title: ImageJ counting clumped cells
body: <p>I have been trying to make a macros for counting the cells in the image. However, I have a hard time removing the overlap between cells and for the program to distinguish between the clumps. </p>
  
  <pre><code>run("8-bit", "stack"); 
  run("Subtract Background...", "rolling=5 light sliding stack"); 
  run("Median...", "radius=1 stack"); 
  run("Unsharp Mask...", "radius=0.8 mask=0.50 stack"); 
  run("Invert LUT"); 
  run("Auto Threshold", "method=Yen white stack"); 
  run("Erode"); 
  run("Erode"); 
  run ("Watershed"); 
  run("Analyze Particles...", "size=200-2000 circularity=0.50-1.00 show=[Count Masks] display exclude clear summarize add in_situ");
  </code></pre>
  
  <p>I am using the macros on a stack of images. </p>
  
  <p>I also tried using GreyscaleReconstruct but I was not that successful either. I used this code </p>
  
  <pre><code>run("Open..."); 
  selectWindow("A.png"); 
  setBatchMode(true); 
  a=getTitle(); 
  run("8-bit"); 
  run("Invert LUT"); 
  run("Gaussian Blur...", "sigma=2"); 
  run("Duplicate...", "title=_seed"); 
  run("Minimum...", "radius=3"); 
  run("GreyscaleReconstruct ", "mask="+a+" seed=_seed create"); 
  imageCalculator("Subtract create", a,"_seed"); 
  selectWindow("Result of "+a); 
  rename("WhiteTopHatReconstructed"); 
  run("Auto Threshold", "method=Otsu white"); 
  setBatchMode(false); 
  run("Analyze Particles...", "size=200-2000 circularity=0.50-1.00 show=[Count Masks] display exclude clear summarize add in_situ"); 
  </code></pre>
  
  <p>Pleas help (either with the first or second code!) Thanks! :) </p>
  
  <p>Here is an image of what am I analyzing.<img src="https://i.stack.imgur.com/Hx0Pp.jpg" alt="enter image description here"></p>