/*  Macros written to count spots in plates. 

This macro was tested on 16 bit images.  It may work on 8 bot Images. 
Color images would need to be converted using Image > Type > 16-bit.

Instructions:
*  Open image and run "Auto Threshold Plate".
*  Draw a circle over the well to be counted.  This may be a region of interest saved
in the ROIManager so that the size is always exactly the same.
*  Run macro "Measure spots in area [q]" or just type the letter q.
*  Drag ROI to next area to be measured and repeat.

*/

macro "Auto Threshold Plate" {
  setAutoThreshold("Default");
  setOption("BlackBackground", true);
  run("Convert to Mask");
  run("Erode");
  run("Dilate");
  run("Watershed"); 
}

macro "Measure spots in area [q]" {
  run("Set Measurements...", "  redirect=None decimal=3");
  original = getImageID;
  run("Duplicate...", " ");
  tempimage = getImageID;
  run("Analyze Particles...", "pixel show=Outlines exclude include summarize");
  outlinesimage = getImageID;
  selectImage(tempimage);
  close();
  selectImage(original);
  selectImage(outlinesimage); 
  selectWindow("Summary");
}