Re: Count cells in stack?

Posted by Fernando Sales on Apr 15, 2008; 5:48pm
URL: http://imagej.273.s1.nabble.com/Count-cells-in-stack-tp3695075p3695076.html

Mike,

if you have a program that segments and identify the cells in each slice of
the stack, you can generate a binary mask and count the number of "islands"
of white pixels (suppose that the cells are white and the backgroung is
black). I've developed a plugin which implements a labelling algorithm to
identify different objects in a binary scene. Then, this way you can count
the number of cells slice by slice.

Cheers,
Fernando
On Fri, Apr 11, 2008 at 3:54 PM, Mike Myerburg <[hidden email]> wrote:

> Hi-
>
> I study polarized cells that form a pseudostratified epithelial layer on
> filters.  I am trying to make a plugin that will count the # of nuclei
> present in a stack.  Because the cells are not a monolayer, I cannot
> accurately count them by making an zprojection and then do standard
> automated counting (the nuclei are occasionally on top of each other). It
> seems that it "should" be possible to make a plugin to analyze the nuclei in
> 3D and then count the number within a stack.
>
> Has something like this already been made?  Any suggestions?
>
> Cheers, Mike
>

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Fernando José Ribeiro Sales
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