The Hierarchic treatment of marine ecological information from spatial networks of benthic platforms

Measuring biodiversity simultaneously in different locations, at different temporal scales, and over wide spatial scales is of strategic importance for the improvement of our understanding of the functioning of marine ecosystems and for the conservation of their biodiversity. Monitoring networks of cabled observatories, along with other docked autonomous systems (e.g., Remotely Operated Vehicles [ROVs], Autonomous Underwater Vehicles [AUVs], and crawlers), are being conceived and established at a spatial scale capable of tracking energy fluxes across benthic and pelagic compartments, as well as across geographic ecotones. At the same time, optoacoustic imaging is sustaining an unprecedented expansion in marine ecological monitoring, enabling the acquisition of new biological and environmental data at an appropriate spatiotemporal scale. At this stage, one of the main problems for an effective application of these technologies is the processing, storage, and treatment of the acquired complex ecological information. Here, we provide a conceptual overview on the technological developments in the multiparametric generation, storage, and automated hierarchic treatment of biological and environmental information required to capture the spatiotemporal complexity of a marine ecosystem. In doing so, we present a pipeline of ecological data acquisition and processing in different steps and prone to automation. We also give an example of population biomass, community richness and biodiversity data computation (as indicators for ecosystem functionality) with an Internet Operated Vehicle (a mobile crawler). Finally, we discuss the software requirements for that automated data processing at the level of cyber-infrastructures with sensor calibration and control, data banking, and ingestion into large data portals.Peer ReviewedPostprint (published version

Quantum-inspired computational imaging

Computational imaging combines measurement and computational methods with the aim of forming images even when the measurement conditions are weak, few in number, or highly indirect. The recent surge in quantum-inspired imaging sensors, together with a new wave of algorithms allowing on-chip, scalable and robust data processing, has induced an increase of activity with notable results in the domain of low-light flux imaging and sensing. We provide an overview of the major challenges encountered in low-illumination (e.g., ultrafast) imaging and how these problems have recently been addressed for imaging applications in extreme conditions. These methods provide examples of the future imaging solutions to be developed, for which the best results are expected to arise from an efficient codesign of the sensors and data analysis tools.Y.A. acknowledges support from the UK Royal Academy of Engineering under the Research Fellowship Scheme (RF201617/16/31). S.McL. acknowledges financial support from the UK Engineering and Physical Sciences Research Council (grant EP/J015180/1). V.G. acknowledges support from the U.S. Defense Advanced Research Projects Agency (DARPA) InPho program through U.S. Army Research Office award W911NF-10-1-0404, the U.S. DARPA REVEAL program through contract HR0011-16-C-0030, and U.S. National Science Foundation through grants 1161413 and 1422034. A.H. acknowledges support from U.S. Army Research Office award W911NF-15-1-0479, U.S. Department of the Air Force grant FA8650-15-D-1845, and U.S. Department of Energy National Nuclear Security Administration grant DE-NA0002534. D.F. acknowledges financial support from the UK Engineering and Physical Sciences Research Council (grants EP/M006514/1 and EP/M01326X/1). (RF201617/16/31 - UK Royal Academy of Engineering; EP/J015180/1 - UK Engineering and Physical Sciences Research Council; EP/M006514/1 - UK Engineering and Physical Sciences Research Council; EP/M01326X/1 - UK Engineering and Physical Sciences Research Council; W911NF-10-1-0404 - U.S. Defense Advanced Research Projects Agency (DARPA) InPho program through U.S. Army Research Office; HR0011-16-C-0030 - U.S. DARPA REVEAL program; 1161413 - U.S. National Science Foundation; 1422034 - U.S. National Science Foundation; W911NF-15-1-0479 - U.S. Army Research Office; FA8650-15-D-1845 - U.S. Department of the Air Force; DE-NA0002534 - U.S. Department of Energy National Nuclear Security Administration)Accepted manuscrip

A new 3-D modelling method to extract subtransect dimensions from underwater videos

