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Reliable prediction of precipitation by numerical weather prediction (NWP) models depends on the appropriate representation of cloud microphysical processes and accurate initial conditions of observations of atmospheric variables. Therefore, to retrieve reasonable cloud distributions, a 1-D variational Ice Cloud Microphysics Data Assimilation System (IMDAS) is developed to improve the predictability of NWP models. The general framework of IMDAS includes the Lin ice cloud microphysics scheme as a model operator, a four-stream fast microwave radiative transfer model in the atmosphere as an observation operator, and a global minimization method that is known as the shuffled complex evolution. IMDAS assimilates the satellite microwave radiometer data set of the Advanced Microwave Scanning Radiometer for the Earth Observing System (AMSR-E) and retrieves integrated water vapor and integrated cloud liquid water content. This new method successfully introduces heterogeneity into the initial state of the atmosphere, and the modeled microwave brightness temperatures agree well with the observations of the Wakasa Bay Experiment 2003 in Japan. It has significantly improved the performance of the cloud microphysics scheme by the intrusion of heterogeneity into the external global reanalysis data, which resultantly improved atmospheric initial conditions.