Canopy

Timely urban-canopy information is essential for linking remote sensing with heat, mobility, and neighborhood planning. We developed an optical GeoAI workflow for Davis, California, using 2022 National Agriculture Imagery Program imagery (0.6 m RGB+NIR). DeepForest generated crown candidates; an NDVI threshold, non-maximum suppression, and box-prompted Segment Anything Model (ViT-B) produced a crown-anchored canopy surface. Analyses used the 25.92 km2 Census TIGER municipal boundary and a 100 m grid. The workflow retained 11,741 candidate crowns and mapped 7.71 km2 of canopy (29.8% of the city). On the identical extent, pixel precision was 0.804, pixel recall was 0.873, and 97.4% of candidate centers agreed with the 2022 USDA/CAL FIRE LiDAR-assisted canopy product (IoU 0.719; Dice 0.837; area recovery 108.5%). Approximately 49% of candidates occurred within 15 m of a road. Canopy was inversely associated with Landsat land-surface temperature (Spearman rho = -0.477; partial rho = -0.551 controlling for built probability), and spatial-lag modeling confirmed clear neighborhood structure. Two transparent attention surfaces combined canopy need with thermal and contextual indicators. The framework provides a reproducible, updateable screening layer that complements structural canopy products and municipal inventories while retaining assumptions, data provenance, and spatial diagnostics for planning interpretation.

Accurate estimation of forest height from satellite imagery is essential for applications such as carbon accounting, biodiversity monitoring, and ecosystem management. While recent deep learning approaches provide accurate predictions, they typically do not quantify predictive uncertainty. This limitation is particularly relevant in geospatial settings characterized by sparse supervision and geographic distribution shift. In this work, we investigate Deep Evidential Regression (DER) for forest height estimation on the TreeUQ benchmark, a large-scale dataset designed for the joint estimation of tree count and average tree height at 10 m resolution, based on Sentinel-1/-2 data as well as tree inventory data over the federal state of Bavaria. To account for the extreme label sparsity of the tree inventory data, we introduce a masked evidential loss for dense geospatial prediction. Using a U-Net architecture with multimodal Sentinel-1 and Sentinel-2 inputs, the proposed approach jointly predicts tree height and associated uncertainty estimates in a single forward pass. Experimental results show that DER achieves predictive performance comparable to a deterministic U-Net while additionally providing well-calibrated uncertainty estimates. These findings demonstrate the potential of evidential learning as an efficient framework for uncertainty-aware forest structure estimation from Earth observation data.

Accurate 3D crop monitoring underpins data-driven precision agriculture by enabling field-scale analysis of plant structure, growth dynamics, and management response. Modern 3D reconstruction methods perform strongly on generic benchmarks, but rendered appearance may not translate into metrically and agronomically useful geometry in crop fields. We introduce UAV3DCrop, a public benchmark of repeated multi-angle unmanned aerial vehicle (UAV) crop surveys. It contains 88,830 RGB images at $5280 \times 3956$ pixels, with a ground sampling distance of 3.6-5.8 mm, from 91 scenes spanning corn, soybean, wheat, and oat. Track A evaluates seven scene-optimized methods -- Neural Radiance Field (NeRF) and 3D Gaussian Splatting (3DGS) variants -- on held-out views, photogrammetry-referenced depth, and canopy-height recovery. Track B tests four pretrained feed-forward models on zero-shot camera-pose and geometry estimation. The scene-optimized methods rank differently across the three targets: Splatfacto-big leads appearance, whereas Scaffold-GS leads depth and is statistically tied with Splatfacto for canopy height. Among feed-forward models, MapAnything leads on seven of the eight metrics, while the remaining models vary more across crops and fail severely on absolute scale in a way that alignment conceals. Repeated acquisitions reveal further sensitivities that differ by output type and by model, associated with position within the acquisition sequence and with tie-point multiplicity. Current 3D reconstruction methods are therefore not yet interchangeable for agronomic use: no single method wins on appearance, geometry, and canopy height at once, and only one of four feed-forward models recovers usable metric scale. The dataset is publicly available at https://link-dev.github.io/UAV3DCrop/

