Many researchers use cell-free systems to study mitochondrial pathways. This usually entails treating populations of cells with different reagents, separating the various cellular components, recombining the components from the different treatments, and studying the effect on mitochondrial processes. The first step in mitochondrial isolation is cell disruption. Although many disruption methods exist, some are better than others for isolating intact mitochondria. Arguably, the simplest is sonication, although this method is better suited to production of whole cell lysates.
Many researchers use mortar and pestle style tissue grinders for organelle isolation.
These shear the cells between the glass wall of the container and the edge of the pestle and tend to be significantly gentler than sonication. This method also requires careful attention to conditions such as stroke force and cooling time. Dounce tissue grinders are specially designed to produce low tissue shearing to keep organelles intact. Other homogenizers aren't as well suited to production of organelles, but have been used with some success. Lab Glass manufactures a wide range of homogenizers with a variety of features for nearly every application.