Automating Tree Crown Delineation in UAV Orthomosaics Without Annotation: An Annotation-Free Framework Coupling DeepForest, Segment Anything, and Unsupervised Clustering

Abstract

Individual-tree-level information on crown distribution and morphology underpins forest inventory, biomass estimation, and carbon accounting. High-resolution Unmanned Aerial Vehicle (UAV) imagery resolves single-tree detail, but automated crown extraction remains difficult: fully supervised segmentation depends on costly pixel-level annotation that generalizes poorly, while the Segment Anything Model (SAM), though training-free, cannot locate trees on its own and existing SAM-based methods restore this ability only by adding task-specific training. We present an end-to-end, annotation-free toolkit for tree crown extraction and ecological analysis. A RetinaNet-based DeepForest detector produces coarse boxes; an adaptive module then removes duplicate boxes and non-vegetation false positives using an intersection-over-union rule and a global greenness index, converting noisy boxes into clean prompts; these prompts drive SAM to decode irregular crown masks without task-specific training; and geometric and texture features are extracted and grouped by principal component analysis and K-means clustering to map ecological patterns. We evaluated the toolkit on multi-biome imagery from the public OAM-TCD dataset. Because pixel-exact metrics are unstable at 10 cm resolution, where wind sway, shadow shift, and small labeling offsets are strongly amplified, we assessed accuracy under an absolute physical-distance tolerance. At a 2.0 m tolerance, consistent with the effective radius of a mature crown, the toolkit reached a precision of 91.25%, a recall of 86.40%, and an F1-score of 88.76%; bootstrap and Monte Carlo resampling confirmed these values are stable. Without manual annotation, it characterized more than 4700 individual crowns and recovered distinct vegetation patterns across geographic settings, offering a highly adaptable, low-cost baseline tool that demonstrates robust performance across the diverse multi-biome scenes within the OAM-TCD dataset.