My_Batch_Subtract_Images.txt

  inputDir = getDirectory("Choose Source Directory ");

  outputDir = getDirectory("Choose Destination Directory ");
  
  setBatchMode(true);
  

  list = getFileList(inputDir);
 
  //for (i=0; i<5; i++) {
  for (i=0; i<list.length-1; i++) {
  
  
     showProgress(i+1, list.length);

     // open first image
     open(inputDir+list[i]);
      
     imageFirst = getTitle;
     idFirst = getImageID;

     // open second image
     open(inputDir+list[i+1]);
      
     imageSecond = getTitle;
     idSecond = getImageID;
     
     imageCalculator("Subtract create 32-bit", imageSecond , imageFirst);

     run("Scale...", "x=0.5 y=0.5 interpolate create title=Scaled");

     //run("8-bit");

     //run("Specify...", "width=1500 height=1750 x=300 y=0");
     //run("Crop");
     
     //selectImage(idImage);
     //close();
     
     
     idImageRes = getImageID;
     
        
     saveAs("TIFF", outputDir+list[i]);
     //saveAs("PGM", outputDir+list[i]);
     //saveAs("Raw Data", outputDir+list[i]);
     
     run("Close All Without Saving");


  }

  showMessage("Finished");