STS-NET: Spatio-Temporal Stress Network for Self-Supervised Crop Stress Detection using Satellite Image Time Series

Plant diseases, resulting from both biotic and abiotic stresses, cause an estimated 20-40% loss in global agricultural yield annually, resulting in economic damages exceeding USD 220 billion. Accurate and scalable stress quantification is essential for precision agriculture, yet traditional manual assessments are labour-intensive and subjective. This paper proposes a unified deep learning pipeline integrating semantic segmentation, regression-based severity estimation, and disease classification. Stress severity is categorised into four levels (Low to Very High) based on the proportion of infected leaf area. Experiments on the Apple Tree Leaf Disease Segmentation dataset (1,641 samples, six classes) evaluate four models: U-Net (MobileNetV2), SegFormer, FCN, and PSPNet. U-Net with MobileNetV2 achieves the best performance with 98.20% pixel accuracy, 0.70 mIoU, and 99.41% detection accuracy at 14.7 ms per image, making it suitable for real-time use. SegFormer performs competitively (mIoU 0.66), while FCN and PSPNet show lower spatial accuracy (approximately 0.49 mIoU). The computed severity index strongly correlates with expert annotations (r = 0.968, R^2 = 0.937), demonstrating the system's reliability for automated crop monitoring and decision support.

Crop type classification from optical satellite time series remains limited in its ability to generalize across growing seasons, particularly when crop phenology shifts due to inter-annual weather variability. This hampers deployment in operational settings where current-year labels are unavailable. In addition, uncertainty quantification is often overlooked, reducing the reliability of such approaches for practical crop monitoring. Inspired by ecophysiological principles, we introduce Thermal Time-based Temporal Sampling ($T^3S$), a simple, model-agnostic method that replaces calendar time with thermal time. By re-indexing satellite observations by cumulative growing degree days, $T^3S$ aligns phenologically equivalent growth stages across years, reducing temporal redundancy while concentrating on the most biologically informative periods. We evaluate $T^3S$ across three architecturally distinct backbones on (i) SwissCrop, a new country-scale, multi-year Sentinel-2 dataset with paired temperature data that we publicly release, and (ii) the cross-region TimeMatch benchmark spanning Denmark and France. Across these settings, $T^3S$ consistently improves cross-year and cross-region crop classification over several state-of-the-art baselines, including thermal positional encoding, with particularly strong gains in uncertainty calibration, robustness under label scarcity, and early-season prediction, while requiring no architectural modification.

Panoptic crop mapping requires both delineating individual agricultural parcels and assigning a crop type to each parcel from satellite image time series. Existing approaches typically rely on dense parcel-level annotations and task-specific model training, which limits their applicability to new regions and growing seasons. We introduce PhenoStitch, a panoptic crop-mapping pipeline that requires no task-specific gradient-based training. A frozen Segment Anything model first oversegments each patch into class-agnostic regions. For each region, optical NDVI and Sentinel-1 backscatter series are summarized by an analytic double-harmonic phenological signature. Adjacent regions are then merged into parcels by minimizing a Potts graph energy, and each parcel is classified by nearest-prototype matching using only (k) labeled parcels per class. A final topology-closure step produces the panoptic map. Under a matched budget of (k=20) parcels per class, corresponding to less than 1% of the available labels, PhenoStitch achieves 20.0 crop mIoU, 76.2 segmentation quality, and 6.2 panoptic quality on PASTIS-R under a 5-fold, 3-seed evaluation. It outperforms the evaluated frozen foundation-model, few-shot, and matched-budget supervised baselines under the same protocol, with a consistent ranking also observed on ZueriCrop. Ablation studies show that radar observations contribute the largest performance gain, while the graph-energy merge and compact phenological signature provide further improvements. These results demonstrate the effectiveness of combining label-free parcel delineation with few-shot phenological recognition for panoptic crop mapping under limited supervision.