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Maxim 4.x (or CCDSoft) + CCDAutoPilot3. Works flawlessly night after night after night after night all from thousands of miles away. Including darks, flats and opening/closing the roof. Multi-targets, meridian flips, camera rotation, and focus. also integrates with the Boltwood Cloud sensor. Perfect for setting up the run, and off to sleep knowing its all getting done, and will be parked and closed down in the morning.
For Comets and asteroids (long target list generated from TheSky database), I use CCDCommander to grab these images for photometry/astrometry work. Its easier to integrate a long target list with this arrangement. also the fact that it'll grab latest coords for these moving targets.