Counting fluorescent cells (from a Image J newbie)

Posted by Denise Johnson on Sep 04, 2008; 5:33pm
URL: http://imagej.273.s1.nabble.com/Counting-fluorescent-cells-from-a-Image-J-newbie-tp3695173.html

Hi all,

I want to be able to take an image of fluorescent cells and use Image J to
get a cell count. The cell counter plugin is not what I’m looking for
since it only keeps a tally of counts after you click on cells one by one.
I want a more automated version of this, where I only have to pull up the
image and press a button for it to count what is there.

This is kind of tricky because my cells “glow” (from calcein-AM or
ethidium) in the image making it hard for the software to "see", I guess
(remember I'm new to Image J). After playing with the software, this it
what I've come up with:

1. I realized that I had to convert the image to a colorized one using the
software (used the LUT tools to color the cells with an opaque color of my
choice).

2. I then "thresholded my image" to exclude everything but the colored
cells, and then asked the software to analyze particles.

In this scenario, I don’t get cell counts, but the percent area the cells
take up.

What am I doing wrong? Can Image J do what I'm asking for?

Denise