// Author's Note: The outline of this script was downloaded by following these instructions:
// Open the script editor in ImageJ/Fiji, select Templates  ▶ ImageJ 1.x  ▶ Batch  ▶ Process Folder (IJ1 Macro).
//

// @File(label = "Input directory", style = "directory") input
// @File(label = "Output directory", style = "directory") output
// @String(label = "File suffix", value = ".tif") suffix

/*
 * Macro template to process multiple images in a folder
 */

// See also Process_Folder.py for a version of this code
// in the Python scripting language.

 dir = getDirectory("Choose a Directory ");
   setBatchMode(true);
   count = 0;
   countFiles(dir);
   n = 0;
   processFiles(dir);
   //print(count+" files processed");
   
   function countFiles(dir) {
      list = getFileList(dir);
      for (i=0; i<list.length; i++) {
          if (endsWith(list[i], "/"))
              countFiles(""+dir+list[i]);
          else
              count++;
      }
  }

   function processFiles(dir) {
      list = getFileList(dir);
      for (i=0; i<list.length; i++) {
          if (endsWith(list[i], "/"))
              processFiles(""+dir+list[i]);
          else {
             showProgress(n++, count);
             path = dir+list[i];
             processFile(path);
          }
      }
  }

  function processFile(path) {
  	//Code following this comment was implemented by the authors
  	//Please modify the parameters to suit your particular implementation
       if (endsWith(path, ".czi")) {
           open(path);
           run("Enhance Contrast", "saturated=0.35");
		   run("Gaussian Blur 3D...", "x=2 y=2 z=2");
		   setOption("BlackBackground", false);
		   run("Make Binary", "method=Li background=Default calculate");
		   run("Remove Outliers...", "radius=4 threshold=50 which=Bright stack");
		   run("Remove Outliers...", "radius=5 threshold=50 which=Dark stack");
           saveAs("TIF",path);
           close();
      }
  }