Underwater Hyperspectral Imaging (UHI): a review of systems and applications for proximal seafloor ecosystem studies

Marine ecosystem monitoring requires observations of its attributes at different spatial and temporal scales that traditional sampling methods (e.g., RGB imaging, sediment cores) struggle to efficiently provide. Proximal optical sensing methods can fill this observational gap by providing observations of, and tracking changes in, the functional features of marine ecosystems non-invasively. Underwater hyperspectral imaging (UHI) employed in proximity to the seafloor has shown a further potential to monitor pigmentation in benthic and sympagic phototrophic organisms at small spatial scales (mm–cm) and for the identification of minerals and taxa through their finely resolved spectral signatures. Despite the increasing number of studies applying UHI, a review of its applications, capabilities, and challenges for seafloor ecosystem research is overdue. In this review, we first detail how the limited band availability inherent to standard underwater cameras has led to a data analysis “bottleneck” in seafloor ecosystem research, in part due to the widespread implementation of underwater imaging platforms (e.g., remotely operated vehicles, time-lapse stations, towed cameras) that can acquire large image datasets. We discuss how hyperspectral technology brings unique opportunities to address the known limitations of RGB cameras for surveying marine environments. The review concludes by comparing how different studies harness the capacities of hyperspectral imaging, the types of methods required to validate observations, and the current challenges for accurate and replicable UHI research

Hyperspectral imaging as a tool for assessing coral health utilising natural fluorescence

Fluorescent proteins are a crucial visualisation tool in a myriad of research fields including cell biology, microbiology and medicine. Fluorescence is a result of the absorption of electromagnetic radiation at one wavelength and its reemission at a longer wavelength. Coral communities exhibit a natural fluorescence which can be used to distinguish between diseased and healthy specimens, however, current methods, such as the underwater visual census, are expensive and time-consuming constituting many manned dive hours. We propose the use of a remotely operated vehicle mounted with a novel hyperspectral fluorescence imaging (HyFI) “payload” for more rapid surveying and data collection. We have tested our system in a laboratory environment on common coral species including Seriatopora spp., Montipora verrucosa, Montipora spp., Montipora capricornis, Echinopora lamellose, Euphyllia ancora, Pocillopora damicornis and Montipora confusa. With the aid of hyperspectral imaging, the coral specimens’ emission wavelengths can be accurately assessed by capturing the emission spectra of the corals when excited with light emitting diodes (395–405 and 440 nm). Fluorescence can also provide an indicator of coral bleaching as shown in our bleaching experiment where we observe fluorescence reduction alongside coral bleaching

High-speed scanless entire bandwidth mid-infrared chemical imaging

Mid-infrared spectroscopy probes molecular vibrations to identify chemical species and functional groups. Therefore, mid-infrared hyperspectral imaging is one of the most powerful and promising candidates for chemical imaging using optical methods. Yet high-speed and entire bandwidth mid-infrared hyperspectral imaging has not been realized. Here we report a mid-infrared hyperspectral chemical imaging technique that uses chirped pulse upconversion of sub-cycle pulses at the image plane. This technique offers a lateral resolution of 15 $\mu$m, and the field of view is adjustable between 800 $\mu$m $\times$ 600 $\mu$m to 12 mm $\times$ 9 mm. The hyperspectral imaging produces a 640 $\times$ 480 pixel image in 8 s, which covers a spectral range of 640-3015 cm$^{-1}$, comprising 1069 wavelength points and offering a wavenumber resolution of 2.6-3.7 cm$^{-1}$. For discrete frequency mid-infrared imaging, the measurement speed reaches a frame rate of 5 kHz, the repetition rate of the laser. As a demonstration, we effectively identified and mapped different components in a microfluidic device, plant cell, and mouse embryo section. The great capacity and latent force of this technique in chemical imaging promise to be applied to many fields such as chemical analysis, biology, and medicine.Comment: 22 pages, 10 figure

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

Sensing Archaeology in the North: The Use of Non-Destructive Geophysical and Remote Sensing Methods in Archaeology in Scandinavian and North Atlantic Territories

