ConvertStackToBinary.txt

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// Converts a stack to binary using locally calculated thresholds

  setBatchMode(true);
  run("Select None");
  run("8-bit");
  id = getImageID;
  for (i=1; i<=nSlices; i++) {
     setSlice(i);
     run("Duplicate...", "title=temp");
     run("Convert to Mask");
     invertingLUT = is("Inverting LUT");
     run("Copy");
     close;
     selectImage(id);
     run("Paste");
     if (i==1 && invertingLUT != is("Inverting LUT"))
         run("Invert LUT");
  }
  run("Select None");

ConvertStackToBinary.txt

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