Creating a 2D matrix from 2 FITS images of unequal dimensions for Radio/FIR correlation
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.