// Generic multiple colour macro for assisting setting of thresholds
// Analyses pixel intensities along a line selection
// for a series of greyscale slices in a stack, each corresponding to a colour channel
// Expandable to any number of colour channels (slices)

// Check for RGB image and convert to greyscale stack
// Breaks if image name includes "(RGB)"
image = getImageID(); selectImage(image); info = getInfo(); 
if (indexOf(info, "(RGB)") >1) {
	getLine(x1,y1,x2,y2,width);
	run("RGB Split");
	run("Convert Images to Stack");
	makeLine(x1,y1,x2,y2);}

Greyscales = 255; if (indexOf(info, "pixel: 16")>1) {Greyscales = 65535;}

setLineWidth(1);
getLine(startx, starty, endx, endy, temp);
stack = getImageID();

selectImage(stack); slices = nSlices();

for (i =0; i<slices; i++) {
	selectImage(stack);
	slice = "slice="+(i+1);
	run("Set Slice...", slice);
	ydata = getProfile();
        	Plot.create(slice, "pixels", "intensity");
        	Plot.setLimits(0, ydata.length, 0, Greyscales);
        	Plot.setLineWidth(1);
	Plot.setColor("red");
	Plot.add("line", ydata);
	Plot.show();
	}