Antoine Caron-Guay

Mark A. Friedl

Changes in Arctic tundra vegetation, driven by climate change, may be inducing major shifts in ecosystem services and the Arctic carbon budg… (see more)et, and altering high latitude feedbacks to the climate system. Field-based studies have documented warming-induced shrub expansion, and remote sensing has revealed heterogeneous, but primarily positive, trends in peak summer greenness across the Arctic. However, efforts to move beyond remotely sensed measures of spectral greening to quantify the spatial extent and rate of shrub expansion have been constrained by spectral similarities among tundra vegetation types, limited ground truth data, low revisit frequency of satellite observations, and sub-pixel heterogeneity of land cover at medium spatial resolution (30 m). To address these challenges, we developed a methodology that integrates high spatial resolution (2 m) commercial satellite imagery with Harmonized Landsat and Sentinel-2 observations in a machine learning framework, and used it to produce annual maps for 2016 to 2023 of sub-pixel land cover fractions at 30-m spatial resolution across three Arctic tundra ecoregions spanning 3.35 × 105 km2 between the Seward and Tuktoyaktuk Peninsulas. Uncertainty was quantified at each pixel via Monte Carlo resampling. Independent accuracy assessments yielded good accuracies (mean squared errors of 15.98% and 11.89% for low-stature vegetation and erect shrub cover, respectively), that were comparable to or exceeded previous mapping efforts. Further, repeat commercial satellite image pairs enabled the first assessment of mapped fractional cover change in Arctic tundra (R2 of 0.46 and 0.55, change direction accuracies of 77% and 78% for low-stature vegetation and erect shrub cover, respectively). This novel, scalable, multi-sensor approach to fractional land cover mapping produced the first annual maps of land cover fractions in the Arctic tundra, which support more accurate representation of vegetation dynamics and their linkages to climate change and disturbance processes.

2026-09-30

Remote Sensing of Environment (published)

Early detection of common reed ( <i>Phragmites australis</i> ) using unoccupied aerial vehicles and deep learning

Mickaël Germain

2026-04-12

Canadian Journal of Remote Sensing (published)

Seeing the forest and the trees: a workflow for automatic acquisition of ultra-high resolution drone photos of tropical forest canopies to support botanical and ecological studies

Vincent Le Falher

Guillaume Tougas

Helene C. Muller-Landau

Gonzalo Rivas-Torres

Thomas R. Walla

Hugo Baudchon

Melvin Hernández

Adrian Buenaño

Anna Weber

Jeffrey Q. Chambers

Jomber Chota Inuma

Fernando Araúz

Jorge Valdes

Andrés Hernández

David Brassfield

P. Sérgio

Vicente Vasquez

Adriana Simonetti … (see 7 more)

Daniel Magnabosco Marra

Caroline de Moura Vasconcelos

Jarol Fernando Vaca

Geovanny Rivadeneyra

José Illanes

Luis A. Salagaje-Muela

Jefferson Gualinga

Tropical forest canopies contain many tree and liana species, and foliar and reproductive characteristics useful for taxonomic identificatio… (see more)n are often difficult to see from the forest floor. As such, taxonomic identification often becomes a bottleneck in tropical forest inventories. Here we present a drone-based workflow to automatically acquire large volumes of close-up, ultra-high resolution photos of selected tree crowns (or specific locations over the canopy) to support tropical botanical and ecological studies ( https://youtu.be/80goMEifpc4 ). Our workflow is built around the small, easy-to-use DJI Mavic 3 Enterprise (M3E) drone, which is equipped with a wide-angle and a telephoto camera. On day one, the pilot maps a forest area of up to ∼200 ha with the wide-angle camera to generate a high-resolution digital surface model (DSM) and orthomosaic using structure-from-motion (SfM) photogrammetry. On subsequent days, the pilot acquires close-up photos with the telephoto camera from up to 300 selected canopy trees per day. These close-up photos are acquired from 6 m above the canopy and contain a high level of visual detail that allows botanists to reliably identify many tree and liana species. The photos are geolocated with survey-grade accuracy using RTK GNSS, thus facilitating spatial co-registration with other data sources, including the photogrammetry products. The primary operational challenge of our workflow is the need to maintain RTK corrections with the drone to ensure that close-up photos are acquired exactly at the predefined locations. The maximum operational range we achieved was 3 km, which would allow the pilot to reach any tree within a ∼2800 ha area from the take-off point. Although our workflow was developed to support taxonomic identification of tropical trees and lianas, it could be extended to any other forest or vegetation type to support botanical, phenological, and ecological studies. We provide harpia , an open-source Python library to program these automatic close-up photo missions with the M3E drone ( https://github.com/traitlab/harpia ). We provide harpia , an open-source Python library to program these automatic close-up photo missions ( https://github.com/traitlab/harpia ). Drone imagery and labelled close-up photo data are not yet publicly available because they were acquired with the goal of publishing benchmark machine learning datasets and models for tree and liana species classification and prior publication of the data would jeopardize this future publication.

2026-01-05

bioRxiv (preprint)

SelvaBox: A high‑resolution dataset for tropical tree crown detection

Hugo Baudchon

Arthur Ouaknine

Martin Weiss

Mélisande Teng

Thomas Walla

Christopher Pal

Detecting individual tree crowns in tropical forests is essential to study these complex and crucial ecosystems impacted by human interventi… (see more)ons and climate change. However, tropical crowns vary widely in size, structure, and pattern and are largely overlapping and intertwined, requiring advanced remote sensing methods applied to high-resolution imagery. Despite growing interest in tropical tree crown detection, annotated datasets remain scarce, hindering robust model development. We introduce SelvaBox, the largest open‑access dataset for tropical tree crown detection in high-resolution drone imagery. It spans three countries and contains more than

2025-12-31

International Conference on Learning Representations (Accept (Poster))

openreview.net

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

Mickaël Germain

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.

2024-06-05

bioRxiv (preprint)