My order to use the tools are like this:
AstroImageJ (demosaic, calibrate, align, stack, my version only Canon EOS!):
http://astrofriend.eu/astronomy/tuto...roduction.html
Fitswork (rgb combining, adjust levels, background elimination):
http://astrofriend.eu/astronomy/tuto...-fitswork.html
After that have done the above, a final touch with some photoprogram.
AIJ (AstroImageJ):
If you have an Canon DSLR you don't need the deBayering process because of the demosaicing in my macro for AIJ.
With that process in AIJ you lower the random noise and take away or reduce the static pattern without need of dark and bias frames, works very good.
Noise:
Where to measure the S/N in the image depends of what's important, the strong stars has very high signal and then high S/N. But if you measure the S/N in a nebula or the weak part of a galaxy, then the S/N is interesting to know. Most of the noise comes from background if not narrow band images.
/Lars