macro.txt

//
dir = getArgument;
dir2 = "',temp,'";
list = getFileList(dir);
open(dir + list[0]);
run("Set Scale...", "distance=',distance.pixel, ' known=',known.distance, ' pixel=1 unit=cm global");
for (i=0; i<list.length; i++) {
  open(dir + list[i]);
  width = getWidth() - ',trim.pixel, ';
  height = getHeight() -',trim.pixel,' ;
  run("Canvas Size...", "width=" + width + " height=" + height + " position=Bottom-Center");
  run("8-bit");
  run("Threshold...");
  setAutoThreshold("Minimum");
  run("Analyze Particles...", "size=',size.arg,' circularity=',circ.arg,' show=Masks display clear record");
  saveAs("Measurements", dir2+list[i]+".txt");
  saveAs("tiff", dir+list[i]+ "_mask.tif")};



// else
dir = getArgument;
dir2 = "',temp,'";
list = getFileList(dir);
open(dir + list[0]);
run("Set Scale...", "distance=',distance.pixel, ' known=',known.distance, ' pixel=1 unit=cm global");
for (i=0;
i<list.length; i++) {
  open(dir + list[i]);
  width = getWidth() - ',trim.pixel, ';
  height = getHeight() -',trim.pixel,' ;
  run("Canvas Size...", "width=" + width + " height=" + height + " position=Bottom-Center");
  run("8-bit");
  run("Threshold...");
  setAutoThreshold("Minimum");
  run("Analyze Particles...", "size=',size.arg,' circularity=',circ.arg,' show=Masks display clear record");
  saveAs("Measurements", dir2+list[i]+".txt")};