When I perform a long image sequence, I setup the instrument, setup auto run, go to bed and let the system run until the number of images are captured. I calculate the number of images that the sequence will be finished when the sun is rising. Now all images are captured but the mount is still running (sometimes to its limits) and the guiding software performs errors because the reference star is invisible.
A great feature would be that the last step in the auto run sequence would be the possibility to call an external program, e.g. a batch file so I could shut down all the running applications, stop the mount and shut down the PC.
