Individual tree-crown detection in RGB imagery using self-supervised deep learning neural networks

Abstract

Remote sensing can transform the speed, scale, and cost of biodiversity and forestry surveys. Data acquisition currently outpaces the ability to identify individual organisms in high resolution imagery. We outline an approach for identifying tree-crowns in RGB imagery while using a semi-supervised deep learning detection network. Individual crown delineation has been a long-standing challenge in remote sensing and available algorithms produce mixed results. We show that deep learning models can leverage existing Light Detection and Ranging (LIDAR)-based unsupervised delineation to generate trees that are used for training an initial RGB crown detection model. Despite limitations in the original unsupervised detection approach, this noisy training data may contain information from which the neural network can learn initial tree features. We then refine the initial model using a small number of higher-quality hand-annotated RGB images. We validate our proposed approach while using an open-canopy site in the National Ecological Observation Network. Our results show that a model using 434,551 self-generated trees with the addition of 2848 hand-annotated trees yields accurate predictions in natural landscapes. Using an intersection-over-union threshold of 0.5, the full model had an average tree crown recall of 0.69, with a precision of 0.61 for the visually-annotated data. The model had an average tree detection rate of 0.82 for the field collected stems. The addition of a small number of hand-annotated trees improved the performance over the initial self-supervised model. This semi-supervised deep learning approach demonstrates that remote sensing can overcome a lack of labeled training data by generating noisy data for initial training using unsupervised methods and retraining the resulting models with high quality labeled data.

Plant phenotyping relevance

RGB画像から個体の樹冠を検出・ delineateする深層学習手法の開発と検証が中心であり、樹冠という植物形態形質を直接推定している。

Code and data availability

The paper uses publicly available NEON airborne LIDAR, RGB orthomosaic, and woody vegetation structure data from the San Joaquin Experimental Range site, and provides its authors' analysis code publicly on GitHub (weecology/DeepLidar, archived on Zenodo). Both are paper-specific, public, and actionable.