CedarCypress3D: an annotated UAV-LiDAR dataset of individual trees in planted cedar and cypress forests

We present a curated multi-platform LiDAR reference dataset from an instrumented ICOS forest plot, explicitly designed to support calibration, benchmarking, and integration of 3D structural data with ecological observations and standard allometric models. The dataset integrates UAV-borne laser scanning (ULS) to measure canopy coverage, terrestrial laser scanning (TLS) for detailed stem mapping, and backpack mobile laser scanning (MLS) with real-time SLAM for efficient sub-canopy acquisition. We focus on the control plot with the most complete and internally consistent registration, where TLS point clouds (~333 million points) are complemented by ULS and MLS data capturing canopy and understory strata. Marker-free, SLAM-aware protocols were used to reduce field and processing time, while manual and automated methods were combined. Final products are available in LAZ and E57 formats with UTM coordinates, together with registration reports for reproducibility. The dataset provides a benchmark for testing registration methods, evaluating scanning efficiency, and linking point clouds with segmentation, quantitative structure models, and allometric biomass estimation. By situating the acquisitions at a long-term ICOS site, it is explicitly linked to 3D structure with decades of ecological and flux measurements. More broadly, it illustrates how TLS, MLS, and ULS can be combined for repeated inventories and digital twins of forest ecosystems.

Detailed structural and species information on individual tree level is increasingly important to support precision forestry, biodiversity conservation, and provide reference data for biomass and carbon mapping. Point clouds from airborne and ground-based laser scanning are currently the most suitable data source to rapidly derive such information at scale. Recent advancements in deep learning improved segmenting and classifying individual trees and identifying semantic tree components. However, deep learning models typically require large amounts of annotated training data which limits further improvement. Producing dense, high-quality annotations for 3D point clouds, especially in complex forests, is labor-intensive and challenging to scale. We explore strategies to reduce dependence on large annotated datasets using self-supervised and transfer learning. Our objective is to improve performance across three tasks: instance segmentation, semantic segmentation, and tree classification using realistic and operational training sets. We observe improvements across all tasks, compared to training from scratch, evaluated with their respective metrics. For instance segmentation, self-supervised learning combined with domain adaptation improves AP50 by 16.98%. For semantic segmentation, self-supervised learning alone improves mIoU by 1.79%. For tree classification, hierarchical transfer learning improves mean Jaccard by 6.07%. To simplify use and encourage uptake, we integrated the tasks into a unified framework, streamlining the process from raw point clouds to tree delineation, structural analysis, and species classification. Pretrained models reduce energy consumption and carbon emissions by ~21%. This open-source contribution aims to accelerate operational extraction of individual tree information from laser scanning point clouds to support forestry, biodiversity, and carbon mapping.

Automated instance segmentation of forest LiDAR point clouds is increasingly critical as forest monitoring moves toward scalable, detailed, 3D measurement. Yet, progress is constrained by label scarcity for tree instances; a single hectare can hold millions of points and hundreds of overlapping, complex crowns, making manual annotation from scratch with raw data laborious and error-prone. Annotations are often corrected from automatic pre-segmentations, but remain costly as these provide no interactive or AI-assisted refinement. Inspired by the promptable paradigm of foundation segmentation models, we propose SelectAnyTree, a promptable instance segmentation model that delineates any individual tree in a 3D forest point cloud from a few clicks. It introduces two key components: Click-to-query prompt encoder and Canopy Height Model (CHM)-guided first prompt. The former turns each click into a single content query, encoding its 3D position and positive/negative polarity together with a pooled local backbone feature. The latter provides treetops as a geometry- and ecologically guided first prompt without any user input. The resulting prompt query is then decoded into one tree mask by a state-space query decoder to efficiently capture long-range context in large-scale forest scenes with linear-time complexity. We evaluate SelectAnyTree in interactive and instance-level settings across seven diverse forest regions and an independent held-out test dataset, demonstrating strong generalization beyond the training domains. It segments a target tree to 78.2 Intersection over Union (IoU) from a single click, 24.8 points above the strongest promptable baseline, and reaches every accuracy target with the fewest clicks, while using far fewer parameters and less inference time than prior promptable models. The source code is available at https://github.com/thanhhff/SelectAnyTree.