Earth Observation regression tasks such as building height, canopy height, and above-ground biomass estimation underpin critical applications in urban planning, forest monitoring, and climate policy, where both accuracy and reliability are critical. Yet most deep learning models yield only deterministic predictions, providing no indication of per-pixel reliability. These regression tasks are inherently challenging due to heterogeneous land surfaces, skewed target distributions, sensor noise, and signal saturation at high target values, making uncertainty (UC) estimation essential for reliable inference. We address this gap by modeling aleatoric uncertainty using year-long Sentinel-1 SAR and Sentinel-2 MSI time series, proposing two complementary approaches: (i) Gaussian UC, which jointly predicts mean and standard deviation under a Gaussian assumption, and (ii) Quantile UC, which estimates the 10th, 50th, and 90th quantiles to capture asymmetric and heteroscedastic error distributions. Both models are evaluated on three representative EO regression tasks at 10 m spatial resolution. Results show that both approaches match or surpass deterministic benchmarks and existing global products, while delivering well-calibrated, interpretable, and operationally useful confidence estimates. Notably, both models outperform the current 10 m state-of-the-art uncertainty-aware model for canopy height estimation. Our implementation will be available at: https://github.com/RituYadav92/EO-Regression-Uncertainty-Estimation

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{ö}lauer 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.

Tree growth determines how much CO2 is sequestered from the atmosphere and temporarily stored in woody biomass. At the same time tree growth is affected by increasing temperatures, more frequent drought periods, late frosts and other extreme events associated with climate change. While continuous measurements of radial (secondary) tree growth using dendrometers are well established, monitoring of shoot elongation (primary growth) has largely been neglected because suitable measurement techniques are lacking. As a result, the effects of climate change on primary tree growth remain insufficiently understood. This work aims at reconstructing native deciduous trees in 3D as a basis for measuring and monitoring shoot elongation over entire tree canopies. Here we explored the use of low-cost UAV photogrammetry and of a multi-camera CraneCam system under real-world conditions. Data were collected in two study areas over an entire growing season. We present sensor evaluations, photogrammetric data acquisition and processing strategies. A special focus is placed on the analysis of the resulting photogrammetric 3D point clouds in terms of accuracy, resolution and completeness. Results demonstrate 3D point accuracies of 5-6 mm for entire trees using consumer-grade UAVs weighing less than 250 g and a 3D reconstruction completeness between 92% and 98% depending on the UAV type. The paper introduces a novel 3Dprinted ground-truth branch to evaluate the capability to reconstructing fine-detail structures such as thin tree shoots. Finally, we discuss operational challenges and initial experiments towards a skeletonization of entire trees based on photogrammetric point clouds.

Designing microbial strains that produce high-value chemicals at commercially viable titers remains a central challenge in metabolic engineering. Existing computational approaches either rely on stoichiometric constraint-based models that cannot learn from experimental data, or apply tabular machine learning to hand-crafted features that discard the relational structure of biological knowledge. We present Canopy, a heterogeneous graph foundation model that integrates ten public and proprietary data sources into a unified knowledge graph (KG) of 6.9M nodes across 13 types and 34 edge types, covering genes, proteins, metabolites, reactions, pathways, strains, and fermentation experiments. Node features are encoded through domain-specific foundation models (ESM-2 for protein sequences, MoLFormer for chemical SMILES, and PubMedBERT for biomedical text), yielding a multi-modal representation within a single graph. We pretrain a Heterogeneous Graph Transformer (HGT) augmented with SignNet positional encodings, Jumping Knowledge aggregation, and virtual nodes using four self-supervised objectives (link prediction, masked node modelling, distance prediction, and contrastive experiment clustering), balanced via learned homoscedastic uncertainty weighting. On the downstream task of fermentation titer prediction, frozen Canopy embeddings achieve $R^{2} = 0.41$ with a lightweight probe, outperforming tabular baselines (best $R^{2} = 0.24$) and homogeneous GNN variants.

