// Measures the mitochondrial morphology of mitochondrial particles in a cell by measuring the area/perimeter ratios[F9]" 
macro "Measure mitochondrial Morphology [F9]" 
{
open();

run("Set Measurements...", "area integrated limit display redirect=None decimal=3");

run("RGB Split");
close();
run("Set Measurements...", "area integrated limit display redirect=None decimal=3");
setTool(2);
 macro "Process RGB Image [F10]"
{
  run("Copy");
  run("Duplicate...","\n");
  run("Paste");
  run("Invert");
  run("Sharpen");
setAutoThreshold();
}
 //run("Threshold...");
 macro "Measure Mitochondria [F11]"
{ 
run("Set Measurements...", "area perimeter circularity redirect=None decimal=2" );
run("Analyze Particles...", "minimum=30 maximum=100000 bins=100 show=Outlines display summarize");
  
for (i=0; i<nResults; i++){
	MP+= getResult('Perim.',i);
                   MA +=getResult('Area', i);
                     MC +=getResult('Circ.', i);
 }

wait(1000);
  s = getString("Are you OK with the outlines of mitochondria in neurons? [y/n+comment]","n");
  if (fromCharCode(charCodeAt(s,0)) == "N") 
    exit;  // Have to start over and fix Macro to fit the right outlines of most cells

else {
AMP= (MP/i);
AMA= (MA/i);
AMC= (MC/i);
Rmorph= (AMA/AMP); // Measures the area perimeter ratio of mitochondria
print(getTitle());  print("Count:" +i); print("Total Area Mitos:" +MA); print("Perimeter Mitos:"+MP); print("Circularity mitos:"+MC); print ("Avg. Perimeter:" +AMP); print ("Avg. Area:" + AMA); print ("Avg. Circularity:"+ AMC); print ("Area/Perim:"+ Rmorph);        
selectWindow("Results");
selectWindow("Log");
}

 for (i=0; i<25; i++){
 s = getString("Do you want to analyze another cell in the same field? [y/n+comment]","n");
  if (fromCharCode(charCodeAt(s,0)) == "n") 
     exit;   // end of program, updated on May 15-2007

else {
 
macro "Process RGB Image [F10]"
{
  run("Clear Results");
  resetThreshold();
  run("Copy");
  run("Duplicate...","\n");
  run("Paste");
  run("Invert");
  run("Sharpen");
setAutoThreshold();
 //run("Threshold...");
}
macro "Measure Mitochondria [F11]"
{ 
run("Set Measurements...", "area perimeter circularity redirect=None decimal=2" );
run("Analyze Particles...", "minimum=30 maximum=100000 bins=100 show=Outlines display summarize");
  
for (i=0; i<nResults; i++){
	MP+= getResult('Perim.',i);
                   MA +=getResult('Area', i);
                     MC +=getResult('Circ.', i);
 }

wait(1000);
  s = getString("Are you OK with the outlines of mitochondria in neurons? [y/n+comment]","n");
  if (fromCharCode(charCodeAt(s,0)) == "N") 
    exit;  // Have to start over and fix Macro to fit the right outlines of most cells
     //Closes all windows except your results which you can transfer to Excel
else {
AMP= (MP/i);
AMA= (MA/i);
AMC= (MC/i);
Rmorph= (AMA/AMP); // Measures the area perimeter ratio of mitochondria
print(getTitle());  print("Count:" +i); print("Total Area Mitos:" +MA); print("Perimeter Mitos:"+MP); print("Circularity mitos:"+MC); print ("Avg. Perimeter:" +AMP); print ("Avg. Area:" + AMA); print ("Avg. Circularity:"+ AMC); print ("Area/Perim:"+ Rmorph);        
selectWindow("Results");
selectWindow("Log");

 macro "Close All Windows [F4]" { 
      while (nImages>0) { 
          selectImage(nImages); 
          close(); 
      } 
}
}
}