Spatio-Temporal Gap Filling of Sentinel-2 NDI45 Data Using a Variance-Weighted Kalman Filter and LSTM Ensemble.

This study aims to reconstruct NDI45 missing values due to cloud cover while outlining the importance of vegetation health for the climate-carbon cycle and the benefits of the NDI45 index for high canopy area indices. The methods include a novel hybrid framework that combines a deterministic Kalman filter (KF) and a clustering-based LSTM network to generate gap-free NDI45 series with 20 m spatial and 5-day temporal resolution. The innovation of the applied method relies on achieving a single-sensor workflow, provides a pixel-level uncertainty map, and minimizes LSTM overfitting through clustering based on a correlation threshold. In the northern Pampas (South America), this hybrid approach reduces the MAE by 22-35% on average and narrows the 95% confidence interval by 25-40% compared to the Kalman filter or LSTM alone. The three-dimensional spatio-temporal analysis demonstrates that the KF-LSTM hybrid provides better spatial homogeneity and reliability across the entire study area. The proposed framework can generate gap-free, high-resolution NDI45 time series with quantified uncertainties, enabling more reliable detection of vegetation stress, yield fluctuations, and long-term resilience trends. These capabilities make the method directly applicable to operational drought monitoring, crop insurance modeling, and climate risk assessment in agricultural systems, particularly in regions prone to frequent cloud cover. The framework can be further extended by including radar backscatter and multi-model ensembles, thus providing a promising basis for the reconstruction of global, high-resolution vegetation time series.