Monitoring canopy height change is essential for understanding carbon sinks and forest dynamics. Remote sensing enables consistent, large-scale observations of such changes, increasingly integrated with deep learning architectures such as Geospatial Foundation Models (GFMs). However, existing methods and datasets frame the problem as binary change detection, which overlooks both the continuous nature of change, especially for vegetation, and the inherent uncertainty in labels. We present the Canopy Height Change (CHC) dataset, providing 3 $\mathrm{m}$ resolution continuous canopy height differences and associated spatially resolved uncertainties across 10598 $\mathrm{km}^2$ of northern and western Spain. The dataset is paired with a co-located time series of PlanetScope satellite imagery. Based on the dataset, we introduce the task of uncertainty-aware change regression, associated metrics and strategies for fine-tuning GFMs. Furthermore, we evaluate state-of-the-art GFMs and highlight promising directions and remaining challenges for advancing continuous canopy height change estimation.

Remote sensing is increasingly relied upon to deliver actionable science for forest and wildfire risk management across large landscapes. Wall-to-wall, annually updated maps are a persistent need for effective forest management. Many planning systems and data collections combine disparate data sources with different purposes, vintages, and prediction quality, which leads to confounding behavior in operational planning systems. We introduce the VibrantForests framework, developed and applied to map forest attributes and provide a coherent foundation for effective forest and wildfire planning. VibrantForests includes a satellite-based forest structure model trained on lidar-derived samples and applied across the contiguous United States to concurrently generate estimates of canopy cover, canopy height, aboveground live tree biomass, basal area, and quadratic mean diameter at 10-meter resolution. We demonstrate predictive capability spanning the full spectrum of forest conditions ranging from sparse-canopy/low-biomass to dense-canopy/high-biomass. Results show that our model extends the range at which saturation is commonly encountered in comparable passive-sensor models, and reduces regression-to-mean behavior that commonly produces overestimation of forest attributes in small/sparse conditions and underestimation in large/dense conditions. The VibrantForests framework addresses a key limitation in large-area forest and wildfire planning by delivering coherent wall-to-wall estimates of management-relevant attributes at annual cadence and 10m resolution.

Accurate modeling of leaf spectral reflectance from physiological and biochemical traits is essential for advancing remote sensing applications in plant science and precision agriculture. Widely used radiative transfer models, such as PROSPECT-PRO, rely on generalized trait-reflectance relationships developed from a wide range of species, which may not fully capture the spectral behavior of specific crops like grapevines. In this study, we developed a trait-to-spectra prediction model using a multi-head attention neural network trained on a grapevine-specific dataset that includes 16 leaf traits measured across multiple varieties, growth stages, and years. The model was evaluated using stratified 5-fold cross-validation and achieved an average coefficient of determination (R^2) of 0.84 and normalized root mean squared error (NRMSE) of 1.52 percent, demonstrating high accuracy and generalizability. When compared to PROSPECT-PRO in forward mode, the neural network exhibited lower mean absolute error (MAE), especially in the near-infrared (NIR) and shortwave-infrared (SWIR) regions. These results emphasize the importance of species-specific modeling approaches and show that integrating biochemical and structural traits into data-driven architectures can significantly improve spectral prediction. The proposed model provides a robust framework for generating accurate leaf-level reflectance data, with potential applications in canopy trait retrieval, vineyard monitoring, and remote sensing-driven crop management.

