Analysis of profile plot

Tags: #<Tag:0x00007fd53e518e78>



I have profile plots like this:

And I would like to write a macro to identify the x coordinates of the beginning and end of the data different from “0” (excluding the high peak on the right).

I have tried to create an array, an index of this array, and then a loop to identify these values but it does not work because I struggle manipulating arrays… Could anyone spare a minute to get me started?


Good day Olivier,

here is a mcro that does what you’ve described:

// IJ-macro begin
// create test image
newImage("Untitled", "8-bit random", 256, 256, 1);
makeRectangle(0, 0, 64, 256);
setBackgroundColor(0, 0, 0);
run("Clear", "slice");
makeRectangle(168, 0, 32, 256);
run("Clear", "slice");
makeRectangle(201, 0, 55, 256);
run("Clear", "slice");
// get desired x-values
run("Select All");
p = getProfile();
zeroBound( p );
p = Array.findMaxima( p, 0 );
Array.sort( p );
print( p[0]+1, p[1] );
run( "Select None" );
function zeroBound( a ) {
	for ( i = 1; i < a.length; i++ ) {
		if ( (a[i] > 0 && a[i-1] == 0) || (a[i-1] > 0 && a[i] == 0) ) a[i-1] = 1; else a[i-1] = 0;
	a[a.length-1] = 0;
// IJ-macro end




Thank you so much Herbie! This does the trick. The only thing is that the coordinates are based on 256 pixels now, instead of the original 1234. I tried to amend your script but didn’t succeed…



I don’t understand

The only thing is that the coordinates are based on 256 pixels now […]

Did you try to understand the macro?

The call


does the same as “Plot Profile”, it gets the values of the profile but without plotting it.

So if you run the macro starting from the comment

// get desired x-values

on your image (not the profile plot), you will get the desired coordinates.

Please learn how to write ImageJ-macros:




Ok, I misunderstood (should have checked the code carefully), I thought you analysed the line plot. Thank you again!