1. A method for determining coordinate positions of light-emitting particles that label at least one component of a sample specimen using a light microscope, the method comprising: activating a subset of the light-emitting particles by illuminating the sample with an activation light beam; capturing a series of images of the light emitted from the subset of particles illuminated with an excitation light beam forming a three-dimensional structured illumination pattern; generating a resolved image of the light-emitting particles from the series of images; and repeatedly activating, capturing, and generating to obtain a number of resolved images that are processed to obtain a super-resolution image of the at least one component, wherein the super-resolution image has a higher resolution than a diffraction limit of the light microscope, wherein illuminating the sample with the activation light beam further comprises illuminating the sample with the activation light beam that stochastically activates the subset of light-emitting particles, and wherein generating the resolved image further comprises: summing the series of images to generate a summed image of the each subset of particles; determining centroid positions of the each subset of particles in the summed image; and resolving centroid positions in the summed image to generate the resolved image.