Re: Problem regarding cell counting

Posted by SARAH ROSE STERLACE on Apr 24, 2014; 7:19pm
URL: http://imagej.273.s1.nabble.com/Problem-regarding-cell-counting-tp5007416p5007420.html

Thank you so much your reply! The macro works pretty well, but conservative
for the positive pictures, however, I also have neighboring regions (to
show the limited spread) that have no fluorescent neurons stained, but do
contain "dust." (or autofluorescence). It seems to recognize and
overestimate in these regions.  I have attached a picture of the
neighboring regions.  When I applied your macro, it came up with 38.
Any thoughts?
I am relatively new to Image J, so please let me know if this is because of
"user error."

thanks!



On Thu, Apr 24, 2014 at 11:15 AM, BioVoxxel <[hidden email]>wrote:

> Hi Sarah,
>
> You might try the following short macro:
>
> run("Subtract Background...", "rolling=100");
> run("Median...", "radius=12");
> run("Minimum...", "radius=8");
> run("Find Maxima...", "noise=2 output=[Count] exclude");
> run("Find Maxima...", "noise=2 output=[Point Selection] exclude");
> run("Revert");
>
> If your images are all similar, this might be able to recognize mist of
> your cells and count them.
>
> regards,
> Jan
>
>
> 2014-04-24 18:54 GMT+02:00 SARAH ROSE STERLACE <[hidden email]>:
>
> > Hello,
> > I am having trouble how to figure out a way to automatically count the
> GFP
> > stain without counting the background. I have been using the ITCN plugin,
> > but I cannot figure out how to have it just count the circles.  Any help
> > would be greatly appreciated.
> > I have been inverting the image, setting it to 8-bit and enhancing the
> > contrast by 3% to show the cells stained deeper in the tissue better to
> see
> > if that would help.  (i have not attached that image because it exceeds
> the
> > size for the email) I am attaching an original image. I have about 100
> > images to count, so if I could figure out how to automate the counting
> that
> > would be awesome!
> >
> > --
> > Sarah R Sterlace, C. Phil
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
>
>
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--
Sarah R Sterlace, C. Phil
my email address: [hidden email]

Behavioral Neuroscience
UCLA
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A225 Franz Hall
Los Angeles, CA 90095-1563

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