A method of imaging with an optical system characterized by a diffraction-limited resolution volume is disclosed. In a sample that includes a plurality of phototransformable optical labels ("PTOLs") distributed in the sample with a density greater than an inverse of the diffraction-limited resolution volume of the optical system, a first subset of the PTOLs in the sample are activated, and the density of the activated PTOLs in the first subset is less than the inverse of the diffraction-limited resolution volume. A first portion of the PTOLs in the first subset of PTOLs is excited. Radiation emitted from the activated and excited PTOLs in the first portion of PTOLs is detected with the imaging optics, and locations of activated and excited PTOLs in the first portion of PTOLs is determined with a sub-diffraction-limited accuracy based on the detected radiation emitted from the activated and excited PTOLs.