// @Integer rmin
// @Integer rmax
// @Integer by
// @String thrMethod
// @Integer min
// @Integer max
// @BigDecimal(stepSize=0.0001) fraction
// @Integer toll
// @File(label="Select the input directory", style="directory") imagesDir
// @File(label="Select an output directory for the points", style="directory") outFolderP
// @File(label="Select an output directory for the objects", style="directory") outFolderO

setBatchMode(true);
run("Input/Output...", "file=.csv");
list = getFileList(imagesDir);

factor=3/sqrt(2);
rmin=factor*rmin-0.5;
rmax=factor*rmax-0.5;
by=floor(factor*by-0.5);
if (by<=0) by=1;
if (rmin<1) rmin = 1;
if (rmax<rmin+1) rmax = rmin+1;

for (i = 0; i < list.length; i++){
  if ( !endsWith(list[i],"/") ){
   IJ.log(list[i]);
   showProgress((i+1)/(list.length));
   open(imagesDir + "/"+ list[i]);
   width=getWidth();
   height=getHeight();
   nslice=nSlices();
   if (max <=0){
   max=width*height*nslice;
   }
   titleOriginal=getTitle();

   run("Duplicate...", "duplicate range="+1+"-"+nslice+" title=temp1");
   run("Duplicate...", "duplicate range="+1+"-"+nslice+" title=temp0");
   run("Median...", "radius=1 stack");
   run("Median...", "radius=2 stack");
   selectWindow("temp1");
   // Bright blob detection with maximum of negative LoG at different scales
   run("32-bit");
   run("MaxLoGs", "min="+rmin+" max="+rmax+" steps="+by);
   rename("max");
   run("Enhance Contrast...", "saturated=0 normalize process_all");
   run("8-bit");
   run("Auto Threshold", "method="+thrMethod+" white stack");
   close("temp1");
   // end detection, a binary mask is generated
   titleTh=getTitle();
   // remove noise with a median filter from the original image
   selectWindow("temp0");
   imageCalculator("Min stack", "temp0" ,"max");
   depth=(nslice+1)/2;
   //setVoxelSize(sX,sY,sZ,"micron");
   //segmentation and object counting
   rename(titleOriginal);
   fileO = outFolderO+"/objects_"+titleOriginal;
   fileP = outFolderP+"/centroids_"+titleOriginal+".csv";
   run("ObjCounter",  "threshold=1 slice="+floor(depth)+" min="+min+" max="+max +" fraction="+fraction+" tolerance="+toll+" validate=true" + " output_objects="+ fileO + " output_points="+fileP);
   close("*");
 }
}