normalization/bin/intensities along a set line

[ejb]

Hi!

I have a line that I am measuring that has a defined fluorescent intensity along it that is very stereotypical. It is at the bottom and the top of this line. I have been using the "plot profile" analysis so far where X is the length and Y is the intensity along this length.
Though in some of my tested condition images, these lines are shorter, but with the same stereotypical distribution of fluorescent intensity.
Is there a plug in for normalizing these varying lengths with the intensities along them? Or some kind of bin function plug in? Can't seem to find exactly what I'm looking for, but have been told it exists...

Thanks!