//Returns an array of indexes of ROIs that match  
 //the given regular expression 
 //
 function findRoisWithName(roiName) {
 nR = roiManager("Count");
 roiIdx = newArray(nR); 
k=0;
 clippedIdx = newArray(0);
 for (r=0; r<nR; r++) {
 roiManager("Select", r);
 rName = Roi.getName();
 if (endsWith(rName, roiName) ) {
 roiIdx[k] = r; k++;
 } } 
if (k>0) {
 clippedIdx = Array.trim(roiIdx,k); 
} 
return clippedIdx;
 };

 function countRoisWithName(roiName) {
 nR = roiManager("Count");
 roiIdx = newArray(nR); 
k=0;
 clippedIdx = newArray(0);
 for (r=0; r<nR; r++) {
 roiManager("Select", r);
 rName = Roi.getName();
 if (endsWith(rName, roiName) ) {
 roiIdx[k] = r; k++;
 } } 

return k;
 };
 if (isOpen("Cell counts"))
;
  else {run("Table...", "name=[Cell counts] width=800 height=600");
     print("[Cell counts]", "\\Headings:Group\	Image\	Genes\	Counts\	Total\	ClassColor");}

    
run("Set Measurements...", "area integrated area_fraction limit display redirect=None decimal=2");
trgroup=getString("Which group are you measuring?","Control monkey");
showMessage("In the next dialog select the file with the RoI set!");
            open();
        ChannelNum= getNumber("How many channels will be counted (2 or 3)?",3);
              if (ChannelNum != 3 && ChannelNum != 2) {
              	exit("This macro is meant to run only on two or three channels!");
              };
              criterion= getString("What measurement will you use to identify a positive cell?","%Area");
              if (criterion != "%Area" && criterion != "Area") {
              	exit("You must chose between %Area and Area!");
              };
              
            geneonename = getString ("What gene/antigen is recorded in the first channel?", "");
       		showMessage("In the next dialog select the "+geneonename+"-image!");
       		open();
       		setAutoThreshold("Triangle dark");
       		filename=getTitle();
       		rename(geneonename); 
       		w=getWidth();
            h=getHeight();
            critsizech1=getNumber("What is the minimum size of the selected measurement that identifies a positive cell in the"+geneonename+"-channel?",2);
            mboundarych1=getNumber("Select the number of scaled units (e.g. mkm) to enlarge nucleus boundary for measurement in the"+geneonename+"-channel?",2);

			newImage("Classified_nuclei_"+filename, "8-bit white",w,h,1);
       		genetwoname = getString ("What gene/antigen is recorded in the second channel?", "");
       		showMessage("In the next dialog select the "+genetwoname+"-image!");
       		open();
       		setAutoThreshold("Triangle dark");
       		rename(genetwoname); 
       		        critsizech2=getNumber("What is the minimum size of the selected measurement that identifies a positive cell in the"+genetwoname+"-channel?",2);
            mboundarych2=getNumber("Select the number of scaled units (e.g. mkm) to enlarge nucleus boundary for measurement in the"+genetwoname+"-channel?",2);

       if (ChannelNum == 3) {
       		
       		genethreename = getString ("What gene/antigen is recorded in the third channel?", "");
       		showMessage("In the next dialog select the "+genethreename+"-image!");
       		open();
       		setAutoThreshold("Triangle dark");
       		rename(genethreename); 		
       		critsizech3=getNumber("What is the minimum size of the selected measurement that identifies a positive cell in the"+genethreename+"-channel?",2);
            mboundarych3=getNumber("Select the number of scaled units (e.g. mkm) to enlarge nucleus boundary for measurement in the"+genethreename+"-channel?",2);

       		n = roiManager("count");
			total=n;					
								for (j=0; j<n; j++) {
								selectImage(geneonename);
								//setAutoThreshold("Otsu dark");
								roiManager("select", j);
							run("Enlarge...", "enlarge=&mboundarych1");
								run("Measure");
								a= getResult(criterion);
								selectImage(genetwoname);
								//setAutoThreshold("Otsu dark");
								roiManager("select", j);
								run("Enlarge...", "enlarge=&mboundarych2");
								run("Measure");
								b= getResult(criterion);
								selectWindow(genethreename);
								//setAutoThreshold("Otsu dark");
								roiManager("select", j);
							run("Enlarge...", "enlarge=&mboundarych3");
								run("Measure");
								c= getResult(criterion);
	if (a<critsizech1) {if (b<critsizech2) {if (c<critsizech3) {roiManager("rename", j+":negative");}
			else {roiManager("rename", j+":"+genethreename);}}
 		else 	{if (c<critsizech3) {roiManager("rename", j+":"+genetwoname);}
		else {roiManager("rename", j+":double_"+genetwoname+"+"+genethreename);}}}
	else {	if (b<critsizech2) {if (c<critsizech3) {roiManager("rename", j+":"+geneonename);}
								else {roiManager("rename", j+":double_"+geneonename+"+"+genethreename);}}
		   else  {if (c<critsizech3) {roiManager("rename", j+":double_"+geneonename+"+"+genetwoname)}
		   						else {roiManager("rename",  j+":triple_"+geneonename+"+"+genetwoname+"+"+genethreename);}}};
								};
 									
