Counting fluorescent cells (from a Image J newbie)

[Denise Johnson]

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

[Sami Badawi-2]

Hi Denise,

When you run ImageJ's particle analyzer you get a report over
properties of all the particles, so the number of particles is just
the number of rows in the report.

The ShapeLogic plugin comes with a particle counter and a color
particle analyzer in that works directly on color images, but only if
either the foreground or the background are relatively uniform in
color and the particles are spatially separated.  Here is a
description: http://www.shapelogic.org/particle.html

-Sami Badawi
http://www.shapelogic.org

On Thu, Sep 4, 2008 at 1:33 PM, Denise Johnson <[hidden email]> wrote:

> 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
>