Autostakkert is the go-to program for stacking from lucky imaging. It's quick, easy, and does a nice job. It will select the best frames and combine them into one image that has more detail and less noise that any individual frame. Just drag-and-drop the video into the Autostakkert window.
Autostakkert lets you choose a contrasty feature as an anchor point for the frame analysis. The ranking of the frames can change quite a bit if you pick a poor feature, so choose wisely.
Autostakkert will analyse every frame in the video and produce a graph to show you the quality of each frame (the sawtooth graph) and put them in order from 0% to 100% (the green graph). Over half of the 1000 frames are better than a 50% quality index. However, only about 50 frames are of 75% quality or higher.
Each red dot surrounded by a green box is an alignment point. Autostakkert will try to match these points on every frame to align them. While you can choose the points manually, I usually just let AS find them automatically.
You have several options when stacking the final image. You can ask it to stack a specific number of frames or the best x percent. I usually stack 50 and 100 frames, out of 1000 total, and compare the resulting images for contrast and noise.
Here are the resulting images from several videos, zoomed in for a closer look. Sometimes it's easy to choose the best, sometimes not. You want the sharpest image with the lowest noise.