Individual mapping of large polymorphic shrubs in high mountains using satellite images and deep learning

Monitoring the distribution and size of long-living large shrubs, such as junipers, is crucial for assessing the long-term impacts of global change on high-mountain ecosystems. While deep learning models have shown remarkable success in object segmentation, adapting these models to detect shrub species with polymorphic nature remains challenging. In this research, we release a large dataset of individual shrub delineations on freely available satellite imagery and use an instance segmentation model to map all junipers over the treeline for an entire biosphere reserve (Sierra Nevada, Spain). To optimize performance, we introduced a novel dual data construction approach: using photo-interpreted (PI) data for model development and fieldwork (FW) data for validation. To account for the polymorphic nature of junipers during model evaluation, we developed a soft version of the Intersection over Union metric. Finally, we assessed the uncertainty of the resulting map in terms of canopy cover and density of shrubs per size class. Our model achieved an F1-score in shrub delineation of 87.87% on the PI data and 76.86% on the FW data. The R2 and RMSE of the observed versus predicted relationship were 0.63 and 6.67% for canopy cover, and 0.90 and 20.62 for shrub density. The greater density of larger shrubs in lower altitudes and smaller shrubs in higher altitudes observed in the model outputs was also present in the PI and FW data, suggesting an altitudinal uplift in the optimal performance of the species. This study demonstrates that deep learning applied on freely available high-resolution satellite imagery is useful to detect medium to large shrubs of high ecological value at the regional scale, which could be expanded to other high-mountains worldwide and to historical and fothcoming imagery. • The largest publicly available dataset of shrubs (8580 individuals). • Application of Mask R-CNN to detect polymorphic plants. • A new data construction approach to overcome the limitations of field surveying methods. • A new model evaluation metric for polymorphic plants. • Model deployment at the regional scale to map and count high-mountain individual shrubs.