setTool("polyline");
waitForUser("Draw a line along the shaft of the dendrite. Change Line Width as needed to cover dendrite."); 
//get current positions and return later
getDisplayedArea(x, y, dwidth, dheight);  
getSelectionCoordinates(xp, yp);//save selected area
Stack.getPosition(channel, slice, frame);// - Returns the current position. 
print(channel, slice, frame);
zoom=getZoom();
// get mean in each channel for branch 
if (selectionType==-1) 
      exit("Area selection required"); 

Stack.setChannel(1);    
getStatistics(area, ch1Mean, min, max, std, histogram);
print(ch1Mean+" ch1 Mean");

Stack.setChannel(2);    
getStatistics(area, ch2Mean, min, max, std, histogram); 
print(ch2Mean+" ch2 Mean");

Stack.setChannel(3);    
getStatistics(area, ch3Mean, min, max, std, histogram);
print(ch3Mean+" ch3 Mean");
  
print(ch1Mean/ch2Mean+" Ch1:Ch2 ratio");
print(ch1Mean/ch3Mean+" Ch2:Ch3 ratio");

origTitle=getTitle();

//if exists delete the normalized channel
//Stack.getDimensions(width, height, channels, slices, frames) ;
//if (channels>3){
//	Stack.setChannel(5);
//	run("Delete Slice", "delete=channel");

//		Stack.setChannel(4);
//	run("Delete Slice", "delete=channel");
//}

Stack.getDimensions(width, height, channels, slices, frames) ;
//if(bitDepth()!=16 ||  channels==3){
//The below is for a first run case. ObjectJ needs to be closed for this to work. 

waitForUser("Close ObjectJ before proceeding. This will note make it happy.");// Next time, you should be able to leave it open."); 
//modify and create new synaptic channels
run("Split Channels");  
//16 bit cov here bc crashes in entire stack up there
selectImage("C1-"+origTitle);
run("16-bit");

selectImage("C2-"+origTitle);
run("16-bit");
run("Duplicate...", "duplicate");
rename("C4-"+origTitle);    
run("Multiply...", "value="+ch1Mean/ch2Mean+" stack"); 
imageCalculator("Subtract stack", "C4-"+origTitle, "C1-"+origTitle);
setMinAndMax(ch1Mean/ch2Mean*2,ch1Mean/ch2Mean*15);

selectImage("C3-"+origTitle);
run("16-bit");
run("Duplicate...", "duplicate");
rename("C5-"+origTitle);    
run("Multiply...", "value="+ch1Mean/ch3Mean+" stack"); 
imageCalculator("Subtract stack", "C5-"+origTitle, "C1-"+origTitle);


run("Merge Channels...", "c1=[C1-"+origTitle+"] c2=[C2-"+origTitle+"] c3=[C3-"+origTitle+"] c4=[C4-"+origTitle+"] c5=[C5-"+origTitle+"] create");
/**
}else{
	print("in option 2");
	autoUpdate(false);
//Stack.setPosition(channel, slice, frame);
	Stack.getDimensions(width, height, channels, slices, frames) ;
	for (i=1;i<=slices;i++){
		ch1P=newArray(width*height);
		ch2P=ch1P;
		ch3P=ch1P;
		setSlice(i*5+0);
		//Stack.setPosition(1,i,1);
		c=0;
		for (w=0;w<width;w++)
			for (h=0;h<height;h++)
				ch1P[c++]=getPixel(w,h);

		c=0;
		setSlice(i*5+1);
		//Stack.setPosition(2,i,1);
		for (w=0;w<width;w++)
			for (h=0;h<height;h++)
				ch2P[c++]=getPixel(w,h);

		c=0;
		setSlice(i*5+2);
		//Stack.setPosition(3,i,1);
		for (w=0;w<width;w++)
			for (h=0;h<height;h++)
				ch3P[c++]=getPixel(w,h);

		c=0;
		//Stack.setPosition(4,i,1);
		setSlice(i*5+3);
		for (w=0;w<width;w++)
			for (h=0;h<height;h++)
				setPixel(w,h,ch2P[c]*ch1Mean/ch2Mean-ch1P[c++]);

		c=0;
		//Stack.setPosition(5,i,1);
		setSlice(i*5+4);
		for (w=0;w<width;w++)
			for (h=0;h<height;h++)
				setPixel(w,h,ch3P[c]*ch1Mean/ch3Mean-ch1P[c++]);

	}
	updateDisplay();
	**/	
//}







//original position
Stack.setPosition(channel, slice, frame); // Sets the position. 
run("Set... ", "zoom="+zoom*100+" x="+(x+dwidth/2)+" y="+(y+dheight/2));//xy abovE ARE top left pos. this gets center
//redraw selected area
out=toString(xp[0])+",";
out=out+toString(yp[0]);
for (i=1;i<lengthOf(xp);i++){
	out=out+","+toString(xp[i]+",");
	out=out+toString(yp[i]);
}
eval("makeLine("+out+")");
Stack.setActiveChannels("10110");