Manual Labelling Artificially Inflates Deep Learning-Based Segmentation Performance on RGB Images of Closed Canopy: Validation Using TLS

Monitoring forest dynamics at an individual tree scale is essential for accurately assessing ecosystem responses to climate change, yet traditional methods relying on field-based forest inventories are labor-intensive and limited in spatial coverage. Advances in remote sensing using drone-acquired RGB imagery combined with deep learning models have promised precise individual tree crown (ITC) segmentation; however, existing methods are frequently validated against human-annotated images, lacking rigorous independent ground truth. In this study, we generate high-fidelity validation labels from co-located Terrestrial Laser Scanning (TLS) data for drone imagery of mixed unmanaged boreal and Mediterranean forests. We evaluate the performance of two widely used deep learning ITC segmentation models - DeepForest (RetinaNet) and Detectree2 (Mask R-CNN) - on these data, and compare to performance on further Mediterranean forest data labelled manually. When validated against TLS-derived ground truth from Mediterranean forests, model performance decreased significantly compared to assessment based on hand-labelled from an ecologically similar site (AP50: 0.094 vs. 0.670). Restricting evaluation to only canopy trees shrank this gap considerably (Canopy AP50: 0.365), although performance was still far lower than on similar hand-labelled data. Models also performed poorly on boreal forest data (AP50: 0.142), although again increasing when evaluated on canopy trees only (Canopy AP50: 0.308). Both models showed very poor localisation accuracy at stricter IoU thresholds, even when restricted to canopy trees (Max AP75: 0.051). Similar results have been observed in studies using aerial LiDAR data, suggesting fundamental limitations in aerial-based segmentation approaches in closed canopy forests.

PointsToWood: A deep learning framework for complete canopy leaf-wood segmentation of TLS data across diverse European forests

Point clouds from Terrestrial Laser Scanning (TLS) are an increasingly popular source of data for studying plant structure and function but typically require extensive manual processing to extract ecologically important information. One key task is the accurate semantic segmentation of different plant material within point clouds, particularly wood and leaves, which is required to understand plant productivity, architecture and physiology. Existing automated semantic segmentation methods are primarily developed for single ecosystem types, and whilst they show good accuracy for biomass assessment from the trunk and large branches, often perform less well within the crown. In this study, we demonstrate a new framework that uses a deep learning architecture newly developed from PointNet and pointNEXT for processing 3D point clouds to provide a reliable semantic segmentation of wood and leaf in TLS point clouds from the tree base to branch tips, trained on data from diverse mature European forests. Our model uses meticulously labelled data combined with voxel-based sampling, neighbourhood rescaling, and a novel gated reflectance integration module embedded throughout the feature extraction layers. We evaluate its performance across open datasets from boreal, temperate, Mediterranean and tropical regions, encompassing diverse ecosystem types and sensor characteristics. Our results show consistent outperformance against the most widely used PointNet based approach for leaf/wood segmentation on our high-density TLS dataset collected across diverse mixed forest plots across all major biomes in Europe. We also find consistently strong performance tested on others open data from China, Eastern Cameroon, Germany and Finland, collected using both time-of-flight and phase-shift sensors, showcasing the transferability of our model to a wide range of ecosystems and sensors.

AI applications in forest monitoring need remote sensing benchmark datasets

With the rise in high resolution remote sensing technologies there has been an explosion in the amount of data available for forest monitoring, and an accompanying growth in artificial intelligence applications to automatically derive forest properties of interest from these datasets. Many studies use their own data at small spatio-temporal scales, and demonstrate an application of an existing or adapted data science method for a particular task. This approach often involves intensive and time-consuming data collection and processing, but generates results restricted to specific ecosystems and sensor types. There is a lack of widespread acknowledgement of how the types and structures of data used affects performance and accuracy of analysis algorithms. To accelerate progress in the field more efficiently, benchmarking datasets upon which methods can be tested and compared are sorely needed. Here, we discuss how lack of standardisation impacts confidence in estimation of key forest properties, and how considerations of data collection need to be accounted for in assessing method performance. We present pragmatic requirements and considerations for the creation of rigorous, useful benchmarking datasets for forest monitoring applications, and discuss how tools from modern data science can improve use of existing data. We list a set of example large-scale datasets that could contribute to benchmarking, and present a vision for how community-driven, representative benchmarking initiatives could benefit the field.