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Deriving thermophysical properties such as thermal inertia from thermal infrared observations provides useful insights into the structure of the surface material on planetary bodies. The estimation of these properties is usually done by fitting temperature variations calculated by thermophysical models to infrared observations. For multiple free model parameters, traditional methods such as Least-Squares fitting or Markov-Chain Monte-Carlo methods become computationally too expensive. Consequently, the simultaneous estimation of several thermophysical parameters together with their corresponding uncertainties and correlations is often not computationally feasible and the analysis is usually reduced to fitting one or two parameters. Data assimilation methods have been shown to be robust while sufficiently accurate and computationally affordable even for a large number of parameters. This paper will introduce a standard sequential data assimilation method, the Ensemble Square Root Filter, to thermophysical modelling of asteroid surfaces. This method is used to re-analyse infrared observations of the MARA instrument, which measured the diurnal temperature variation of a single boulder on the surface of near-Earth asteroid (162173) Ryugu. The thermal inertia is estimated to be $295 \pm 18$ $\mathrm{J\,m^{-2}\,K^{-1}\,s^{-1/2}}$, while all five free parameters of the initial analysis are varied and estimated simultaneously. Based on this thermal inertia estimate the thermal conductivity of the boulder is estimated to be between 0.07 and 0.12 $\mathrm{W\,m^{-1}\,K^{-1}}$ and the porosity to be between 0.30 and 0.52. For the first time in thermophysical parameter derivation, correlations and uncertainties of all free model parameters are incorporated in the estimation procedure which is more than 5000 times more efficient than a comparable parameter sweep.