tool for surrounding dots

[Johannes Breu]

I have confocal images of neurons with stained synaptic proteins. I am
looking for a tool that marks all dots beyond a defined intensity. I would
prefer doing so without thresholding before. I thought I could use  Analyze
Particle but there only threshold images are allowed. I would be happy if I
had an image where all the dots are surrounded so that I could do something
with this surronded (=activated) parts of the image. If I say "activated" I
mean I would like to be able to measure these activated zones or maybe
extract etc

Thanks Johannes

[Sami Badawi-2]

Hi Johannes,

The ShapeLogic plugin has a color particle analyzer that will do some
particle measurements. Chose ShapeLogic menu item "RGB Color Particle
Analyzer", and set the background color to 0, 0, 0. This should work
both on gray and RGB images.

http://www.shapelogic.org/particle.html
http://www.shapelogic.org/colocalization.html

Not sure ShapeLogic it will measure the things you are interested in.
Otherwise on June 26 2008 there were a thread on the ImageJ mailing
list called: "rgb measure", where Wayne Rasband had a very interesting
suggestion that you might be able to modify for your need:

http://article.gmane.org/gmane.comp.java.imagej/10890

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

On Mon, Nov 10, 2008 at 12:08 PM, J Breu <[hidden email]> wrote:

> I have confocal images of neurons with stained synaptic proteins. I am
> looking for a tool that marks all dots beyond a defined intensity. I would
> prefer doing so without thresholding before. I thought I could use  Analyze
> Particle but there only threshold images are allowed. I would be happy if I
> had an image where all the dots are surrounded so that I could do something
> with this surronded (=activated) parts of the image. If I say "activated" I
> mean I would like to be able to measure these activated zones or maybe
> extract etc
>
> Thanks Johannes
>