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Microcanonical instanton theory offers the promise of providing rate constants for chemical reactions including quantum tunneling of atoms over the whole temperature range. We discuss different rate expressions, which require the calculation of stability parameters of the instantons. The traditional way of obtaining these stability parameters is shown to be numerically unstable in practical applications. We provide three alternative algorithms to obtain such stability parameters for non-separable systems, i.e., systems in which the vibrational modes perpendicular to the instanton path couple to movement along the path. We show the applicability of our algorithms on two molecular systems: H 2 + OH → H 2 O + H using a fitted potential energy surface and HNCO + H → NH 2 CO using a potential obtained on-the-fly from density functional calculations.