Marra, D. M. | Search bioRxiv

bioRxiv2025

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

Tropical forest canopies contain many tree and liana species, and foliar and reproductive characteristics useful for taxonomic identification 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). Data/code for peer review statementWe 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.

ecology↗

bioRxiv2022

Tracking canopy gap dynamics across four sites in the Brazilian Amazon

Background information to give context to the studyCanopy gaps are the most evident manifestation of how disturbances disrupt forest landscapes. The size distribution and return frequency of gaps, and subsequent recovery processes, determine whether the old-growth state can be reached. The aim or research questionWe used remote sensing metrics to compare the disturbance regime of four Amazon regions based on the size distribution of gaps, their dynamics and geometric characteristics. A brief summary of the methodology usedWe assessed gap dynamics at four sites in the central, central eastern, southeastern, and northeastern regions of the Brazilian Amazon using repeated airborne laser scanning surveys. We developed a novel analysis to quantify four possible stages of gap dynamics: formation, expansion, persisting and recovering. For that, we overlapped layers of gap locations from two consecutive airborne laser scanning surveys. Key results with some significance measuresThe gap fraction in our study sites varied between 1.26% to 7.84%. All the sites have similar proportion of gaps among size classes. What notably changed between sites was not the gap size-distribution, but the relative importance of stages of gap dynamics. Growing and persisting rates were greatest in the site with the stronger seasonal variation in climate, lower annual precipitation, higher mean wind speed and higher solar radiation. The conclusions, which address the main aimsThe concept of stability reflects the tendency of a system to quickly return to a position of equilibrium when disturbed. We showed that gap dynamics varied among sites, with one example of low recovery rate contrasted to three other sites with faster recovery. Our results support that such as assessing the size distribution of gaps, investigating their return frequency and severity is crucial for understanding forest dynamics at the landscape and regional scales.

ecology↗