In August 2018, a group of experts working with terrestrial/marine geophysics and remote sensing methods to explore archaeological sites in Denmark, Finland, Norway, Scotland and Sweden gathered together for the first time at the Workshop ‘Sensing Archaeology in The North’. The goal was to exchange experiences, discuss challenges, and consider future directions for further developing these methods and strategies for their use in archaeology. After the event, this special journal issue was arranged to publish papers that are based on the workshop presentations, but also to incorporate work that is produced by other researchers in the field. This paper closes the special issue and further aims to provide current state-of-the-art for the methods represented by the workshop. Here, we introduce the aspects that inspired the organisation of the meeting, a summary of the 12 presentations and eight paper contributions, as well as a discussion about the main outcomes of the workshop roundtables, including the production of two searchable databases (online resources and equipment). We conclude with the position that the ‘North’, together with its unique cultural heritage and thriving research community, is at the forefront of good practice in the application and development of sensing methods in archaeological research and management. However, further method development is required, so we claim the support of funding bodies to back research efforts based on testing/experimental studies to: explore unknown survey environments and identify optimal survey conditions, as well as to monitor the preservation of archaeological remains, especially those that are at risk. It is demonstrated that remote sensing and geophysics not only have an important role in the safeguarding of archaeological sites from development and within prehistorical-historical research, but the methods can be especially useful in recording and monitoring the increased impact of climate change on sites in the North

Macroalgal assemblages as indicators of the ecological status of marine coastal systems: A review

Abstract Macroalgae have been utilized as biological indicators of ecosystem health in many monitoring programs worldwide. These programs have utilized various methods to quantify macroalgal community structures. The aim of this study was to provide an overview of current progress by reviewing techniques and methods in both monitoring programs and impact evaluation studies that use macroalgal assemblage data. A total of 215 papers were selected and divided into four categories: macroalgal assemblage monitoring, macroalgal mapping, developing and employing ecological indices based on macroalgae, and developing and employing generic ecological indices including macroalgae. The number and goals of macroalgal monitoring programs are very different among geographical areas. In Europe, the recent European Union Directives led to the development of indices as tool to monitor the ecological quality of coastal systems. In other geographic regions, most studies focused on mapping the distribution of kelps or Fucales. This demonstrates the necessity to harmonize marine macroalgal monitoring, identifying common metrics and approaches in sampling design, field measurements, taxonomic resolution and data management, in order to develop standardized procedures which may allow data obtained to be compared

The Future of Coral Reefs

This volume contains a series of papers prepared for presentation at the 14th International Coral Reef Symposium, originally planned for July 2020 in Bremen, Germany, but postponed until 2021 (online) and 2022 (in person) because of the COVID-19 pandemic. It contains a series of papers illustrating the breadth of modern studies on coral reefs and the response of the reef science community to the threats that coral reefs now face, above all from climate change. The first group of papers focus on the biology of a selection of reef organisms, ranging from sea fans to coral dwelling crabs. The next group describe studies of coral communities and ecological interactions in regions as diverse as Florida, Kenya, Colombia, and Norway. Further papers describe investigations into the effects of global warming (in the Maldives and in Timor-Leste) and of other impacts (UV blockers, ocean acidification). The final two papers describe the latest applications of satellite and camera technology to the challenge of mapping and monitoring reefs

Underwater hyperspectral imagery to create biogeochemical maps of seafloor properties

This chapter presents aspects of underwater hyperspectral imaging (UHI) techniques aimed at mapping biogeochemical objects of interest (OOI) on the seafloor. Case examples of instrument-carrying platforms and biogeochemical applications are given. We discuss how to create high resolution, georeferenced, optically corrected digital underwater maps of different habitats, minerals, substrates, and organisms. Corrections for platform speed and direction, inherent optical properties (IOP), optical path length, dynamic positioning, and pitch/roll/yaw are discussed in the context of using UHI-based optical fingerprints (i.e. spectral reflectance in visible wavelengths) of different targets to create maps that can help discriminate, identify, and quantify OOI, and provide statistical information on relevant seafloor features. © 2013 Woodhead Publishing Limited. All rights reserved

Obtaining Hyperspectral Signatures for Seafloor Massive Sulphide Exploration

Seafloor massive sulphide (SMS) deposits are hosts to a wide range of economic minerals, and may become an important resource in the future. The exploitation of these resources is associated with considerable expenses, and a return on investment may depend on the availability of multiple deposits. Therefore, efficient exploration methodologies for base metal deposits are important for future deep sea mining endeavours. Underwater hyperspectral imaging (UHI) has been demonstrated to be able to differentiate between different types of materials on the seafloor. The identification of possible end-members from field data requires prior information in the form of representative signatures for distinct materials. This work presents hyperspectral imaging applied to a selection of materials from the Loki’s Castle active hydrothermal vent site in a laboratory setting. A methodology for compensating for systematic effects and producing the reflectance spectra is detailed, and applied to recover the spectral signatures from the samples. The materials investigated were found to be distinguishable using unsupervised dimensionality reduction methods, and may be used as a reference for future field application