Fine-tuning is often believed to reduce uncertainty and diversity in large language models, but existing analyses overlook output length, a key confounder, and therefore fail to capture how uncertainty is distributed across an entire generation rollout. To address this, we propose Canopy Entropy ($\mathrm{CE}^\star$), a measure that views language generation from a tree perspective, where ``canopy'' represents the space of all possible rollouts, making $\mathrm{CE}^\star$ naturally quantify the effective size of the generation space. $\mathrm{CE}^\star$ jointly captures uncertainty in both the output length $N$ and the generated sequence $Y_{1:N}$ -- indeed, we show that it equals to total Shannon entropy $H(N, Y_{1:N}\mid X)$, where $X$ denotes the prompt. This formulation yields interpretable metrics, including a length-entropy correlation term $ρ(N, r_N)$, where $r_N$ is the entropy rate, quantifying information conveyance efficiency by indicating whether longer outputs are more or less informative per token. Empirically, across tasks and model families, we find that fine-tuned models consistently exhibit stronger positive correlation $ρ(N, r_N)$, even when total entropy decreases. Furthermore, after controlling for model family, task, prompt, and output-length effects, we find that fine-tuning nearly triples the correlation strength between entropy rate and semantic diversity, suggesting that aligned models convert token uncertainty into semantic diversity more efficiently. Overall, these results demonstrate that fine-tuning does not simply reduce uncertainty, but fundamentally reorganizes it into more informative and semantically meaningful generations. Our code is available at https://github.com/WeiyiTian/canopy-entropy.

Integrating machine learning (ML) with physical models (PM) has emerged as a promising way of retrieving geophysical parameters from remote sensing data. In this context, a ML model for estimating forest height from TanDEM-X interferometric coherence measurements has recently been proposed, that constrains the learning process through a PM. While the features used for training and inversion where selected to ensure the physical consistency of the solutions, they could not resolve all height / structure and baseline / terrain slope ambiguities in the data. To improve this, the extension of the feature space with optical Landsat data is proposed able to provide complementary information on forest type or structure. The extended model is applied and validated on several TanDEM-X acquisitions over the Gabonese Lopé national park site and assessed against airborne LiDAR measurements. Results show a 13.5% reduction in RMSE and a 16.6% reduction in MAE compared to the original hybrid model, confirming the added value of multispectral inputs.

Accurate quantification of forest coverage and combustible biomass (fuel load) is critical for wildfire risk assessment and ecosystem management. However, traditional methods relying on airborne LiDAR or field surveys are cost-prohibitive and time-intensive, while satellite imagery often lacks the vertical resolution required for canopy volume analysis. This paper proposes a novel, automated pipeline for rapid forest inventory using virtual remote sensing data derived from Google Earth Studio (GES). Our approach first generates low-altitude orbital imagery and camera poses for a target region. For dense 3D reconstruction, we employ Pi-Long, developed within the VGGT-Long framework. This model serves as a scalable extension of the Pi-3 feed-forward Transformer architecture. To address the inherent scale ambiguity in monocular reconstruction, we introduce a metric recovery module that aligns the reconstructed trajectory with GES ground truth poses via Sim(3) Umeyama optimization. The metric-scale point cloud is then orthogonally projected into Bird's-Eye-View (BEV) height and density maps. Finally, we employ a watershed-based segmentation algorithm combined with height variance analysis to classify tree species (conifer vs. broadleaf), calculate Leaf Area Index (LAI), and estimate total fuel load. Experimental results demonstrate that this pipeline offers a scalable, cost-effective alternative to physical scanning, enabling near-real-time estimation of forest biomass with high geometric consistency.

