//  Macro for ImageJ written by Michael Cammer 20140620 
//  If you publish data processed using these macros, please acknowledge the OCS Microscopy Core at NYU Langone Medical Center
//  and properly cite ImageJ as described at http://rsbweb.nih.gov/ij/docs/faqs.html
//=====================================================================


macro "To RGB  [q]" {
  requires("1.49a");

  //  user enters these colors as needed
  colors = newArray("Red", "Red", "Green",  "Blue", "Green", "Red", "Cyan");
  maxes = newArray(4095, 4095, 4095, 4095);
  mins = newArray(150, 150, 150, 450, 150);
  //  user enters title of channels as needed



  titles = newArray("DNA", "RedStuff", "GFP", "Far-Red","trans");

  

  Stack.getDimensions(width, height, channels, slices, frames);

  Stack.setDisplayMode("composite");

  // This needs to be coded to have channels turned on or off
  Stack.setActiveChannels("101100000");

  for (c=0; c<channels; c++) {
    Stack.setChannel(c+1);
    run(colors[c]);
    setMinAndMax(mins[c], maxes[c]);
  }

  run("RGB Color");
  run("Scale Bar...", "width=25 height=5 font=18 color=[Light Gray] background=None location=[Lower Left] bold");
  run("Tiff...");

}  // end