Different Results from Color Threshold Macro

Posted by acbernal on Feb 11, 2015; 9:55pm
URL: http://imagej.273.s1.nabble.com/Different-Results-from-Color-Threshold-Macro-tp5011573.html

Hi everyone,

When I use the GUI to adjust the color threshold of an image, I get the results that I desire. Whenever I do this then subsequently click the "Macro" button I get a printout of the auto-generated macro for the color threshold modification.

My problem is that when I run this auto-generated macro on the same image I started with, the end result is different from when I manually adjust the color threshold. The manual protocol results in an image where the particles are colored red for easy counting with the particle analyzer. When I run the automated version of the protocol in my macro, the resulting picture is almost completely white.

Any help would be greatly appreciated. Here is the macro:

	open(currentImage);
	run("Invert");
	run("Color Threshold...");
	// Color Thresholder 1.48v
	// Autogenerated macro, single images only!
	min=newArray(3);
	max=newArray(3);
	filter=newArray(3);
	a=getTitle();
	run("HSB Stack");
	run("Convert Stack to Images");
	selectWindow("Hue");
	rename("0");
	selectWindow("Saturation");
	rename("1");
	selectWindow("Brightness");
	rename("2");
	min[0]=210;
	max[0]=255;
	filter[0]="pass";
	min[1]=0;
	max[1]=255;
	filter[1]="pass";
	min[2]=170;
	max[2]=170;
	filter[2]="pass";
	for (i=0;i<3;i++){
  	     selectWindow(""+i);
  	     setThreshold(min[i], max[i]);
 	     run("Convert to Mask");
 	     if (filter[i]=="stop")  run("Invert");
	}
	imageCalculator("AND create", "0","1");
	imageCalculator("AND create", "Result of 0","2");
	for (i=0;i<3;i++){
  	     selectWindow(""+i);
  	     close();
	}
	selectWindow("Result of 0");
	close();
	selectWindow("Result of Result of 0");
	rename(a);
	// Colour Thresholding-------------