file=getTitle();

framescounter=11;  //number of frames
frequency=1;	//frames frequency
Type=1
setTool("polygon");
Dialog.create("Number of frames");
Dialog.create("Frames frequency in min")
Dialog.create("Single Point (0) or Kinetics (1)")
Dialog.addNumber("Number of frames: ", framescounter);
Dialog.addNumber("Frames frequency in min: ", frequency);
Dialog.addNumber("Single Point (0) or Kinetics (1)", Type);
Dialog.show();
framescounter=Dialog.getNumber();
frequency=Dialog.getNumber();
Type=Dialog.getNumber();

if (Type==0) {

run("Enhance Contrast", "auto");      //it makes easier to select the cell

waitForUser('Please go to 1st frame, draw the cell area and press OK.');
run("Clear Results");
run("Set Measurements...", "area integrated limit redirect=None decimal=0");
run("Measure");
Total_first=getResult('IntDen');   // Total intensity at the first frame
run("Clear Results");

waitForUser('Please go to the desired frame and press OK.');
run("Measure");
Total_final=getResult('IntDen');   //Total Intensity at the last frame
run("Clear Results");

waitForUser('Please go to 1st frame, draw the PHOTOCONVERTED cell area and press OK.');
run("Measure");
Inside_first=getResult('IntDen');   //Intensity of the photoconverted area at the first frame
	Outside_first=Total_first-Inside_first;	//to calculate the outside intensity (Outside= Total-Inside)
	run("Clear Results");
	waitForUser('Please go to the desired frame and press OK.');
	run("Measure");
	Inside_final=getResult('IntDen');	//Intensity of the photoconverted area at the last frame
	Outside_final=Total_final-Inside_final;	//to calculate the outside intensity
	run("Clear Results");
	Motile_Fraction=(Outside_final-(Outside_first*(Total_final/Total_first)))/(Total_final-(Outside_first*(Total_final/Total_first)));	// basically  Motiliy= Outside last frame/ total last frame       (there is a blackground correction in the equation)
	print ("DATA_OBTAINED_FROM_FILE:",file);
	print ("Outside_Initial_Intensity:",	Outside_first );
	print ("Outside_Final_Intensity:",	Outside_final);
	print ("Total_Initial_Intensity:",	Total_first);
	print ("Total_Final_Intensity:",	Total_final);
	print ("Motile_Intensity:",	Motile_Fraction);

}

else 
{



run("Enhance Contrast", "auto");      //it makes easier to select the cell
	

waitForUser('Please go to 1st frame, draw the cell area and press OK.');
run("Clear Results");
run("Auto Threshold", "method=IsoData white stack");
run("Set Measurements...", "area integrated limit redirect=None decimal=0");
Total= newArray(framescounter+1);
for (i=1;i<=framescounter;i++)
	{
	run("Measure");
	Total[i]=getResult('IntDen');
	run("Clear Results");
	run("Next Slice [>]");
	}
for (i=1;i<=framescounter;i++)
	{
		run("Previous Slice [<]");
	}

waitForUser('Make sure to be in the 1st frame, draw the PHOTOCONVERTED cell area and press OK.');
newArray(framescounter);
Inside= newArray(framescounter+1);
Outside=  newArray(framescounter+1);
for (i=1;i<=framescounter;i++)
	{	
	run("Measure");
	Inside[i]=getResult('IntDen');   //Intensity of the photoconverted area at the first frame
	Outside[i]=Total[i]-Inside[i];	//to calculate the outside intensity (Outside= Total-Inside)
	run("Clear Results");
	run("Next Slice [>]");
	}
print ("Motile_Fraction_OBTAINED_FROM_FILE:",file);
i=1;
Total1=Total[i];
Outside1=Outside[i];
print("Time_in_min, Motile_Fraction");
Motile_Fraction= newArray(framescounter+1);
for (i=1; i<=framescounter;i++)
	{	
	Motile_Fraction[i]=(Outside[i]-Outside1*(Total[i]/Total1))/(Total[i]-Outside1*(Total[i]/Total1));
	Framefrequency= frequency * (i) - frequency;
	print(Motile_Fraction[i]);
	}

}