Hi all,
Here is my take on the problem ...
Are you capturing RAW subs from the DSLR?
My firm belief, now, is that you CANNOT 'calibrate' images from a DSLR if you have saved these in any mode OTHER than RAW. This is because you will have NO KNOWLEDGE of the 'settings' used by the camera's 'internal' deBayer algorithm. The software could, understandably, use a totally different 'white point' for Darks than for Lights, for example. This would mean that you would NOT be able to use those Darks in your post-acquisition calibration steps.
If you are capturing RAW subs, then your next challenge is adequate temperature correlation between Lights and Darks - almost impossible in a camera never designed for temperature stability - far less temperature control.
The best you can hope for here is that the temperatures of any two frames exposed 'consecutively', are going to be relatively 'similar'. Some DSLRs (like my Olympus e500) take advantage of this fact and will automagically take a second 'Dark' exposure immediately after the Light sub, and then do the dark-subtraction BEFORE (internally) converting to RGB (if this is what you asked for) whever you have the "Noise Reduction" feature enabled.
But even this is far from ideal because, as we all know, the usefulness of a Dark Frame can be enhanced by 'statistical averaging' of 'many' individual darks. But you cannot (usefully) do this because you do NOT have the ability to 'temperature match' your Darks.
The only workaround I can come up with is to collect Lights and Darks (or Flats and FlatDarks) in a "Dark-Light-Dark-Light-Dark" sequence, and to then, manually, 'average' each pair of Darks surrounding each Light, before then using THAT, temporary, MasterDark to correct the associated Light.
Sure, it is a long-winded process, but it is the penalty that has to he paid for using a non-ideal DSLR instead of a dedicated astro-cam.
And, remember, you will have to repeat the D-L-D-L-D sequence for your Flats as well, an then will have to combine your calibrated Flats to give you a MasterFlat, which then needs to be applied to each Dark-calibrated Light.
Only then can you consider deBayering your calibrated Lights, and only thereafter can these be aligned and stacked.
There is nothing 'difficult' about any of these steps - you just have to be meticulous in the control of your data. It wouldn't take much for you to make mistakes, and I don't know of any software that can automate ANY of these steps - except, maybe, one of the 'scriptable' image acqusition programs that may allow the DLDLDLDLD.... sequence to be automated.
Does anybody agree with my thoughts ......
Cheers,