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
Bibliographic record
Abstract
Abstract 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 statement 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.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.002 | 0.001 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.003 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.015 | 0.012 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".