data/imagej_macro/counting_spots/macro_counting_metric.txt

// Open this macro from ImageJ
// Change the input_dir: a directory which contain 8 images of same wavelength. 
// or a big folder image, and define the pattern of image as image_fn below. 
// then run entire macro: run macro from menu bar or Cmd + R in mac, ctrl + R in other os sys I think. 

input_dir="/Users/hoatran/Documents/BCCRC_projects/merfish/XP2059_FOV25/";


output_dir=input_dir+"counting_spots/";

if(!File.exists(output_dir)) 
      File.mkdir(output_dir);

for (r=1; r<=8; r++) {

//r=8;



image_fn="merFISH_0"+r+"_025_05.TIFF";

open(input_dir+image_fn);
short_name = substring(image_fn,0,indexOf(image_fn,'.TIFF'));

run("8-bit");

run("Enhance Contrast...", "saturated=0.2 normalize");

run("Convolve...", "text1=[-1 -1 -1 -1 -1\n-1 -1 -1 -1 -1\n-1 -1 24 -1 -1\n-1 -1 -1 -1 -1\n-1 -1 -1 -1 -1\n] normalize");

//open(input_dir+"demo/mask.tif");

selectWindow(image_fn);

//imageCalculator("AND create", image_fn,"mask.tif");

//selectWindow("mask.tif");

//close();

//selectWindow("Result of "+image_fn);

//selectWindow(image_fn);

nBins = 256;  

row = 0;

getHistogram(values, counts, nBins);

for (i=250; i<nBins; i++) {

      setResult("Value", row, values[i]);

      setResult("Count", row, counts[i]);

      row++;

}

updateResults();


saveAs("Results",output_dir+short_name+"_hist.csv");

//selectWindow("Result of "+image_fn);
selectWindow(image_fn);
saveAs("Tiff",output_dir+image_fn);

run("Close All"); 

//selectWindow(image_fn);

//close();
run("Close All");
list = getList("window.titles");
if(list.length>0){
  	for (i=0; i<list.length; i++){
  		winame = list[i];
	  	print(winame);
  		selectWindow(winame);
	  	run("Close");
	}
	}
}