Use full resolution for each frame. For focus stacking, it’s generally best to capture as much data as possible and downsize later if needed.

Lowering resolution at capture is a blunt way to reduce noise because it throws away both detail and noise. Starting with the highest-resolution source files gives the stacking software more image information to work with, which is especially helpful for fine detail.

If the final image ends up larger than you need, resize the finished stacked image afterward rather than reducing resolution before capture.

A practical tip from microscope stacking experience: take the images quickly and in sequence, since slight subject drift or movement can affect alignment. It can also help to frame a little wider than usual so you have room to crop after stacking.