Underwater video transects have become a common tool for quantitative analysis of the seafloor. However a major difficulty remains in the accurate determination of the area surveyed as underwater navigation can be unreliable and image scaling does not always compensate for distortions due to perspective and topography. Depending on the camera set-up and available instruments, different methods of surface measurement are applied, which make it difficult to compare data obtained by different vehicles. 3-D modelling of the seafloor based on 2-D video data and a reference scale can be used to compute subtransect dimensions. Focussing on the length of the subtransect, the data obtained from 3-D models created with the software PhotoModeler Scanner are compared with those determined from underwater acoustic positioning (ultra short baseline, USBL) and bottom tracking (Doppler velocity log, DVL). 3-D model building and scaling was successfully conducted on all three tested set-ups and the distortion of the reference scales due to substrate roughness was identified as the main source of imprecision. Acoustic positioning was generally inaccurate and bottom tracking unreliable on rough terrain. Subtransect lengths assessed with PhotoModeler were on average 20 % longer than those derived from acoustic positioning due to the higher spatial resolution and the inclusion of slope. On a high relief wall bottom tracking and 3-D modelling yielded similar results. At present, 3-D modelling is the most powerful, albeit the most time-consuming, method for accurate determination of video subtransect dimensions

Mapping and classification of ecologically sensitive marine habitats using unmanned aerial vehicle (UAV) imagery and object-based image analysis (OBIA)

Nowadays, emerging technologies, such as long-range transmitters, increasingly miniaturized components for positioning, and enhanced imaging sensors, have led to an upsurge in the availability of new ecological applications for remote sensing based on unmanned aerial vehicles (UAVs), sometimes referred to as “drones”. In fact, structure-from-motion (SfM) photogrammetry coupled with imagery acquired by UAVs offers a rapid and inexpensive tool to produce high-resolution orthomosaics, giving ecologists a new way for responsive, timely, and cost-effective monitoring of ecological processes. Here, we adopted a lightweight quadcopter as an aerial survey tool and object-based image analysis (OBIA) workflow to demonstrate the strength of such methods in producing very high spatial resolution maps of sensitive marine habitats. Therefore, three different coastal environments were mapped using the autonomous flight capability of a lightweight UAV equipped with a fully stabilized consumer-grade RGB digital camera. In particular we investigated a Posidonia oceanica seagrass meadow, a rocky coast with nurseries for juvenile fish, and two sandy areas showing biogenic reefs of Sabelleria alveolata. We adopted, for the first time, UAV-based raster thematic maps of these key coastal habitats, produced after OBIA classification, as a new method for fine-scale, low-cost, and time saving characterization of sensitive marine environments which may lead to a more effective and efficient monitoring and management of natural resource

Automated classification of three-dimensional reconstructions of coral reefs using convolutional neural networks

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hopkinson, B. M., King, A. C., Owen, D. P., Johnson-Roberson, M., Long, M. H., & Bhandarkar, S. M. Automated classification of three-dimensional reconstructions of coral reefs using convolutional neural networks. PLoS One, 15(3), (2020): e0230671, doi: 10.1371/journal.pone.0230671.Coral reefs are biologically diverse and structurally complex ecosystems, which have been severally affected by human actions. Consequently, there is a need for rapid ecological assessment of coral reefs, but current approaches require time consuming manual analysis, either during a dive survey or on images collected during a survey. Reef structural complexity is essential for ecological function but is challenging to measure and often relegated to simple metrics such as rugosity. Recent advances in computer vision and machine learning offer the potential to alleviate some of these limitations. We developed an approach to automatically classify 3D reconstructions of reef sections and assessed the accuracy of this approach. 3D reconstructions of reef sections were generated using commercial Structure-from-Motion software with images extracted from video surveys. To generate a 3D classified map, locations on the 3D reconstruction were mapped back into the original images to extract multiple views of the location. Several approaches were tested to merge information from multiple views of a point into a single classification, all of which used convolutional neural networks to classify or extract features from the images, but differ in the strategy employed for merging information. Approaches to merging information entailed voting, probability averaging, and a learned neural-network layer. All approaches performed similarly achieving overall classification accuracies of ~96% and >90% accuracy on most classes. With this high classification accuracy, these approaches are suitable for many ecological applications.This study was funded by grants from the Alfred P. Sloan Foundation (BMH, BR2014-049; https://sloan.org), and the National Science Foundation (MHL, OCE-1657727; https://www.nsf.gov). The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript