Below you see the distiphallus of Scathophaga lutaria. The side view on the left side is taken in artificial Canada Balsam, with the best resolution possible. On the right side you see a ventro-caudal view, showing the internal structures. On the right and bottom margin, you can clearly see how the alignment algorithm tracked the rotation of the object, while I was taking the series of ~30 exposures.

In this case it is important to use a video (USB, microscope) camera and not an SLR body, because the series must be taken as fast as possible, say with one exposure per second. With one hand on the fine drive of the microscope and the other one on the mouse, this is quite easy.