Landsat-Sentinel-2 Algal Bloom Mapping Using Vision Transformers: Model Description, Implementation, and Examples

Remote sensing techniques have been increasingly utilised in aquatic applications in recent years. A common challenge in using optical satellite data is the presence of missing observations due to cloud cover. These data gaps can lead to missed detection of critical events, such as algal blooms, in lakes of high interest to water authorities. As a result, enhancing the completeness of optical satellite datasets is crucial for improving the monitoring and prediction of algal blooms. In this study, we compared a traditional data imputation method (i.e., linear interpolation) with deep learning models for reconstructing missing spectral bands across four lakes with historical records of algal blooms. The deep learning models adopted include CNN-based architectures (i.e., CNN, Inception Resnet, and Autoencoder) and CNN-LSTM-based architectures (i.e., CNN-LSTM, Resnet-LSTM, and Autoencoder-LSTM). Our results demonstrated that deep learning models substantially outperformed the baseline linear interpolation method in imputing spectral band values within artificially masked regions. Among these models, CNN delivered the best performance across most lakes. Furthermore, we evaluated the performance of algal bloom indices (i.e., Green/Red and NDCI) derived from the imputed imagery by comparing them with the observed data. Our results demonstrate that deep learning models are effective for imputing missing data in PlanetScope SuperDove imagery, enabling more reliable applications in water monitoring.

Timely monitoring of coastal water quality is critical for environmental protection, yet conventional satellite workflows rely on downlink and ground processing, introducing latency that can limit responsiveness to rapidly evolving turbidity events. To address this limitation, we propose AquaCubeAI, a lightweight machine-learning approach for onboard estimation of coastal water turbidity from {\Phi}sat-2 multispectral imagery. By shifting inference from the ground segment to the satellite, AquaCubeAI aims to enable lower-latency, more responsive, and more operationally useful turbidity monitoring under the strict compute and bandwidth constraints of spaceborne platforms. The model is trained on simulated {\Phi}sat-2 acquisitions spatially aligned with Copernicus Marine Service (CMEMS) High-Resolution Ocean Color (HR-OC) turbidity products over selected localized coastal sites spanning four European marine macro-regions. To provide a realistic evaluation of generalization in the presence of spatial correlation, we adopt a spatial block splitting protocol that mitigates data leakage between training and evaluation subsets. The main contributions of this work are: (i) a scalable dataset generation pipeline pairing simulated {\Phi}sat-2 multispectral patches with CMEMS HR-OC turbidity labels across selected localized European coastal sites; (ii) a compact Multi-Layer Perceptron (MLP)-based turbidity regressor trained under a leakage-aware geospatial split and tailored to embedded constraints; and (iii) a reformulation for dense spatial prediction via parameter sharing, enabling turbidity mapping and simple threshold-based anomaly masks for onboard decision logic. Embedded deployment on an Intel Myriad Vision Processing Unit (VPU) further confirms the feasibility of low-power hardware and supports low-latency inference from multispectral inputs.

Recent deep learning methods for Landsat and Sentinel-2 reflectance time series reconstruction remain limited by restricted spectral coverage, limited geographic scalability, or patch-based designs with short temporal contexts. We present HLS-GPT, a large-scale generative pretrained Transformer model for reconstructing NASA Harmonized Landsat Sentinel-2 30 m surface reflectance for all bands, any date, and any pixel location. HLS-GPT uses a hierarchical Transformer architecture to handle the different spectral band configurations of Landsat and Sentinel-2 and operates on single-pixel 12-month time series. To capture geographic and seasonal variability, the model was trained with nine years of HLS time series from more than 0.25 million training pixels across the conterminous United States. A random cropping and masking strategy extracts 12-month periods with varying start dates across epochs, masks 50% of valid observations, and trains the model to reconstruct the masked reflectance values from the remaining observations. Evaluation using more than 62,000 independent test pixels shows robust reconstruction under diverse land surface conditions, including complex crop phenology and sparse, irregular observations. Leave-one-observation-out evaluation achieved reconstruction RMSE below 0.026 for all HLS spectral bands, with relative RMSE below 35% for visible bands and below 13% for other bands. Red-edge band errors were comparable to red and near-infrared errors despite the absence of red-edge bands on Landsat. Sensitivity analyses that randomly masked 10% to 90% of test observations showed only modest degradation when 10% to 50% of observations were masked, with all-band RMSE below 0.028. Image reconstruction over nine independent 109 by 109 km CONUS HLS tiles further demonstrates that HLS-GPT outperforms two conventional methods and the NASA-IBM Prithvi model.