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);  
print(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+"ch1Mean");

Stack.setChannel(2);    
getStatistics(area, ch2Mean, min, max, std, histogram); 
print(ch2Mean+"ch1Mean");

Stack.setChannel(3);    
getStatistics(area, ch3Mean, min, max, std, histogram);
print(ch3Mean+"ch1Mean");
  
print(ch1Mean/ch2Mean+"ratio");
print(ch1Mean/ch3Mean+"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");
}


//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");

//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");