 neg = findRoisWithName(":negative");
 g1=findRoisWithName(":"+geneonename);	
 g2=findRoisWithName(":"+genetwoname);
 g3=findRoisWithName(":"+genethreename);
 g12=findRoisWithName(":double_"+geneonename+"+"+genetwoname);
 g13=findRoisWithName(":double_"+geneonename+"+"+genethreename);
 g23=findRoisWithName(":double_"+genetwoname+"+"+genethreename);
 g123=findRoisWithName(":triple_"+geneonename+"+"+genetwoname+"+"+genethreename);

if (lengthOf(neg)>0 ) { 								
roiManager("select", neg);//draw negative
setForegroundColor(0, 0, 0);
selectWindow("Classified_nuclei_"+filename);
roiManager("Fill");}


if (lengthOf(g1)>0 ) {
roiManager("select", g1);//draw gene1
setForegroundColor(20, 20, 20); 
selectWindow("Classified_nuclei_"+filename);
roiManager("Fill");}


if (lengthOf(g2)>0 ) {
roiManager("select", g2);//draw gene2
setForegroundColor(53, 53, 53); 
selectWindow("Classified_nuclei_"+filename);
roiManager("Fill");}


if (lengthOf(g3)>0 ) {
roiManager("select",g3 );//draw gene3
setForegroundColor(119, 119, 119); //gene3
selectWindow("Classified_nuclei_"+filename);
roiManager("Fill");}


if (lengthOf(g12)>0 ) {
roiManager("select", g12);//draw gene1&gene2
setForegroundColor(73, 73, 73); //gene1&gene2
selectWindow("Classified_nuclei_"+filename);
roiManager("Fill");}

if (lengthOf(g13)>0 ) {
roiManager("select",g13 );//draw gene1&gene3
setForegroundColor(139, 139, 139); //gene1&gene3
selectWindow("Classified_nuclei_"+filename);
roiManager("Fill");}

if (lengthOf(g23)>0 ) {
roiManager("select", g23);//draw gene2&gene3
setForegroundColor(169, 169, 169); //gene2&gene3
selectWindow("Classified_nuclei_"+filename);
roiManager("Fill");}


if (lengthOf(g123)>0 ) {
roiManager("select", g123);//draw gene1&gene2&gene3
 setForegroundColor(192, 192, 192); //gene1&gene2&gene3
selectWindow("Classified_nuclei_"+filename);
roiManager("Fill");}


//print ("Group","	","Image","	","negative", "	",geneonename+"-only","	",genetwoname+"-only","	",genethreename+"-only","	",geneonename +" and "+genetwoname,"	",geneonename+" and "+genethreename,"	",genetwoname+" and "+genethreename,"	",geneonename+" and "+genetwoname+" and "+genethreename);
negativecount = countRoisWithName(":negative");
gene1count = countRoisWithName(":"+geneonename);
gene2count = countRoisWithName(":"+genetwoname);
gene3count = countRoisWithName(":"+genethreename);
gene1and2count = countRoisWithName(":double_"+geneonename+"+"+genetwoname);
gene1and3count = countRoisWithName(":double_"+geneonename+"+"+genethreename);
gene2and3count = countRoisWithName(":double_"+genetwoname+"+"+genethreename);
gene1and2and3count = countRoisWithName(":triple_"+geneonename+"+"+genetwoname+"+"+genethreename);
//print (trgroup,"	",filename,"	",negativecount,"	",gene1count,"	",gene2count,"	",gene3count,"	",gene1and2count,"	",gene1and3count,"	",gene2and3count,"	",gene1and2and3count);
print("[Cell counts]", trgroup+ "	"+filename+"	"+"negative	"+negativecount+"	"+total+"	"+ 0);
print("[Cell counts]", trgroup+ "	"+filename+"	"+geneonename+"	"+gene1count+"	"+total+"	"+ 20);
print("[Cell counts]", trgroup+ "	"+filename+"	"+genetwoname+"	"+gene2count+"	"+total+"	"+ 53);
print("[Cell counts]", trgroup+ "	"+filename+"	"+genethreename+"	"+gene3count+"	"+total+"	"+ 119);
print("[Cell counts]", trgroup+ "	"+filename+"	"+geneonename+"+"+genetwoname+"	"+gene1and2count+"	"+total+"	"+ 73);
print("[Cell counts]", trgroup+ "	"+filename+"	"+geneonename+"+"+genethreename+"	"+gene1and3count+"	"+total+"	"+ 139);
print("[Cell counts]", trgroup+ "	"+filename+"	"+genetwoname+"+"+genethreename+"	"+gene2and3count+"	"+total+"	"+ 169);
print("[Cell counts]", trgroup+ "	"+filename+"	"+geneonename+"+"+genetwoname+"+"+genethreename+"	"+gene1and2and3count+"	"+total+"	"+ 192);
    exit ("Classification&Counting finished!");
    };
       		
