[Nomalize Line Profile] Normalizes line profiles by making use of the Straighten command followed by scaling #Macro #ImageJ #Fiji #BIOP

Normalize_Line_Straighten.ijm

/*
 * Normalizes line profiles by making use of the Straighten command followed by scaling
 * By Olivier Burri, BioImaging And Optics Platform
 * In Response to http://forum.imagej.net/t/average-pixels-with-line-tool/6408?u=oburri
 * 
 * OUTPUT is the values of the line profile as a results table
 * 	Column name is the image name. 
 * 	the number of rows corresponds to the normalization length normLength 
 */

normLength = 200; //px the final length you want

lineWidth = 10; // Line thickness to average intensities along the perpendicular axis

imageName = getTitle();


run("Straighten...", "title=SubImage line="+lineWidth);
run("Scale...", "x=- y=- width="+normLength+" height="+lineWidth+" interpolation=Bilinear create");
run("Line Width...", "line="+lineWidth);
makeLine(0,lineWidth/2, normLength, lineWidth/2);

data = getProfile();

for(i=0; i<normLength; i++) {
	setResult(imageName, i, data[i]);
}