//Appends the value to the array
//Returns the modified array
function appendToArray(value, array) {
    temparray=newArray(lengthOf(array)+1);
    for (i=0; i<lengthOf(array); i++) {
        temparray[i]=array[i];
    };
    temparray[lengthOf(temparray)-1]=value;
    array=temparray;
    filelist=array;
    return array;
};

function thresmeas() {
// Color Thresholder 1.50i
// Autogenerated macro, single images only!
min=newArray(3);
max=newArray(3);
filter=newArray(3);
a=getTitle();
run("HSB Stack");
run("Convert Stack to Images");
selectWindow("Hue");
rename("0");
selectWindow("Saturation");
rename("1");
selectWindow("Brightness");
rename("2");
min[0]=165;
max[0]=175;
filter[0]="pass";
min[1]=0;
max[1]=255;
filter[1]="pass";
min[2]=55;
max[2]=255;
filter[2]="pass";
for (i=0;i<3;i++){
  selectWindow(""+i);
  setThreshold(min[i], max[i]);
  run("Convert to Mask");
  if (filter[i]=="stop")  run("Invert");
}
imageCalculator("AND create", "0","1");
imageCalculator("AND create", "Result of 0","2");
for (i=0;i<3;i++){
  selectWindow(""+i);
  close();
}
selectWindow("Result of 0");
close();
selectWindow("Result of Result of 0");
rename(a);
// Colour Thresholding-------------
};

function countcells() {
run("Analyze Particles...", "size=300-Infinity pixel show=Nothing display clear summarize");
};

run("Set Measurements...", "area display redirect=None decimal=3");
resopen = isOpen("Results");
sumopen = isOpen("Summary");
if (resopen == 1) {
selectWindow("Results");
run("Close");
};
if (sumopen == 1) {
selectWindow("Summary");
run("Close");
};

var filelist;
name = getTitle;
path=getDirectory("image");
list=getFileList(path); 
filelist = newArray();
selectWindow(name);
close();

for(i=0;i<list.length;i++) {
	name = list[i];
	filetype = endsWith(name,".tif");
	fluotype = endsWith (name,"C001.tif");
	if (filetype == 1 && fluotype == 1) {
		appendToArray(name, filelist);
	};
};

for(i=0;i<filelist.length;i++) {
	open(path+filelist[i]);
	thresmeas();
	countcells();
	selectWindow(filelist[i]);
	close();
};
selectWindow("Summary");