				n = roiManager("count");
				total=n;
								for (j=0; j<n; j++) {
								selectWindow(geneonename);
								//setAutoThreshold("Otsu dark");
								roiManager("select", j);
								run("Enlarge...", "enlarge=&mboundarych1");
								run("Measure");
								a= getResult(criterion);
								selectWindow(genetwoname);
								//setAutoThreshold("Otsu dark");
								roiManager("select", j);
								run("Enlarge...", "enlarge=&mboundarych2");
								run("Measure");
								b= getResult(criterion);
								
if (a<critsizech1) 
			{if (b<critsizech2) {roiManager("rename", j+":negative");}
				else {roiManager("rename", j+":"+genetwoname);}}
 else 	{if (b<critsizech2) {roiManager("rename", j+":"+geneonename);}
				else {roiManager("rename", j+":double_"+geneonename+"+"+genetwoname);}}; 
								};
 neg = findRoisWithName(":negative");
 g1=findRoisWithName(":"+geneonename);	
 g2=findRoisWithName(":"+genetwoname);
 g12=findRoisWithName(":double_"+geneonename+"+"+genetwoname);


if (lengthOf(neg)>0 ) { 						
roiManager("select", neg);//draw negative
setForegroundColor(0, 0, 0); 
selectWindow("Classified_nuclei_"+filename);
roiManager("fill");}

if (lengthOf(g1)>0 ) {
roiManager("select", g1);//draw gene1
setForegroundColor(20, 20, 20); 
selectWindow("Classified_nuclei_"+filename);
roiManager("Fill");}

if (lengthOf(g2)>0 ) {
roiManager("select", g2);//draw gene2
setForegroundColor(53, 53, 53); 
selectWindow("Classified_nuclei_"+filename);
roiManager("Fill");}

if (lengthOf(g12)>0 ) {
roiManager("select",g12 );//draw gene1&gene2
setForegroundColor(73, 73, 73); //gene1&gene2
selectWindow("Classified_nuclei_"+filename);
roiManager("Fill");}

//print ("Group","	","Image","	","negative", "	",geneonename+"-only","	",genetwoname+"-only","	",genethreename+"-only","	",geneonename +" and "+genetwoname,"	",geneonename+" and "+genethreename,"	",genetwoname+" and "+genethreename,"	",geneonename+" and "+genetwoname+" and "+genethreename);
negativecount = countRoisWithName(":negative");
gene1count = countRoisWithName(":"+geneonename);
gene2count = countRoisWithName(":"+genetwoname);
gene1and2count = countRoisWithName(":double_"+geneonename+"+"+genetwoname);			
//print (trgroup,"	",filename,"	",negativecount,"	",gene1count,"	",gene2count,"	","NA","	",gene1and2count,"	","NA","	","NA","	","NA");
 print("[Cell counts]", trgroup+ "	"+filename+"	"+"negative	"+negativecount+"	"+total+"	"+ 0);
print("[Cell counts]", trgroup+ "	"+filename+"	"+geneonename+"	"+gene1count+"	"+total+"	"+ 20);
print("[Cell counts]", trgroup+ "	"+filename+"	"+genetwoname+"	"+gene2count+"	"+total+"	"+ 53);
print("[Cell counts]", trgroup+ "	"+filename+"	"+geneonename+"+"+genetwoname+"	"+gene1and2count+"	"+total+"	"+ 73);

 
 exit ("Classification&Counting finished!");
 ///       setBatchMode(true);

  
        


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