Semantic segmentation of seagrass habitat from drone imagery based on deep learning: A comparative study

Intertidal macroalgal habitats are major components of temperate coastal ecosystems. Their distribution was studied using field sampling and hyperspectral remote mapping on a rocky shore of Porspoder (western Brittany, France). Covers of both dominating macroalgae and the sessile fauna were characterized in situ at low tide in 24 sampling spots, according to four bathymetric levels. A zone of ca. 17,000 m2 was characterized using a drone equipped with a hyperspectral camera. Macroalgae were identified by image processing using two classification methods to assess the representativeness of spectral classes. Finally, a comparison of the remote imaging data to the field sampling data was conducted. Seven seaweed classes were distinguished by hyperspectral pictures, including five different species of Fucales. The maximum likelihood (MLC) and spectral angle mapper (SAM) were both trained using image-derived spectra. MLC was more accurate to classify the main dominating species (Overall Accuracy (OA) 95.1%) than SAM (OA 87.9%) at a site scale. However, at sampling points scale, the results depend on the bathymetric level. This study evidenced the efficiency and accuracy of hyperspectral remote sensing to evaluate the distribution of dominating intertidal seaweed species and the potential for a combined field/remote approach to assess the ecological state of macroalgal communities.

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Seaweed Habitats on the Shore: Characterization through Hyperspectral UAV Imagery and Field Sampling

Background Seagrass beds are essential habitats in coastal ecosystems, providing valuable ecosystem services, but are threatened by various climate change and human activities. Seagrass monitoring by remote sensing have been conducted over past decades using satellite and aerial images, which have low resolution to analyze changes in the composition of different seagrass species in the meadows. Recently, unmanned aerial vehicles (UAVs) have allowed us to obtain much higher resolution images, which is promising in observing fine-scale changes in seagrass species composition. Furthermore, image processing techniques based on deep learning can be applied to the discrimination of seagrass species that were difficult based only on color variation. In this study, we conducted mapping of a multispecific seagrass bed in Saroma-ko Lagoon, Hokkaido, Japan, and compared the accuracy of the three discrimination methods of seagrass bed areas and species composition, i.e., pixel-based classification, object-based classification, and the application of deep neural network. Methods We set five benthic classes, two seagrass species (Zostera marina and Z. japonica), brown and green macroalgae, and no vegetation for creating a benthic cover map. High-resolution images by UAV photography enabled us to produce a map at fine scales (<1 cm resolution). Results The application of a deep neural network successfully classified the two seagrass species. The accuracy of seagrass bed classification was the highest (82%) when the deep neural network was applied. Conclusion Our results highlighted that a combination of UAV mapping and deep learning could help monitor the spatial extent of seagrass beds and classify their species composition at very fine scales.

Species level mapping of a seagrass bed using an unmanned aerial vehicle and deep learning technique

Abstract Biological traits analysis (BTA) links community structure to both ecological functions and response to environmental drivers through species’ attributes. In consequence, it has become a popular approach in marine benthic studies. However, BTA will reach a dead end if the scientific community does not acknowledge its current shortcomings and limitations: (a) uncertainties related to data origins and a lack of standardized reporting of trait information; (b) knowledge gaps on the role of multiple interacting traits on driving the organisms’ responses to environmental variability; (c) knowledge gaps regarding the mechanistic links between traits and functions; (d) a weak focus on the spatial and temporal variability that is inherent to the trait expression of species; and, last but not least, (e) the large reliance on expert knowledge due to an enormous knowledge gap on the basic ecology of many benthic species. BTA will only reach its full potential if the scientific community is able to standardize and unify the reporting and storage of traits data and reconsider the importance of baseline observational and experimental studies to fill knowledge gaps on the mechanistic links between biological traits, functions, and environmental variability. This challenge could be assisted by embracing new technological advances in marine monitoring, such as underwater camera technology and artificial intelligence, and making use of advanced statistical approaches that consider the interactive nature and spatio‐temporal variability of biological systems. The scientific community has to abandon some dead ends and explore new paths that will improve our understanding of individual species, traits, and the functioning of benthic ecosystems.

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Biological traits approaches in benthic marine ecology: Dead ends and new paths

Seagrass meadows are one of the blue carbon ecosystems that continue to decline worldwide. Frequent mapping is essential to monitor seagrass meadows for understanding change processes including seasonal variations and influences of meteorological and oceanic events such as typhoons and cyclones. Such mapping approaches may also enhance seagrass blue carbon strategy and management practices. Although unmanned aerial vehicle (UAV) aerial photography has been widely conducted for this purpose, there have been challenges in mapping accuracy, efficiency, and applicability to subtidal water meadows. In this study, a novel method was developed for mapping subtidal and intertidal seagrass meadows to overcome such challenges. Ground truth seagrass orthophotos in four seasons were created from the Futtsu tidal flat of Tokyo Bay, Japan, using vertical and oblique UAV photography. The feature pyramid network (FPN) was first applied for automated seagrass classification by adjusting the spatial resolution and normalization parameters and by considering the combinations of seasonal input data sets. The FPN classification results ensured high performance with the validation metrics of 0.957 overall accuracy (OA), 0.895 precision, 0.942 recall, 0.918 F1-score, and 0.848 IoU, which outperformed the conventional U-Net results. The FPN classification results highlighted seasonal variations in seagrass meadows, exhibiting an extension from winter to summer and demonstrating a decline from summer to autumn. Recovery of the meadows was also detected after the occurrence of Typhoon No. 19 in October 2019, a phenomenon which mainly happened before summer 2020.

Mapping of Subtidal and Intertidal Seagrass Meadows via Application of the Feature Pyramid Network to Unmanned Aerial Vehicle Orthophotos

Intertidal seagrass plays a vital role in estimating the overall health and dynamics of coastal environments due to its interaction with tidal changes. However, most seagrass habitats around the globe have been in steady decline due to human impacts, disturbing the already delicate balance in the environmental conditions that sustain seagrass. Miniaturization of multi-spectral sensors has facilitated very high resolution mapping of seagrass meadows, which significantly improves the potential for ecologists to monitor changes. In this study, two analytical approaches used for classifying intertidal seagrass habitats are compared—Object-based Image Analysis (OBIA) and Fully Convolutional Neural Networks (FCNNs). Both methods produce pixel-wise classifications in order to create segmented maps. FCNNs are an emerging set of algorithms within Deep Learning. Conversely, OBIA has been a prominent solution within this field, with many studies leveraging in-situ data and multiresolution segmentation to create habitat maps. This work demonstrates the utility of FCNNs in a semi-supervised setting to map seagrass and other coastal features from an optical drone survey conducted at Budle Bay, Northumberland, England. Semi-supervision is also an emerging field within Deep Learning that has practical benefits of achieving state of the art results using only subsets of labelled data. This is especially beneficial for remote sensing applications where in-situ data is an expensive commodity. For our results, we show that FCNNs have comparable performance with the standard OBIA method used by ecologists.

Brandon Lewis Hobley

Papers

Semi-Supervised Segmentation for Coastal Monitoring Seagrass Using RPA Imagery