II-b FWHM - Measure Lengths Scripts

Updated 1,970 Days AgoPublic

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//open an image 
run("Confocal Series (2.2MB)");
image_Name = getTitle();

//get some informations about the image
getDimensions(image_width, image_height, image_channels, image_slices, image_frames);
getVoxelSize(voxel_width, voxel_height, voxel_depth, voxel_unit);

// here we'll make a line in the middle of the image
y_line = image_height/2;
makeLine(0, y_line ,image_width , y_line);

// then we'll create a new iamge by re-slicing
// re-sampling through this line in the z-direction
run("Reslice [/]...", "output="+voxel_depth+" slice_count=1");
selectWindow("Reslice of "+image_Name);

// Now you could draw a line and get the length of this line 
// ther is a live measure in the main ImageJ/Fiji bar when you draw it 
// or you can measure
setTool("line");
while (roiManager("Count") < 1  ){
	waitForUser("Please make a line");
		if (selectionType > -1 ){
		roiManager("Add");
		roiManager("Measure");
	}
}

// do some cleaning of the environment before starting
run("Close All");
run("Clear Results");

// open an image 
// we need a sampling that is larger than the object
// in the previous image stop there were not enough z 
// above and below the object
run("T1 Head (2.4M, 16-bits)");
image_Name = getTitle();

//get some informations about the image
getDimensions(image_width, image_height, image_channels, image_slices, image_frames);
getVoxelSize(voxel_width, voxel_height, voxel_depth, voxel_unit);

// here we make a line
makeLine(0, 90, 256, 90);

// then we create a new image by re-slicing
run("Reslice [/]...", "output="+voxel_depth+" slice_count=1");
selectImage(nImages);
resliceImage = getTitle();

//Let's make a line
makeLine(25, 67, 240, 67);
waitForUser("We'll make a profile through this line and 'fit' a gaussian formula on it");
fitGaussian();
waitForUser("The inhomogenity of the signal causes trouble ");

// Let's blur a bit the image
selectImage(resliceImage);
run("Duplicate...", "title=["+resliceImage+"-Blurred]");
run("Gaussian Blur...", "sigma=5");
waitForUser("So we blur the image a bit before doing the fitting");
makeLine(25, 67, 240, 67);
fitGaussian();

selectImage(resliceImage+"-Blurred");
waitForUser("But this is still not 'perfect' \nbecause the length of the line you used \nwill affect your fitting and the results");
makeLine(0, 67, image_width, 67);
fitGaussian();



selectImage(resliceImage+"-Blurred");
waitForUser("One possible way is to fit a 'SuperGaussian', \nbut it needs estimates(see function below)");
makeLine(0, 67, image_width, 67);
fitSUPERGaussian();


// companion function to make the math for FWHM
function fitGaussian(){
	
	y = getProfile();
	x = Array.getSequence(lengthOf(y));
	Fit.doFit("Gaussian", x, y) ;
	Fit.plot;
			
	sortedParameter = Fit.p(3); // parameter d of gaussian
	rSquared = Fit.rSquared ; 
			
	FWHM = (2 * sqrt( 2 * log(2) ) ) * sortedParameter ;// http://fr.wikipedia.org/wiki/Largeur_%C3%A0_mi-hauteur
	setResult("FWHM ("+voxel_unit+")", nResults, FWHM * voxel_height);
	setResult("Label",nResults-1,image_Name);
	setResult("rSquared",nResults-1,rSquared);
	updateResults();
	selectWindow("Results");
}


function fitSUPERGaussian(){

	getVoxelSize(voxel_width, voxel_height, voxel_depth, voxel_unit);

	yCurrent = getProfile();											
	xPlot = Array.getSequence(lengthOf(yCurrent));			
			
	pidiv2 = PI/2;
	formulaString = "y = a + b * exp( "+pidiv2+"*(-pow ( abs(x-c), e/2 ) ) / ( pow( d* "+pidiv2+" , e/2 ) ) )";
	
	pourcentOfMax = 50	; // percent of the Maxmimal value of the Gaussian you want to consider as the diameter, 50 = FWHM
	fractionOfMax   = 1/pourcentOfMax *100; 
	
	baseline=0;
	maxOfCurve = 255;
	centerOfCurve = 125 ;
	fullWithFactor = 200; // estimated diameter
	gamma = 2 // is close to 2 for a gaussian
	initialGuesses = newArray(baseline, maxOfCurve, centerOfCurve, fullWithFactor, gamma);
	
	Fit.doFit(formulaString, xPlot, yCurrent,initialGuesses);
	Fit.plot();	
	parameterA	= Fit.p(0); 	// baseLine 
	parameterB 	= Fit.p(1);	// top - baseLine
	parameterC  = Fit.p(2);		// center
	parameterD 	= Fit.p(3);	// function of FW 
	parameterE 	= Fit.p(4);	// N, the great lord gamma
	rSquared 	= Fit.rSquared;
	
	radius 	=  parameterD * pow( (2/PI), (2/parameterE) - 1 ) * pow ( log(fractionOfMax), 2/parameterE) ; // in pixel
	
	setResult("FWHM ("+voxel_unit+")", nResults, 2*radius*voxel_width);
	setResult("Label",nResults-1,image_Name);
	setResult("rSquared",nResults-1,rSquared);
	updateResults();
	selectWindow("Results");

}