Re: Count cells in stack?

Posted by simon andrews (BI) on Apr 14, 2008; 9:44am
URL: http://imagej.273.s1.nabble.com/Count-cells-in-stack-tp3695075p3695081.html

On 11 Apr 2008, at 19:54, Mike Myerburg 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.

I've got a plugin which detects objects in 3D which might work for  
this purpose.  It's designed to measure 3D distances between objects,  
but should be able to be used to simply count objects if that's all  
you wanted to do.  It doesn't have any special facility for  
identifying nuclei but just builds features out of groups of voxels  
which are sufficiently bright.

It's not quite yet at a stage where I'm ready to make a public  
release, but if you want to try it send me a mail off list and I'll  
send you a copy.  If you want to you can send me an example image  
stack and I can run the plugin on it here to see if I can get it to  
do what you want.

TTFN

Simon.