//Get info on stack
getDimensions(width, height, channels, slices, frames);
title = getTitle();

//Get current position
Stack.getPosition(channel, slice, frame);

currentSlice = 0;
currentFrame = 0;

for (currentSlice=1; currentSlice<=slices; currentSlice++)
{
	//Duplicate just the current slice
	selectWindow(title);
	run("Duplicate...", "title=[&title] duplicate channels=1-3 slices=&currentSlice frames=1-&frames");
	rename("Duplicate");
	run("Median...", "radius=.5");

	//Copy out all of the color channels
	selectWindow("Duplicate");
	run("Duplicate...", "title=Blue duplicate channels=1 slices=1 frames=1-&frames");
	selectWindow("Duplicate");
	run("Duplicate...", "title=Green duplicate channels=2 slices=1 frames=1-&frames");
	selectWindow("Duplicate");
	run("Duplicate...", "title=Red duplicate channels=3 slices=1 frames=1-&frames");

	//Clean up the green channel by subtracting the Red bleedthrough
	//imageCalculator("Subtract create stack", "Green","Red");
	//selectWindow("Result of Green");
	//rename("GFP");
	selectWindow("Duplicate");
	run("Duplicate...", "title=GFP duplicate channels=2 slices=&currentSlice frames=1-&frames");

	//Copy out the blood channel
	selectWindow("Red");
	run("Duplicate...", "title=Blood duplicate channels=1 frames=1-&frames");

	//Reorder in order to average the time series
	run("Stack to Hyperstack...", "order=xyctz channels=1 slices=&frames frames=1 display=Composite");
	run("Z Project...", "start=1 stop=&frames projection=[Average Intensity]");
	rename("AVG_Blood");
	run("Copy");

	newImage("AVG_" + currentSlice, "16-bit color-mode label", width, height, 1, 1, frames);
	for(currentFrame=1; currentFrame<=frames; currentFrame++)
	{
		selectWindow("AVG_" + currentSlice);
		Stack.setPosition(1, 1, currentFrame);
		run("Paste");
	}

run("Merge Channels...", "c1=AVG_" + currentSlice + " c2=GFP c3=Blue create ignore");
selectWindow("Merged");
rename("AVG_" + currentSlice);

selectWindow("Green");
close();
selectWindow("Red");
close();
selectWindow("Blood");
close();
selectWindow("AVG_Blood");
close();
selectWindow("Duplicate");
close();
}

selectWindow("AVG_" + 1);
rename("Merged")
for (currentSlice=1; currentSlice<slices; currentSlice++)
{
	run("Concatenate...", "  title=[Merged] open image1=Merged image2=AVG_" + currentSlice+1 + " image3=[-- None --]");	
}

run("Stack to Hyperstack...", "order=xyctz channels=&channels slices=&slices frames=&frames display=Composite");

rename(title + " BloodAvg'd");
resetMinAndMax();