The role that organelle analysis has played in understanding biology is studied. Organelle analysis enables a more specific description of the molecular, biochemical, and physiological processes associated with diseases, embryonic development, tissue differentiation, organism aging, disease treatments, and organism response to pathogens. Confocal microscopy has become a routine tool for investigating subcellular organization, organelle networks, and organelle dynamics in cellular and tissue samples. Most organelles have a dynamic, three-dimensional (3D) organization inside the cell, which is tightly connected to their physiological functions. Due to this, a single 2D image inherently limits the information acquired about the distribution of a particular property within the organelle. The combination of subcellular fractionation with 'omic' technologies has become a powerful resource to characterize and catalogue the various subcellular environments in a cell.