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Ash,
Take the darks /after/ your imaging session is complete.
If you're really concerned about the temperature changing that much from the beginning of your imaging run to the end of it, then, take a few (half-an-hour's) worth of dark frames before you begin imaging. Combine them with the ones at the end of the run.
I've never done this; always taken darks at the end of my imaging run and never had any problems, at all.
Regards,
Humayun
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