The use of hyperspectral imaging in marine applications is limited, largely due to the cost-prohibitive nature of the technology and the risk of submerging such expensive electronics. Here, we examine the use of low-cost (<5000 GBP) hyperspectral imaging as a potential addition to the marine monitoring toolbox. Using coral reefs in Bermuda as a case study and a trial for the technology, data was collected across two reef morphologies, representing fringing reefs and patch reefs. Hyperspectral data of various coral species, Montastraea cavernosa, Diploria labyrinthiformis, Pseudodiploria strigosa, and Plexaurella sp., were successfully captured and analyzed, indicating the practicality and suitability of underwater hyperspectral imaging for use in coral reef assessment. The spectral data was also used to demonstrate simple spectral classification to provide values of the percentage coverage of benthic habitat types. Finally, the raw image data was used to generate digital elevation models to measure the physical structure of corals, providing another data type able to be used in reef assessments. Future improvements were also suggested regarding how to improve the spectral data captured by the technique to account for the accurate application of correction algorithms.

Rising oceanic temperatures create more frequent coral bleaching events worldwide and as such there exists a need for rapid, non-destructive survey techniques to gather greater and higher definition information than that offered by traditional spectral based monitoring systems. Here, we examine thermally induced laboratory bleaching of Montipora capricornis and Montipora confusa samples, utilising hyperspectral data to gain an understanding of coral bleaching from a spectral standpoint. The data revealed several characteristic spectral peaks that can be used to make health determinations. The fluorescence peaks are attributed to fluorescent proteins (FPs) and Chlorophyll-a fluorescence. The reflectance peaks can be attributed to Chlorophyll absorption and accessory pigments such as Peridinin and Diadinoxanthin. Each characteristic spectral peak or ‘marker’ allows for observation of each aspect of coral health and hence, simultaneous monitoring of these markers using hyperspectral imaging techniques provides an opportunity to better understand the processes occurring during bleaching and the rates at which they occur relative to one another.

This study is the first known observation of biofluorescence in the lumpfish (Cyclopterus lumpus). Individual lumpfish were illuminated with blue excitation lighting for photography with both hyperspectral and filtered multispectral cameras. All photographed juvenile lumpfish (n = 11) exhibited green biofluorescence. Light emissions were characterised with two peaks observed at 545 and 613 nm, with the greatest intensity along the tubercles of the high crest and the three longitudinal ridges. Further research on the dynamics of biofluorescence through the lifecycle of this species is required.

Monitoring the health of coral reefs is essential to understanding the damaging impacts of anthropogenic climate change as such non-invasive methods to survey coral reefs are the most desirable. Optics-based surveys, ranging from simple photography to multispectral satellite imaging are well established. Herein, we review these techniques, focusing on their value for coral monitoring and health diagnosis. The techniques are broadly separated by the primary method in which data are collected: by divers and/or robots directly within the environment or by remote sensing where data are captured above the water’s surface by planes, drones, or satellites. The review outlines a new emerging technology, low-cost hyperspectral imagery, which is capable of simultaneously producing hyperspectral and photogrammetric outputs, thereby providing integrated information of the reef structure and physiology in a single data capture.

Monitoring the health of coral reefs is essential to understand the damaging impacts of anthropo-genic climate change. Non-invasive methods to survey coral reefs are the most desirable and op-tics-based surveys, ranging from simple photography to multispectral satellite imaging are well es-tablished. Herein, we review these techniques, focusing on their value for coral monitoring and health diagnosis. A new, low-cost hyperspectral imaging technique using linear variable filters is also described. This system is capable of simultaneously producing hyperspectral and photogrammetric outputs, which provides integrated information of reef structure and physiology.

Rapidly and repeatedly ascertaining the health status of coral reefs is an ever more pressing issue as part of activities to understand and monitor the damaging impacts of climate change. A combination of increasing ocean temperatures, acidity and frequency of extreme storm events continues to alter the marine environment beyond what sensitive organisms, such as coral, can cope with. It is therefore vital to establish technologies and validated methods to provide a metric or indication into the health of these organisms. There are currently many surveys and techniques used by coral scientists to uncover insights into the status and assessment of coral reefs, from colour wheels to multispectral satellite surveys. Here we outline an array of current techniques and methods focused specifically on coral monitoring and health diagnosis, ranging across the length scales from simple diver-based surveyance to satellite remote sensing. The technique of using hyperspectral fluorescence imaging is also introduced as a viable novel addition to aid and extend the current toolbox of available technologies.

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.

The use of low-cost, Remotely Operated Vehicle (ROV) and underwater photogrammetry techniques for 3D reconstruction of shallow hydrothermal vent sites around Paleochori Bay, Milos Island, Greece. Characterising venting fields through interactive bathymetry models produced from still images taken from camera onboard ROV flown over areas of interest in double raster pattern. First time the shallow venting fields on Milos have been actively surveyed using ROV. Areas were successfully surveyed and the bathymetry was reconstructed using SfM photogrammetry with a ~10 cm scale resolution. A diverse range of benthic habitats were surveyed and the resulting topographic models will act as a baseline, providing further characterisation of the vent systems and any evolving seafloor morphology associated with mineral deposition.

With the development of ever more powerful micro-computers, the cost and capabilities of robotic systems for environmental surveying using remotely control systems continues to decrease and improve. Historically, submarine exploration was restricted to companies or organisations with considerable finances and resources; however, the last decade has seen the advent of 'low cost' remotely operated vehicles (ROV). These cost anywhere from $400-$40,000 and provide an opportunity for wider participation in ocean exploration. However, with 60% of the world's seafloor lying at depths in excess of 1000 m and current low cost ROVs typiclly depth limited to just 100 m, there is presently an inability to "go deep" affordably. This review assesses the state of the art for deep ROV technologies and identifies the primary technological hurdles to overcome in order to facilitate proliferation of low cost ROVs for deep ocean exploration with an emphasis on their application to mineral and ore prospecting.

"Autonomous vehicles for ore prospecting: robots in the air and water." Applied Earth Science, 126(2), pp. 91–92

The development of low-cost, open-source Remotely Operated Vehicle (ROV) systems has provided almost unrestricted access for researchers looking to monitor the marine environment in ever greater resolution. Sampling microbial communities from the marine environment, however, still usually relies on Niskin-bottle sampling (ROV or Conductivity-Temperature-Depth sampler (CTD) based), a method which introduces an inaccuracy and variability that is incompatible with metatranscriptomic analysis, for example. Here, we describe a versatile, easily-replicated platform which achieves in situ mRNA preservation, via the addition of RNAlater to filtered microbial cells, to enhance ROV or CTD functionality.