Creating a 2D matrix from 2 FITS images of unequal dimensions for Radio/FIR correlation I have two images of NGC 6946:

item       description        size (pixels)    scale (arcseconds/pixel)
 1.     70 micron MIPS FITS     241 x 241           4.5 
 2.     20 cm VLA FITS          512 x 512           2.0  


I need to create a matrix with 2 columns (70 micron vs 20 cm), where each column will store the values at each pixel in such a way that the central pixel coordinate of each image coincides, so that I can plot for Radio/FIR correlation. 

How should I perform such task in python?
If you have the WCS for both images, you can use the astropy reproject module. Once you have projected image 1 onto image 2, the (x,y)th pixel from the output will correspond to the (x,y)th pixel from image 2. 

Then you can flatten both images with numpy, and assemble them into a 2-column array.