ImageJ is capable of applying any of the major image operations hence it can be used in your application. I am not aware of a ready made plugin specific to your requirement. However, a couple of image subtraction operations might be enough to get what you need.

Obviously, OpenCV also can be used and I would go for it because I am more familiar with it.

You may check the following link and look into the section "Differential Reflection" to get an idea. http://physics.oregonstate.edu/~stephsam/dokuwiki/doku.php?id=hyperspectral_microscopy_image_analysis_using_imagej

hi, this domain is my favorite,i love hyperspectral technology and i have similar future plan project,i saw few researchers work on this domain and none of them spent their time on ImageJ or openCV,i saw them designing good deep neural nets for such problem,i recommend you applying yann lecunn's Lenet5 for your problem. i have no idea about ImageJ but for your work deep neural nets are more preferred(i read few papers on it before),i have collected a beautiful book on this technology and i believe you must read that book and thank me later,the book is stored in my github repository,if you have time and want to read for further research then download it from here : https://github.com/mobassir94/Technical-Books-Collection/blob/master/Hyperspectral%20Imaging%20for%20Food%20Quality%20by%20Da%20Wen%20Sun.pdf

thanks!!!!!!!! :)

if you want it in Matlab either by using DFT,

fft2(imagematrix)

or using DCT

dct2(imagematrix)

or using Discrete wavelet transform

dwt2(imagematrix)