
//Example macro that does a diffusion analysis on a results table of tracking 
//data. The required format is as generated by the Manual Tracking plugin 
//http://rsbweb.nih.gov/ij/plugins/track/track.html
//assuming Results table column headings: Track > Slice > X > Y
//It requires many tracks and many time points!
//The analysis uses the time ensemble average method described in Charsooghi, MA et al 2011
//http://www.sciencedirect.com/science/article/pii/S0010465510003620

//Get number of tracks (nTracks)
nTracks = 0;
for (a=0; anTracks)
    {
     nTracks = getResult("Track",a);
    	}
    	else{};
}

//Find the track length for each track - write track length to results table
//some variables
Track=1;
L_Track=0;

//work though tracks and determine length
for (i=0; imaxslice)
    {
     maxslice = getResult("Slice",b);
    	}
    	else{};
}

//get first slice
minslice = maxslice;
for (c=0; cgetResult("Track", i-u)) {}
	
	else { if (getResult("T_Length", i)>=u && getResult("Track", i-u)==getResult("Track", i)) {
	B9 = getResult("X", i);
	B8 = getResult("X", i-u);
	C9 = getResult("Y", i);
	C8 = getResult("Y", i-u);
	disx2 = (B9-B8)*(B9-B8);
	disy2 = (C9-C8)*(C9-C8);
	dis2 = (disx2 + disy2);
	r_total = r_total+dis2;	
	divide++;
			}	
		}
	}
}
time = Array.concat(time, u);	
MSD = Array.concat(MSD, (r_total)/divide);
r_total=0;
divide=0;
}

Fit.doFit("Straight Line", time, MSD);
intercept = d2s(Fit.p(0),6);
slope = d2s(Fit.p(1),6);
r2 = d2s(Fit.rSquared,3);
print("slope = "+slope);
print("intercept = "+intercept);
print("R^2 = "+r2);
Fit.plot();

//Richard Mort 26/01/2013