// macros by Michael Cammer Nov 2014
// If images are published, please credit the Microscopy Core at NYU Langone.  http://ocs.med.nyu.edu/microscopy

// This is for opening an RGB file saved in .nd2 format taken with the inverted
// Nikon microscope in Dept Path 5th floor MSB.
// Brightfield or Phase Contrast images taken on this microscope in color
// have three 12 bit channels.
// This macro displays them, converts to 8 bits, and saves in the same folder.

//  File handling could be added to automatically process all files in a directory/folder.

//  Also, a pause could be added while the user adjusts the color balance.



//=============================================================
macro "16 bit RGB to 8 bit RGB" {
  requires("1.49k");
  t = getTitle();
  path = getInfo("image.directory");
  t = replace(t , ".nd2", "");    t = replace(t , ".tif", "");   t = replace(t , ".TIF", ""); t = replace(t , ".ND2", ""); 
  rename(t);
  Stack.setChannel(1);
  run("Red");
  Stack.setChannel(2);
  run("Green");
  Stack.setChannel(3);
  run("Blue");
  Stack.setDisplayMode("composite");
  Stack.setActiveChannels("1110");
  run("RGB Color");
  t2 = getTitle();
  saveAs("Tiff", ""+path+t2);
}  // end