In order to monitor greenhouse gases including $CO_2$, various types of surface-, aircraft-, and satellite-based measurement projects have been conducted. These data help understand the variations of greenhouse gases and are used in atmospheric inverse modeling systems to simulate surface fluxes for greenhouse gases. CarbonTracker is a system for estimating surface $CO_2$ flux, using an atmospheric inverse modeling method, based on only surface observation data. Because of the insufficient surface observation data available for accurate estimation of the surface $CO_2$ flux, additional observations would be required. In this study, a system that assimilates aircraft $CO_2$ measurement data in CarbonTracker (CT2013B) is developed, and the estimated results from this data assimilation system are evaluated. The aircraft $CO_2$ measurement data used are obtained from the Comprehensive Observation Network for Trace gases by the Airliner (CONTRAIL) project. The developed system includes the preprocessor of the raw observation data, the observation operator, and the ensemble Kalman filter (EnKF) data assimilation process. After preprocessing the raw data, the modeled value corresponding spatially and temporally to each observation is calculated using the observation operator. These modeled values and observations are then averaged in space and time, and used in the EnKF data assimilation process. The modeled values are much closer to the observations and show smaller biases and root-mean-square errors, after the assimilation of the aircraft $CO_2$ measurement data. This system could also be used to assimilate other aircraft $CO_2$ measurement data in CarbonTracker.
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