// **********************************************************************
// declare global variable
//var mypath="c:/";
  
// **********************************************************************
// "color_images"
// Macro for artery imaging
// Fabrice Duprat march 2013
// This macro
// All images are from the same name prefixe "imagename" and an incremential extension number for each set of images  (.001, .002, ...)
// Red channel (1) image : "path/imagename1.number"
// Green channel (2) image : "path/imagename2.number"
// Blue channel (3) image : "path/imagename3.number"
// Fluorescent channel (4) image : "path/imagename4.number"
// Fluorescent channel (5) image : "path/imagename5.number"

//
// If you are using this script for a research article, please cite this web page: https://www.ipmc.cnrs.fr/~duprat/scripts/
//


macro "color_images"

{

// Fluorescent channel to add to the color image
mychannel = 5;
mycolor = "Yellow";	// Choose color for fluorescent "Red", "Green", "Blue", "Cyan", "Magenta", "Yellow"

while (1)	{

//run("Close All");
redimage = File.openDialog("Choose RED image (channel 1)");
open(redimage);
rename("RED");

size = lengthOf(redimage);
filename = substring(redimage, 0, size -5);	// Path + name without channel number
fileext = substring(redimage,size-4, size);

// Make the file name of the other channel images to analyse in the same set
greenimage = filename + "2" + fileext;
open(greenimage);
rename("GREEN");

blueimage = filename + "3" + fileext;
open(blueimage);
rename("BLUE");

fluoimage =  filename + mychannel  + fileext;
open(fluoimage);
rename("FLUO");
run(mycolor);

run("Merge Channels...", "red=RED green=GREEN blue=BLUE gray=*None* ");
run("Duplicate...", "title=COMPOSITE");

imageCalculator("Add", "COMPOSITE","FLUO");
fileext = substring(fileext,1, 4);		// extension without the "."

run("Images to Stack", "name="+ filename + "_color" + fileext + " title=[] use");

saveAs("Tiff", filename + "_color" + fileext +".tif");

}	// end of while



}	// end of macro