Normalising XY data by Z-direction in stacks

Posted by jamescleverley on
URL: http://imagej.273.s1.nabble.com/Normalising-XY-data-by-Z-direction-in-stacks-tp3685096.html

Hi All,

I am using ImageJ to process spatial XANES maps where we map an area in X-Y and each image is taken at a different energy over a specific element K-edge.  By combining into a stack the Z direction represents energy step and the pixel records intensity.  Because the data is slightly noisy and I am only interested in peak positions I would like to normalise the data in the stack  by z-direction so that the intensities at each X-Y position are scaled throughout the Z-direction to between 0 and 1. In other words if I plot a Z-profile for a single pixel in the stack it will show a profile scaled between 0 and 1.

I have searched high and low but can't seem to find the method to do this exact problem.  Does anyone have a suggestion?

Thanks

James