Tree species mapping in Denmark: A comparison of spectral-temporal features with geospatial foundation model embeddings
Authors: Alkiviadis Koukos, Spyros Kondylatos, Thomas Nord-Larsen, Lotte Nyborg, Christian Tøttrup, Kenneth Grogan
Organizations: aEO Centre of Excellence, DHI, Agern Alle 5, Hørsholm, 2970, Denmark · bDepartment of Geoscience and Natural Resource Management, University of Copenhagen, Øster Voldgade 10, Copenhagen, 1350, Denmark · ceometrics, Strandvejen 273C, Charlottenlund, 2920, Denmark
Abstract
We map tree species across Denmark using National Forest Inventory plots and EO data, while evaluating the potential of foundation models for large-scale forest characterization. We compare two alternative input representations for tree species classification: (i) manually engineered spectral-temporal features (STF) derived from multi-temporal Sentinel-1 and Sentinel-2 observations, and (ii) embeddings generated by the EO FMs TESSERA and AlphaEarth. Both representations are complemented with canopy height information. Random forest, XGBoost, and Multi-Layer Perceptron (MLP) classifiers are evaluated for all input representations, with separate assessments for pure and mixed forest stands. The STF-based MLP achieves the highest classification performance, yielding macro F1 scores of 0.843 and 0.653 for pure and mixed stands, respectively. The MLP trained on TESSERA embeddings delivers competitive performance for pure stands, achieving results within 1.1 percentage points of the best-performing model. TESSERA consistently outperforms STF-based models when fewer than approximately 25% of training plots are available, demonstrating a substantial advantage under limited training data. Multi-year observations systematically improve classification accuracy relative to single-year inputs, while ablation experiments reveal the complementary contributions of Sentinel-1 backscatter, spectral indices, and canopy height data. The best-performing model is subsequently applied at the national scale to generate a 10 m tree species map of Denmark. Area-adjusted validation indicates an overall map accuracy of 79.9%. The resulting map, released as an open-access product, is the first high-resolution national tree species map of Denmark and provides a valuable resource for forest monitoring, ecological research, and land management applications.
Although tree species classification from Moderate Resolution Imaging Spectroradiometer (MODIS) time series data is critical for supporting various environmental applications, it is a challenging task due to several key difficulties: the subtle signature differences among tree species, strong spatial-spectral-temporal information coupling, and the difficulty of modeling large-scale topological context information. To better address these challenges, this paper presents a novel Graph-regulated Disentangled Sparse Mamba model (GDS-Mamba) for enhanced tree species classification, with the following contributions. (1) First, to improve large-scale context modeling, we design a mini-batch graph-regulated approach that explicitly explores topological correlation effects among input images. (2) Second, to disentangle the high-dimensional spatial-spectral-temporal information coupling for improved feature extraction, we propose a novel disentangling Mamba architecture tailored for capturing independent spatial patterns, spectral signatures, and temporal phenology behaviors in MODIS time series. (3) Third, to improve efficiency and subtle feature learning, we design novel sparse token approaches that adaptively learn the optimum subset of tokens to better address the correlation decay problem that bottlenecks standard Mamba models. Extensive experiments using large-scale annual MOD13Q1 data across two Canadian provinces (i.e., Alberta and Saskatchewan) achieved an overall accuracy of 93.94% in Alberta and 80.19% in cross-provincial evaluations, outperforming twelve state-of-the-art classification models.
The shift from stand-level to individual-tree-level forest assessments supports improved species mapping and biodiversity monitoring, particularly in boreal ecosystems where tree species like aspen (Populus tremula L.) play a keystone role. Airborne laser scanning (ALS) is the standard for such inventories, but a major limitation for developing improved species classification methods is the small number of publicly available ALS datasets containing high-quality, field-validated reference data. Recently, multispectral ALS data has shown promise for tree species classification, but the progress is hindered by the lack of open multispectral ALS datasets with high-quality field reference data. This paper presents and details an open multispectral ALS dataset for tree species classification that was used before its public release for an international benchmarking study of machine learning and deep learning classification methods in a related publication by Taher et al.,(2026). The dataset comprises 6326 segment-level point clouds of individual trees representing nine species in southern Finland. The point cloud data has been acquired using two multispectral laser scanning systems each operating at three laser wavelengths: a helicopter-borne system (HeliALS) with a point density exceeding 1000 points\m2 and an Optech Titan system with approximately 35 points\m2. Furthermore, we present a crowdsourcing application that facilitates the collection of high-quality field reference data of tree species in an efficient and scalable manner. Our article showcases the versatility of the open dataset by presenting new analyses on species classification using multispectral data building upon the initial findings of Taher et al.,(2026).
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.
Thomas Boudras, Martin Schwartz, Rasmus Fensholt +6