The first step in processing your exposures should be the dark frame subtraction and flat-field correction. Some programs, like CCDSoft, call this process image reduction, whereas other programs, like Maxim DL, call this image calibration. Most image processing programs have a routine to perform this efficiently on all of your images. Make sure that the dark frames match the temperature, the exposure time, and the bin mode of your light exposures. Also, confirm that your flat fields match the optical system of your light exposures. See the section on "Combining Images" for suggestions on dark frame and flat-field combining.
Your calibrated images should be saved in a different folder from your raw images. This way, if your images are not calibrated correctly, you can repeat the process on your raw images. The calibrated image should be virtually free of the scattered hot pixels that plague the raw image. Vignetting and dust shadows should be improved substantially.
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