//Smooths and Cleans up Skeleton for GB analysis  Peter J. Lee 2/4/2015 11:49 AM
//dir = getInfo("image.directory");
name = getTitle();
//path = dir+name;
//print("\Smoothed Macro White Skeleton 4-Connected Macro Started on" +name);

//if (!is(“binary”)) 
//    restoreExit(“Sorry, you need a binary image for this macro!”);

getPixel(0, 0)	
if (((getPixel(0, 0))!=0 || (getPixel(0, 1))!=0 || (getPixel(1, 0))!=0 || (getPixel(1, 1))!=0))
    run("Invert"); 

/* Sometimes the outline procedure will leave a pixel border around the outside - this next step checks for this. */
/* i.e. the corner 4 pixels should now be all black, if not, we have a "border issue". */

if (((getPixel(0, 0))+(getPixel(0, 1))+(getPixel(1, 0))+(getPixel(1, 1))) != 0 ) 
		restoreExit("Border Issue");
		
run("Gaussian Blur...", "sigma=1.50");
setAutoThreshold("Default dark");
//run("Threshold...");
setThreshold(67, 255);
setOption("BlackBackground", false);
run("Convert to Mask");
//selectWindow("Close"); 
//run("Close");

// skeleton3.txt by G. Landini
// a skeletonization algorithm, different from the one in ImageJ
// similar to skeleton1 but 4-connected
// 3 Dec 2003
// uses BinaryThin2_.class available from http://www.mecourse.com/landinig/software/software.html
// assumes a white object on a black background
run("BinaryThin2 ", "kernel_a='1 1 1 2 1 2 0 0 0 ' kernel_b='2 1 1 0 1 1 0 0 2 ' rotations='rotate 45' iterations=-1 white");
// PruneAll by G. Landini
// a pruning algorithm, different from the one in ImageJ
// prunes all branches of a skeleton leaving only the closed loops
// 8-connected
// 4 Dec 2003
// uses BinaryThin_.class available from http://www.mecourse.com/landinig/software/software.html
// assumes a white object on a black background
run("BinaryThin ", "kernel_a='0 2 2 0 1 0 0 0 0'  rotations='rotate 45' iterations=-1 white");
print("\Smoothed White Skeleton 4-Connected Macro Finished on " +name);