This dataset presents data obtained from detecting fluorescence of single atoms trapped in a two-dimensional deep optical lattice. The data was obtained by measuring scattered photons with a high-numerical-aperture objective and imaged on an electron multiplying CCD camera. The data set includes the point spread functionof our imaging system, the number of photons scattered per atom, the position of the atoms and the losses,as well as the size of the cloud and the total value of the fluorescence of all the atoms. The analysis of this data allowed us to characterize the performance of our imaging system and the distribution of the atoms in the optical lattice.