_DKR_FRAP_Analysis.txt

macro "_DKR_FRAP_Analysis"
{

//define and setup
bleach_timepoint =   4;     //frame number that shows first bleached image
bleachsize       =  10;     //diameter in pixels
run("Set Measurements...", "  mean display redirect=None decimal=2");

//adaptive mode searches for greatest-bleached point and places coords there, 
//otherwise at center of image
adaptive         =  "FALSE";

if(isOpen("Results")){
	selectWindow("Results");
	run("Close"); 
	}
	
//set image stats
stack=File.name;
getDimensions(width, height, channels, slices, frames);
wide=width;
high=height;


if(adaptive=="TRUE"){
	//to determine the most bleached point, we subtract pre from post-bleached slices
	selectImage(stack);
	setSlice(bleach_timepoint-1);
	run("Duplicate...", "title=prebleached");
	
	selectImage(stack);
	setSlice(bleach_timepoint);
	run("Duplicate...", "title=bleached");
	
	//find the bleach point
	run("Calculator Plus", "i1=bleached i2=prebleached operation=[Subtract: i2 = (i1-i2) x k1 + k2] k1=1 k2=0 create");
	selectImage("prebleached");
	close();
	selectImage("bleached");
	close();
	selectImage("Result");
	run("Find Maxima...", "noise=100 output=[Point Selection]");
	
	//make a ROI before measuring
	getSelectionCoordinates(xCoord,yCoord);
	x=(xCoord[0])-(bleachsize/2);
	y=(yCoord[0])-(bleachsize/2);
	run("Specify...", "width="+bleachsize+" height="+bleachsize+" x="+x+" y="+y+" oval");
	}

else{
	x=(wide/2)-(bleachsize/2);
	y=(high/2)-(bleachsize/2);
	run("Specify...", "width="+bleachsize+" height="+bleachsize+" x="+x+" y="+y+" oval");
	}

waitForUser("move ROI is desired");

no=roiManager("count");
roiManager("add");
selectImage(stack);	
roiManager("Select", no);
roiManager("Multi Measure");

saveAs("Measurements", "C:\\Users\\dkrozelle\\Desktop\\"+stack+".xls");
if(File.exists("C:\\Users\\dkrozelle\\Desktop\\"+stack+".xls")){
	selectWindow("Results");
	run("Close"); 
	}
}