The response of thin films of Bi$_2$Se$_3$ to a strong perpendicular magnetic field is investigated by performing magnetic bandstructure calculations for a realistic multi-band tight-binding model. Several crucial features of Landau quantization in a realistic three-dimensional topological insulator are revealed. The $n=0$ Landau level is absent in ultra-thin films, in agreement with experiment. In films with a crossover thickness of five quintuple layers, there is a signature of the $n=0$ level, whose overall trend as a function of magnetic field matches the established low-energy effective-model result. Importantly, we find a field-dependent splitting and a strong spin-polarization of the $n=0$ level which can be measured experimentally at reasonable field strengths. Our calculations show mixing between the surface and bulk Landau levels which causes the character of levels to evolve with magnetic field.
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