The software is ImageJ, free for anyone who wants to use it. Google and name and you should find it easily
This is not a test target and so you need to dig a little further. The plot of the image is far more complex, which is why just using resolving power to make some sort of grid to define "equivalent MP" does not really work--you are not going to find convenient line pairs and line pairs in and of themselves do not describe an image (it is just a quantification of system that allows comparison, but does not have enough detail to express image formation or perception). Since the 645D has a pixel pitch of 6um, the image does actually provide clear separation of detail between 1-2 pixels or 6um-12um. You can see that in the image and if you analyze the plot, it is there as well--as in other areas of the image. You will also see it is defining edges very well. Just taking peaks on the plot will not work.
This is also a low contrast target which would lower the resolving power of the system. Which suggests that the Rayleigh criterion/limit, which you use in your post, is far too crude to model real systems. Actually, the Rayleigh limit is really just a useful learning tool, but it is out of date.