Go to http://github.com/toddstavish/puncta-analyzer and follow the following instructions for installing Puncta Analyzer

Install JDK

Install maven

Fork the puncta analyzer repo

Execute 'mvn compile' in project directory (where the pom.xml is located)

Create a 'PunctaAnalyzer' directory in the your ImageJ plugins directory

Copy all of the class files (bytecode) in target/classes to plugins/PunctaAnalyzer

Z-project images if necessary

Open an image in FIJI and use Ctrl+A to select all or select a specific region of interest

Run Puncta Analyzer using Analyze>Puncta Analyzer

Select Red channel and Green channel boxes to analyze those channels. Also select background subtraction for the red and green channels. Click set results file and save results and select a folder to save to.

Click OK with the default 50 pixel rolling ball radius for subtract background

Threshold the red channel using the slider

Click OK with the default 50 pixel rolling ball radius for subtract background

Threshold the red channel using the slider

Enter any desired restrictions on the analyze particles function such as a minimum pixel size.

Click yes to save result to file

Close all windows and proceed to the next image