouldn't affect anything.

My problem isn't that I'm missing nuclei, but that the rawintden values are misreporting (specifically, they are occasionally reporting WAY too many nuclei). Dilating the output mask would not help me in this case.

Thanks in advance for any help.