The high-fidelity analysis of many-body quantum states of indistinguishable atoms requires the accurate counting of atoms. Here we report the tomographic reconstruction of an atom-number-resolving detector. The tomography is performed with an ultracold rubidium ensemble that is prepared in a coherent spin state by driving a Rabi coupling between the two hyperfine clock levels. The coupling is followed by counting the occupation number in one level. We characterize the fidelity of our detector and show that a negative-valued Wigner function is associated with it. Our results offer an exciting perspective for the high-fidelity reconstruction of entangled states and can be applied for a future demonstration of Heisenberg-limited atom interferometry.