PhenoEmbed: Self-Supervised Multispectral UAV Time-Series Embeddings for Individual Tree Crown Phenology

Tree crowns are a challenging target for resilient AI because they are not static objects: their spectral response, internal texture, translucency, and apparent boundaries change substantially across the growing season. We develop PhenoEmbed, a self-supervised crown-centric temporal embedding model trained with contrastive and masked reconstruction objectives on HeideBench, an 18-date UAV multispectral time-series benchmark for forest crown phenology in D"olauer Heide. The model treats seasonal crown dynamics as phenological appearance change driven by leaf emergence, canopy closure, senescence, and leaf-off conditions. Segmented tree crown polygons are retained as object anchors to extract aligned crown-centered crops through time, allowing one 256-dimensional vector summarizing seasonal crown appearance to be learned per tree. On 5,885 crop-safe crowns, the exported embeddings show structured low-dimensional organization, with the first two principal components explaining 25.1% of variance and nearest-neighbor retrieval producing a median top-1 cosine similarity of 0.946. Compared with handcrafted temporal features and a learned mean-pooling baseline, PhenoEmbed yields substantially more compact nearest-neighbor structure, while ablations show that the contrastive loss, masked reconstruction loss, and explicit seasonal time features each affect the structure of the learned embedding space. These results support PhenoEmbed as a reusable forest crown representation learner and motivate future downstream tests of whether such features improve tree-level models under seasonal change.