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.

In this study we applied for the first time Fully Convolutional Neural Networks (FCNNs) to a marine bathymetric dataset to derive morphological classes over the entire Irish continental shelf. FCNNs are a set of algorithms within Deep Learning that produce pixel-wise classifications in order to create semantically segmented maps. While they have been extensively utilised on imagery for ecological mapping, their application on elevation data is still limited, especially in the marine geomorphology realm. We employed a high-resolution bathymetric dataset to create a set of normalised derivatives commonly utilised in seabed morphology and habitat mapping that include three bathymetric position indexes (BPIs), the vector ruggedness measurement (VRM), the aspect functions and three types of hillshades. The class domains cover ten or twelve semantically distinct surface textures and submarine landforms present on the shelf, with our definitions aiming for simplicity, prevalence and distinctiveness. Sets of 50 or 100 labelled samples for each class were used to train several U-Net architectures with ResNet-50 and VGG-13 encoders. Our results show a maximum model precision of 0.84 and recall of 0.85, with some classes reaching as high as 0.99 in both. A simple majority (modal) voting combining the ten best models produced an excellent map with overall F1 score of 0.96 and class precisions and recalls superior to 0.87. For target classes exhibiting high recall (proportion of positives identified), models also show high precision (proportion of correct identifications) in predictions which confirms that the underlying class boundary has been learnt. Derivative choice plays an important part in the performance of the networks, with hillshades combined with bathymetry providing the best results and aspect functions and VRM leading to an overall deterioration of prediction accuracies. The results show that FCNNs can be successfully applied to the seabed for a morphological exploration of the dataset and as a baseline for more in-depth habitat mapping studies. For example, prediction of semantically distinct classes as “submarine dune” and “bedrock outcrop” can be precise and reliable. Nonetheless, at present state FCNNs are not suitable for tasks that require more refined geomorphological classifications, as for the recognition of detailed morphogenetic processes.

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 environmental conditions that sustain seagrass. Miniaturization of multi-spectral sensors has facilitated very high resolution mapping of seagrass meadows, which significantly improve 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, however FCNNs are an emerging set of algorithms within Deep Learning with sparse application towards seagrass mapping. Conversely, OBIA has been a prominent solution within this field, with many studies leveraging in-situ data and multiscale 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 standard OBIA method used by ecologists, while also noting an increase in performance for mapping ecological features that are sparsely labelled across the study site.