run("Colors...", "foreground=white background=black selection=yellow");
run("Options...", "iterations=1 black count=1");

//
// All image calculation using logical operators take zero values as zero and 255 as "one" in the case below
// So inverted luts only change black to white and white to black but zero stays zero meaning black was zero and after
// inverting the LUT white is now zero.
// Anything measured needs to have value 255
// So 255 or '1' is the object



// Required ImageJ version 
requires("1.43u");
// requires threshold colour RGBtoLAB
AssessFibrosis();

function AssessFibrosis() {

	
	exclude_high_th=72;
	lumen_low_th=240;
	fibrosis_high_th=130;
	name= getTitle
	image_name = File.name;
	OriginalImage = getImageID();
	run("Duplicate...", "title=total_area");
	
	// Obtain total area
	TotalArea = getImageID();
	selectImage(TotalArea);
	min=newArray(3);
        	max=newArray(3);
        	filter=newArray(3);
        	a=getTitle();
        	run("RGB Stack");
        	run("Convert Stack to Images");
        	selectWindow("Red");
        	rename("0");
        	selectWindow("Green");
        	rename("1");
        	selectWindow("Blue");
        	rename("2");
        	min[0]=0;
        	max[0]=250;
        	filter[0]="pass";
        	min[1]=0;
        	max[1]=250;
        	filter[1]="pass";
        	min[2]=0;
        	max[2]=250;
        	filter[2]="pass";
        	for (i=0;i<3;i++){
          	   selectWindow(""+i);
          	   setThreshold(min[i], max[i]);
          	   run("Make Binary", "thresholded remaining");
          	   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------------
       	 run("8-bit");

	//Now obtain fibrosis component
	selectImage(OriginalImage);
	run("Duplicate...", "title=fibrosis_area");
	FibrosisImage = getImageID();
	selectImage(FibrosisImage);
	min=newArray(3);
            max=newArray(3);
            filter=newArray(3);
	a=getTitle();
	run("RGBtoLab ");
	run("RGB Stack");
	run("Convert Stack to Images");
	selectWindow("Red");
	rename("0");
	selectWindow("Green");
	rename("1");
	selectWindow("Blue");
	rename("2");
	min[0]=0;
	max[0]=lumen_low_th-1;
	filter[0]="pass";
	min[1]=fibrosis_high_th;
	max[1]=255;
	filter[1]="pass";
	min[2]=0;
	max[2]=255;
	filter[2]="pass";
	for (i=0;i<3;i++){
  		selectWindow(""+i);
  		setThreshold(min[i], max[i]);
  		run("Make Binary", "thresholded remaining");
  		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------------
	run("8-bit");
	run("Set Measurements...", "area limit redirect=None decimal=3");
	selectImage("total_area");
        	// We need the size of the exclusion part
        	totarea=0;
        	run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00 show=Nothing clear");
        	for (i=0; i<nResults; i++) {
        		totarea = totarea + getResult("Area",i);
	// Fibrosis
	selectImage("fibrosis_area");
	totarea_fibrosis=0;
	run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00 show=Nothing clear");
	for (i=0; i<nResults; i++) {
		totarea_fibrosis = totarea_fibrosis+ getResult("Area",i);
	}
	run("Clear Results");
	setResult("Total area fibrosis (pixels) "+ name, 0, totarea_fibrosis);
	setResult("Total area of clot (pixels)" + name, 0, totarea);
	setResult("percent fibrosis (pixels)" +name,0, totarea_fibrosis/totarea);
        	updateResults();
        	selectWindow("Results" );
       	run("Text..."); // File>Save As>
	selectWindow("fibrosis_area");
	saveAs("Tiff..."); // File>Save As.\>
	selectWindow("total_area");
	saveAs("Tif...") // File>Save As.\>
	
	
}// End of macro