Étienne Laliberté

Bringing SAM to new heights: Leveraging elevation data for tree crown segmentation from drone imagery

Mélisande Teng

Etienne Lalibert'e

Information on trees at the individual level is crucial for monitoring forest ecosystems and planning forest management. Current monitoring … (see more)methods involve ground measurements, requiring extensive cost, time and labor. Advances in drone remote sensing and computer vision offer great potential for mapping individual trees from aerial imagery at broad-scale. Large pre-trained vision models, such as the Segment Anything Model (SAM), represent a particularly compelling choice given limited labeled data. In this work, we compare methods leveraging SAM for the task of automatic tree crown instance segmentation in high resolution drone imagery in three use cases: 1) boreal plantations, 2) temperate forests and 3) tropical forests. We also study the integration of elevation data into models, in the form of Digital Surface Model (DSM) information, which can readily be obtained at no additional cost from RGB drone imagery. We present BalSAM, a model leveraging SAM and DSM information, which shows potential over other methods, particularly in the context of plantations. We find that methods using SAM out-of-the-box do not outperform a custom Mask R-CNN, even with well-designed prompts. However, efficiently tuning SAM end-to-end and integrating DSM information are both promising avenues for tree crown instance segmentation models.

2025-06-05

ArXiv (preprint)

arxiv.org

Bringing SAM to new heights: Leveraging elevation data for tree crown segmentation from drone imagery

Mélisande Teng

Etienne Lalibert'e

Information on trees at the individual level is crucial for monitoring forest ecosystems and planning forest management. Current monitoring … (see more)methods involve ground measurements, requiring extensive cost, time and labor. Advances in drone remote sensing and computer vision offer great potential for mapping individual trees from aerial imagery at broad-scale. Large pre-trained vision models, such as the Segment Anything Model (SAM), represent a particularly compelling choice given limited labeled data. In this work, we compare methods leveraging SAM for the task of automatic tree crown instance segmentation in high resolution drone imagery in three use cases: 1) boreal plantations, 2) temperate forests and 3) tropical forests. We also study the integration of elevation data into models, in the form of Digital Surface Model (DSM) information, which can readily be obtained at no additional cost from RGB drone imagery. We present BalSAM, a model leveraging SAM and DSM information, which shows potential over other methods, particularly in the context of plantations. We find that methods using SAM out-of-the-box do not outperform a custom Mask R-CNN, even with well-designed prompts. However, efficiently tuning SAM end-to-end and integrating DSM information are both promising avenues for tree crown instance segmentation models.

2025-06-01

arXiv (published)

doi.org

arxiv.org

Assessing SAM for Tree Crown Instance Segmentation from Drone Imagery

Mélisande Teng

Etienne Lalibert'e

2025-03-26

ArXiv (preprint)

arxiv.org

Assessing SAM for Tree Crown Instance Segmentation from Drone Imagery

Mélisande Teng

Etienne Lalibert'e

2025-03-26

ArXiv (preprint)

doi.org

arxiv.org

OpenForest: a data catalog for machine learning in forest monitoring

Arthur Ouaknine

Teja Kattenborn

Etienne Lalibert'e

David Rolnick

2025-02-27

Environmental Data Science (published)

doi.org

arxiv.org

Early Detection of an Invasive Alien Plant (Phragmites australis) Using Unoccupied Aerial Vehicles and Artificial Intelligence

Antoine Caron-Guay

Mickaël Germain

Étienne Laliberté

The combination of unoccupied aerial vehicles (UAVs) and artificial intelligence to map vegetation represents a promising new approach to im… (see more)prove the detection of invasive alien plant species (IAPS). The high spatial resolution achievable with UAVs and recent innovations in computer vision, especially with convolutional neural networks, suggest that early detection of IAPS could be possible, thus facilitating their management. In this study, we evaluated the suitability of this approach for mapping the location of common reed (Phragmites australis subsp. australis) within a national park located in southern Quebec, Canada. We collected data on six distinct dates during the growing season, covering environments with different levels of reed invasion. Overall, model performance was high for the different dates and zones, especially for recall (mean of 0.89). The results showed an increase in performance, reaching a peak following the appearance of the inflorescence in September (highest F1-score at 0.98). Furthermore, a decrease in spatial resolution negatively affected recall (18% decrease between a spatial resolution of 0.15 cm pixel−1 and 1.50 cm pixel−1) but did not have a strong impact on precision (2% decrease). Despite challenges associated with common reed mapping in a post-treatment monitoring context, the use of UAVs and deep learning shows great potential for IAPS detection when supported by a suitable dataset. Our results show that, from an operational point of view, this approach could be an effective tool for speeding up the work of biologists in the field and ensuring better management of IAPS.

2024-06-06

bioRxiv (preprint)

doi.org

Arbuscular and ectomycorrhizal tree seedling growth is inhibited by competition from neighboring roots and associated fungal hyphae

V. Parasquive

Jacques Brisson

Étienne Laliberté

P. L. Chagnon

2024-05-28

Plant and Soil (published)

doi.org

Coordination among leaf and fine-root traits along a strong natural soil fertility gradient