1. A microscopy system for creating three dimensional images using probe molecules, comprising: a sample stage for mounting a sample, said sample containing the probe molecules; an optional activation light source configured to illuminate the sample with an activation light and to activate probe molecules in at least one subset of the 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 the 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 readout 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 an edge of the objective lens and a region proximal to a center of the objective lens; a beam splitter positioned to split the luminescence into at least two luminescence beams corresponding to at least two object planes in the sample; at least one camera positioned to capture a plurality of images by detecting the luminescence from the at least one subset of the probe molecules when the beam path of the light beam is directed through the region of the objective lens proximal to the edge of the objective lens and when the beam path of the light beam is directed through the region proximal to the center of the objective lens and capture the plurality of images; and an image construction module which combines the plurality of captured images from the at least two luminescence beams and constructs a three dimensional image using the plurality of captured images.