Distribution_shapes.ijm

macro "spheroids_penetration_profile" {
	
//getting the position of drawn ellipse

roiManager("Add");

//calculating of the ellipse center 


//resolution of profile (the number of nested circles)
n=100;

//initialization of arrays
a=newArray(n);
s=newArray(n);
s1=newArray(n);
a1=newArray(n);
ss=newArray(n);

//calculation of increments
si=1/n;


//calculation of total fluorescnce signal and pixels area from each nested circle
for (i=n; i>=1; i-=1){ 
scalefactor = si*(i-1);

scaletext="x="+d2s(scalefactor, 3)+" y="+d2s(scalefactor, 3)+" centered";	

run("Scale... ", scaletext);
getStatistics(area, mean);
roiManager("Select", 0);
s[i-1]=mean*area;
a[i-1]=area;
}

//calculation of total intensity and area of the rims (between circles)
for (i=n-1; i>=1; i-=1){ 
s1[i]=s[i]-s[i-1];
a1[i]=a[i]-a[i-1];
}

//caclulation of mean fluorescnce intensity of the rims
s1[0]=s[0];
a1[0]=a[0];
 for (i=n-1; i>=0; i-=1){ 
ss[i]=s1[i]/a1[i]; 
}

//plotting of the result profile
Plot.create("","r","Int",ss);
roiManager("Delete");