Automated Image Analysis of Offshore Infrastructure Marine Biofouling

Supplementary Materials: The following are available online at www.mdpi.com/2077-1312/6/1/2/s1 Acknowledgments: This project was funded by the Natural Environmental Research Council (NERC) project No.: NE/N019865/1. The authors would like to thank Melanie Netherway and Don Orr, from our project partner (company requested to remain anonymous) for the provision of survey footage and for supporting the project. In addition, many thanks to Oscar Beijbom, University California Berkley for providing guidance and support to the project. Additional thanks to Calum Reay, Bibby Offshore; George Gair, Subsea 7; and Alan Buchan, Wood Group Kenny for help with footage collection and for allowing us to host workshops with them and their teams, their feedback and insights were very much appreciated.Peer reviewedPublisher PD

Repeatable semantic reef-mapping through photogrammetry and label-augmentation

In an endeavor to study natural systems at multiple spatial and taxonomic resolutions, there is an urgent need for automated, high-throughput frameworks that can handle plethora of information. The coalescence of remote-sensing, computer-vision, and deep-learning elicits a new era in ecological research. However, in complex systems, such as marine-benthic habitats, key ecological processes still remain enigmatic due to the lack of cross-scale automated approaches (mms to kms) for community structure analysis. We address this gap by working towards scalable and comprehensive photogrammetric surveys, tackling the profound challenges of full semantic segmentation and 3D grid definition. Full semantic segmentation (where every pixel is classified) is extremely labour-intensive and difficult to achieve using manual labeling. We propose using label-augmentation, i.e., propagation of sparse manual labels, to accelerate the task of full segmentation of photomosaics. Photomosaics are synthetic images generated from a projected point-of-view of a 3D model. In the lack of navigation sensors (e.g., a diver-held camera), it is difficult to repeatably determine the slope-angle of a 3D map. We show this is especially important in complex topographical settings, prevalent in coral-reefs. Specifically, we evaluate our approach on benthic habitats, in three different environments in the challenging underwater domain. Our approach for label-augmentation shows human-level accuracy in full segmentation of photomosaics using labeling as sparse as 0.1%, evaluated on several ecological measures. Moreover, we found that grid definition using a leveler improves the consistency in community-metrics obtained due to occlusions and topology (angle and distance between objects), and that we were able to standardise the 3D transformation with two percent error in size measurements. By significantly easing the annotation process for full segmentation and standardizing the 3D grid definition we present a semantic mapping methodology enabling change-detection, which is practical, swift, and cost-effective. Our workflow enables repeatable surveys without permanent markers and specialized mapping gear, useful for research and monitoring, and our code is available online. Additionally, we release the Benthos data-set, fully manually labeled photomosaics from three oceanic environments with over 4500 segmented objects useful for research in computer-vision and marine ecology

Comparative image analysis approaches to assess ecological effects of macroalgal removal on inshore reefs of Magnetic Island, Australia

Macroalgae removal is a proposed management option in the GBR to reverse declines in inshore coral reef health. Automated image analysis (AIA) is a valuable tool to assess benthic community assemblages. This study compared the accuracy of benthic community assemblages assessed through the AIA program CoralNet to manual image analysis. The ecological effect of macroalgae removal on benthic community composition was also investigated on established permanent quadrats (5x5 m) for reefs at Florence and Arthur Bay, Magnetic Island. Control and treatment quadrats (n=3 respectively) were photographed before and after macroalgae removal over 6 months. The results obtained by AIA and manual approaches were consistent, with macroalgae cover is approximately 77%-87% in all quadrats before macroalgal removal. Through the monitoring period, a small increase in coral cover in the macroalgal removal quadrats was observed in Florence and Arthur Bay (an increase of 1.8% and 0.1%, respectively). CoralNet was demonstrated to be robust for assessing reef benthic cover with no significant difference in recorded benthic categories when compared to the manual approach. CoralNet was accurate for identifying broad benthic categories, but less effective than manual image analyses for lower taxonomic categories (i.e., genus or species level)

Automatic Hierarchical Classification of Kelps utilizing Deep Residual Feature

Across the globe, remote image data is rapidly being collected for the assessment of benthic communities from shallow to extremely deep waters on continental slopes to the abyssal seas. Exploiting this data is presently limited by the time it takes for experts to identify organisms found in these images. With this limitation in mind, a large effort has been made globally to introduce automation and machine learning algorithms to accelerate both classification and assessment of marine benthic biota. One major issue lies with organisms that move with swell and currents, like kelps. This paper presents an automatic hierarchical classification method (local binary classification as opposed to the conventional flat classification) to classify kelps in images collected by autonomous underwater vehicles. The proposed kelp classification approach exploits learned feature representations extracted from deep residual networks. We show that these generic features outperform the traditional off-the-shelf CNN features and the conventional hand-crafted features. Experiments also demonstrate that the hierarchical classification method outperforms the traditional parallel multi-class classifications by a significant margin (90.0% vs 57.6% and 77.2% vs 59.0%) on Benthoz15 and Rottnest datasets respectively. Furthermore, we compare different hierarchical classification approaches and experimentally show that the sibling hierarchical training approach outperforms the inclusive hierarchical approach by a significant margin. We also report an application of our proposed method to study the change in kelp cover over time for annually repeated AUV surveys.Comment: MDPI Sensor

Automated Activity Estimation of the Cold-Water Coral Lophelia pertusa by Multispectral Imaging and Computational Pixel Classification

The cold-water coral Lophelia pertusa builds up bioherms that sustain high biodiversity in the deep ocean worldwide. Photographic monitoring of the polyp activity represents a helpful tool to characterize the health status of the corals and to assess anthropogenic impacts on the microhabitat. Discriminating active polyps from skeletons of white Lophelia pertusa is usually time-consuming and error-prone due to their similarity in color in common RGB camera footage. Acquisition of finer resolved spectral information might increase the contrast between the segments of polyps and skeletons, and therefore could support automated classification and accurate activity estimation of polyps. For recording the needed footage, underwater multispectral imaging systems can be used, but they are often expensive and bulky. Here we present results of a new, light-weight, compact and low-cost deep-sea tunable LED-based underwater multispectral imaging system (TuLUMIS) with eight spectral channels. A brunch of healthy white Lophelia pertusa was observed under controlled conditions in a laboratory tank. Spectral reflectance signatures were extracted from pixels of polyps and skeletons of the observed coral. Results showed that the polyps can be better distinguished from the skeleton by analysis of the eight-dimensional spectral reflectance signatures compared to three-channel RGB data. During a 72-hour monitoring of the coral with a half-hour temporal resolution in the lab, the polyp activity was estimated based on the results of the multispectral pixel classification using a support vector machine (SVM) approach. The computational estimated polyp activity was consistent with that of the manual annotation, which yielded a correlation coefficient of 0.957

Perspectives in visual imaging for marine biology and ecology: from acquisition to understanding

Durden J, Schoening T, Althaus F, et al. Perspectives in Visual Imaging for Marine Biology and Ecology: From Acquisition to Understanding. In: Hughes RN, Hughes DJ, Smith IP, Dale AC, eds. Oceanography and Marine Biology: An Annual Review. 54. Boca Raton: CRC Press; 2016: 1-72