Tree-involved crashes represent a critical subset of run-off-road (ROR) collisions, often resulting in fatal or severe injuries due to high-energy impacts. This study develops a comprehensive analytical framework to identify and quantify risk factors contributing to crash severity in tree-involved collisions using the Crash Report Sampling System (CRSS) database spanning 2020-2023. The modeling framework follows a multi-step process. First, a machine learning based classification model (CatBoost) identifies key factors associated with binary crash injury severity (KA: fatal or incapacitating injury versus BC: non-incapacitating or possible injury). Second, SHapley Additive exPlanations (SHAP) tool is used to quantify and visualize the marginal effects of top influential factors on crash severity. Third, a binary logistic regression model estimates factor effects and validates SHAP-derived importance measures. Finally, SHAP interaction plots examine the combined effects of key contributing factors. Results reveal restraint non-use as the most influential predictor, with unrestrained occupants nearly three times more likely to experience severe outcomes due to ejection risk. Vehicle age, speeding violations, and driver impairment demonstrate substantial effects, reflecting reduced crashworthiness, increased impact forces, and reduced control capabilities. Critical interactions emerge between lighting conditions and vehicle age, speeding and lighting conditions, restraint use and vehicle age, and road surface and speeding, demonstrating additive risk effects with specific interactions. These findings provide critical insights for targeted safe system-based interventions, including enhanced seat belt enforcement, speed management in reduced visibility conditions, and vehicle fleet modernization.

Hyperspectral tree species classification is challenging due to limited and imbalanced class labels, spectral mixing (overlapping light signatures from multiple species), and ecological heterogeneity (variability among ecological systems). Addressing these challenges requires methods that integrate biological and structural characteristics of vegetation, such as canopy architecture and interspecific interactions, rather than relying solely on spectral signatures. This paper presents a biologically informed, semi-supervised deep learning method that integrates multi-sensor Earth observation data, specifically hyperspectral imaging (HSI) and airborne laser scanning (ALS), with expert, ecological knowledge. The approach relies on biologically inspired pseudo-labelling over a precomputed canopy graph, yielding accurate classification at low training cost. In addition, ecological priors on species cohabitation are automatically derived from reliable sources using large language models (LLMs) and encoded as a cohabitation matrix with likelihoods of species occurring together. These priors are incorporated into the pseudo-labelling strategy, effectively introducing expert knowledge into the model. Experiments on a real-world forest dataset demonstrate 5.6% improvement over the best reference method. Expert evaluation of cohabitation priors reveals high accuracy with differences no larger than 15%.

Accurate estimation of forest biomass, a major carbon sink, relies heavily on tree-level traits such as height and species. Unoccupied Aerial Vehicles (UAVs) capturing high-resolution imagery from a single RGB camera offer a cost-effective and scalable approach for mapping and measuring individual trees. We introduce BIRCH-Trees, the first benchmark for individual tree height and species estimation from tree-centered UAV images, spanning three datasets: temperate forests, tropical forests, and boreal plantations. We also present DINOvTree, a unified approach using a Vision Foundation Model (VFM) backbone with task-specific heads for simultaneous height and species prediction. Through extensive evaluations on BIRCH-Trees, we compare DINOvTree against commonly used vision methods, including VFMs, as well as biological allometric equations. We find that DINOvTree achieves top overall results with accurate height predictions and competitive classification accuracy while using only 54% to 58% of the parameters of the second-best approach.

High-resolution mapping of canopy height is essential for forest management and biodiversity monitoring. Although recent studies have led to the advent of deep learning methods using satellite imagery to predict height maps, these approaches often face a trade-off between data accessibility and spatial resolution. To overcome these limitations, we present SERA-H, an end-to-end model combining a super-resolution module (EDSR) and temporal attention encoding (UTAE). Trained under the supervision of high-density LiDAR-derived Canopy Height Models (CHM), our model generates 2.5 m resolution height maps from freely available Sentinel-1 and Sentinel-2 (10 m) time series data. Evaluated against an open-source benchmark dataset in France, SERA-H, with a MAE of 2.6 m and R2 of 0.82, not only outperforms standard Sentinel-1/2 baselines but also approaches the accuracy of methods based on commercial very high-resolution imagery (e.g., SPOT-6/7), while relying solely on freely available data. These results demonstrate that combining high-resolution ALS supervision with the spatio-temporal information embedded in Sentinel time series enables the reconstruction of spatial detail finer than the native resolution of the input imagery. By approaching the accuracy of costly commercial imagery, SERA-H opens the possibility of mapping temperate forests using publicly available data with high revisit frequency.