Most cells are transparent or colorless and therefore staining helps make them visible and thus they can be studied under the microscope in better detail. Staining usually works by using a dye that stains some of the cell components a bright color, together with a counterstain that stains the rest of the cell a different color.
There are many different ways of staining. The method used can either be non-specific where most of the cells are stained in much the same way, or specific where particular components within the cell or tissue are stained selectively.