When applying generalised MSER methods to free energy calculations, a practical question is whether they should be applied to the overall time series (e.g. after combining all λ state gradients using thermodynamic integration), or applied individually to the gradients/perturbed energies from each window. As the optimal truncation points are expected to vary substantially between states, the former approach may reduce the quantity of data unnecessarily discarded, while the latter should reduce noise in the time series. We have not fully answered this question, but we have shown that the N n 0 window method appears to offer reasonable performance on synthetic data fit both to the overall stage free energy change (Table ) and to a single noisy λ state (Section S7). These heuristics appear suitable for both approaches.