It can be done on isolated cell using dyes such as Mitotrackers which are very useful to visualize mitochondria by confocal microscope. Depending on the number/density of the mitochondria in the cell type you are studying, the analysis might require a specific software with an "object detection" function which allow the identification of each mitochondria. By adjusting the concentration of the dye, you should be able to identify all the mitochondria even if your cell type presents a large amount of mitochondria.