1. A microscopy system for creating three dimensional images using probe molecules, comprising: a sample stage for mounting a sample; an activation light source configured to illuminate the sample with an activation light and to activate probe molecules in at least one subset of probe molecules; a readout light source configured to illuminate the sample with a readout light and to cause luminescence in the at least one subset of probe molecules; an acoustic optical tunable filter (AOTF) configured for fine tuning a power of the activation light source and the readout light source; an objective lens configured to direct a light beam from the light source toward the sample; a total internal reflection fluorescence condenser configured to alter a beam path of the light beam between a region proximal to a side of the objective lens and a region proximal to a center of the objective lens; at least one camera positioned to capture a plurality of images by detecting the luminescence from the at least one subset of probe molecules when the beam path of the light beam is directed through a region of the objective lens proximal to a side of the objective lens and when the beam path of the light beam is directed through a region of the objective lens proximal to a center of the objective lens and capture a plurality of images; and an image construction module configured to combine the plurality of captured images from the at least two luminescence beams and construct a three dimensional image using the plurality of captured images.