Semantic Segmentation of Coral Reefs Using Convolutional Neural Networks: A Case Study in Kiritimati, Kiribati
Bibliographic record
Abstract
Habitat complexity plays a critical role in coral reef ecosystems by enhancing habitat availability, increasing ecological resilience, and offering coastal protection. Structure-from-motion (SfM) photogrammetry has become a standard approach for quantifying habitat complexity in reef monitoring programs. However, a major bottleneck remains in the two-dimensional (2D) classification of benthic cover in three-dimensional (3D) models, where experts are required to manually annotate individual colonies and identify coral species or taxonomic groups. With recent advances in deep learning and computer vision, automated classification of benthic habitats is possible. While some semi-automated tools exist, they are often limited in scope or do not provide semantic segmentation. In this investigation, we trained a convolutional neural network with the ResNet101 architecture on three years (2015, 2017, and 2019) of human-annotated 2D orthomosaics from Kiritimati, Kiribati. Our model accuracy ranged from 71% to 95%, with an overall accuracy of 84% and a mean intersection of union of 0.82, despite highly imbalanced training data, and it demonstrated successful generalizability when applied to new, untrained 2023 plots. Successful automation depends on training data that captures local ecological variation. As coral monitoring efforts move toward standardized workflows, locally developed models will be key to achieving fully automated, high-resolution classification of benthic communities across diverse reef environments.
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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 | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
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".