var milled;
var scale;
var name;
var horse;
var leg;
var section;
var site;
var confocal;
var left;

macro "Show Dialog... [b]" {

open();
name = getTitle();

open();
confocal = getTitle();

sync = isOpen("Sync Windows 1.4.1");

if (sync == false)
	run("Sync Windows");

//Set scale automagically
//This macro is for use with 200x images
//At 2048x2048 resolution
//and 0.2160 microns per pixel

//  The following section gets useful information from the filename
   horse = substring(name, 0, 2);
   leg = substring(name, 2, 3);
   section = substring(name, 3, 4);
   site = substring(name, 4,6);

res = getHeight();

if (res==1024)
	scale = 1.7448;
else if (res==2048)
	scale = 0.2160;
//failsafe value
else
	scale = 1;

//need to have a line selection for line width to work
makeLine(1,1,0,0);

if (res==1024)
	run("Line Width...", "line=10");
else if (res==2048)
	run("Line Width...", "line=25");
else
	run("Line Width...", "line=1");

//give the BSE window the focus
selectWindow(name);

//Make a dialog box
Dialog.create("Specimen Information");
Dialog.addCheckbox("Lateral to left (uncheck if to right)", true);
Dialog.addNumber("Scale", scale, 4, 6, "µm / pixel")
Dialog.show();
left = Dialog.getCheckbox();
scale = Dialog.getNumber();
setVoxelSize(scale, scale, 1, "micron");

selectWindow(confocal);
setVoxelSize(scale, scale, 1, "micron");
selectWindow(name);

//use logical values to reassign site to the correct side (lateral to left)

siten = parseInt(site);

if (left==false && siten == 11)
	site = 17;
else if (left==false && siten == 12)
	site = 16;
else if (left==false && siten == 13)
	site = 15;
else if (left==false && siten == 15)
	site = 13;
else if (left==false && siten == 16)
	site = 12;
else if (left==false && siten == 17)
	site = 11;
else if (left==false && siten == 14)
	site = 14;
else if (left==true)
	site = siten;
else
	site = 99;

}


macro "Calcein and qBSE [t]" {
    requires("1.34h");                           
    var bmmd;
    var fraction;

//get the pixel information from inside the ROI    
 getRawStatistics(count, mean, min, max, std, histogram);

//use these lines to manually control the threshold
lower=1;
upper=255;

    for (k=0; k<lower; k++) {
        background = background + histogram[k];
        fraction = (count - background) / count;
    }
   
    for(j=lower; j<upper; j++) {
        cumulative = cumulative + histogram[j];
         av = av + j * histogram[j];
        bmmd = av / cumulative;
    }
   
modep=0;
    mode = 0;
    for (p=lower; p<upper; p++) {
   
        if (mode < histogram[p]) {
        mode = histogram[p];
        modep = p;
    }
    }


 
//get the coordinates of the ends of the straight line selection
getLine(a,b,c,d,w);

//calculate line length - go pythagoras
thickness=scale*sqrt((a-c)*(a-c)+(b-d)*(b-d));

//the next line prints results in a log window 
print(horse, " \t", leg, "\t", section, "\t", site,"\t", modep, " \t", mean, " \t", bmmd, " \t", fraction, "\t", thickness, "\t", " \n");                

//draw a 10 micron radius circle to guide unbiased placement of next ROI

selectWindow(confocal);

r=20/scale;
x=a-r/2;
y=b-r/2;
makeOval(x,y,r,r);
                }