// First version of Cell Count Apoptosis macro for Image J version 1.42 and higher.
macro "Measure Cell Number and Apoptosis Based on Nuclear Area open image [F9]" 
{
  requires("1.33j"); // setFont() added in 1.33j
  newImage("Welcome Frame", "RGB white", 550, 100, 1);

  setColor(0, 0, 0);
  x=50; y=20;

  setFont("SansSerif" , 16, "bold");
  y += 30;
  setColor(0, 0, 255);
  drawString("Welcome to the ImageJ Cell Count/Apoptosis Marcro by Ruben K. Dagda" x, y);

open();
print ("press F8= processes image for ensuing quantifications");
print ("press F7= quantify both cell  number and apoptosis using DAPI")
print ("press F4= closes all unused windows");
print(getTitle());  print("Warning: Make sure that you use only the DAPI channel (10X images only) in RGB mode before proceeding");
}
macro "Process DAPI Image [F8]"
{ 
  run("Clear Results");

run("Color Threshold...", "Thresholding method=Yen");
 
}

{
   macro "Measure [F7]" { 
	run("Clear Results");
	run("Set Measurements...", "area circularity   redirect=None decimal=3");
	run("Analyze Particles...", "size=30-10000 show=Ellipses display clear summarize list"); 
        for (i=0; i<nResults; i++){MA += getResult('Area', i);
}
run("Distribution...", "parameter=Area or=1 and=30-160");
A=(getResult('Area distribution Count')/i)*100;

print(getTitle());  print( "count:" +i);  
selectWindow("Summary");
selectWindow("Results");
selectWindow("Log");
}
 macro "Close All Windows [F4]" { 
      while (nImages>0) { 
          selectImage(nImages); 
          close(); 
      } 
     //Closes all windows except your results which you can transfer to Excel
}

}