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Montes-Herrera JC, Cimoli E, Cummings VJ, D'Archino R, Nelson WA, Lucieer A, Lucieer V. Quantifying pigment content in crustose coralline algae using hyperspectral imaging: A case study with Tethysphytum antarcticum (Ross Sea, Antarctica). JOURNAL OF PHYCOLOGY 2024; 60:695-709. [PMID: 38558363 DOI: 10.1111/jpy.13449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 04/04/2024]
Abstract
Crustose coralline algae (CCA) are a highly diverse group of habitat-forming, calcifying red macroalgae (Rhodophyta) with unique adaptations to diverse irradiance regimes. A distinctive CCA phenotype adaptation, which allows them to maximize photosynthetic performance in low light, is their content of a specific group of light-harvesting pigments called phycobilins. In this study, we assessed the potential of noninvasive hyperspectral imaging (HSI) in the visible spectrum (400-800 nm) to describe the phenotypic variability in phycobilin content of an Antarctic coralline, Tethysphytum antarcticum (Hapalidiales), from two distinct locations. We validated our measurements with pigment extractions and spectrophotometry analysis, in addition to DNA barcoding using the psbA marker. Targeted spectral indices were developed and correlated with phycobilin content using linear mixed models (R2 = 0.64-0.7). Once applied to the HSI, the models revealed the distinct phycoerythrin spatial distribution in the two site-specific CCA phenotypes, with thin and thick crusts, respectively. This study advances the capabilities of hyperspectral imaging as a tool to quantitatively study CCA pigmentation in relation to their phenotypic plasticity, which can be applied in laboratory studies and potentially in situ surveys using underwater hyperspectral imaging systems.
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Affiliation(s)
- Juan C Montes-Herrera
- Institute for Marine and Antarctic Studies, College of Sciences and Engineering, University of Tasmania, Hobart, Tasmania, Australia
| | - Emiliano Cimoli
- Institute for Marine and Antarctic Studies, College of Sciences and Engineering, University of Tasmania, Hobart, Tasmania, Australia
| | - Vonda J Cummings
- National Institute of Water and Atmospheric Research, Wellington, New Zealand
| | - Roberta D'Archino
- National Institute of Water and Atmospheric Research, Wellington, New Zealand
| | - Wendy A Nelson
- National Institute of Water and Atmospheric Research, Wellington, New Zealand
- Tāmaki Paenga Hira Auckland Museum & School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Arko Lucieer
- School of Geography, Planning, and Spatial Sciences, College of Sciences and Engineering, University of Tasmania, Hobart, Tasmania, Australia
| | - Vanessa Lucieer
- Institute for Marine and Antarctic Studies, College of Sciences and Engineering, University of Tasmania, Hobart, Tasmania, Australia
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Liu H, Summers N, Chen YC, Løvås HS, Johnsen G, Koestner D, Sætre C, Hamre B. Pixelwise immersion factor calibration for underwater hyperspectral imaging instruments. OPTICS EXPRESS 2024; 32:19854-19880. [PMID: 38859110 DOI: 10.1364/oe.523641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 04/30/2024] [Indexed: 06/12/2024]
Abstract
In situ spectral reflectance initially captured at high spatial resolution with underwater hyperspectral imaging (UHI) is effective for classification and quantification in oceanic biogeochemical studies; however, the measured spectral radiance is rarely used as an absolute quantity due to challenges in calibration of UHI instruments. In this paper, a commercial UHI instrument was calibrated for radiometric flat field response and pixelwise immersion effect to support in situ measurement of absolute spectral radiance. The radiometric and immersion factor calibrations of the UHI instrument were evaluated quantitatively through comparative experiments with a spectroradiometer and a spectrometer. Results show that the immersion factor of the center pixel of the tested UHI instrument was 1.763 in pure water at 600 nm, and the averaged difference in immersion factor between the center and edge pixel of the UHI instrument in the visible light band was only 1∼3% across its half angle field of view of 35° in air. The new calibration coefficients were further used to calculate the spectral radiance of transmitted sunlight through ice algae clusters in sea ice measured by the UHI instrument during an Arctic under-ice bio-optical survey.
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Santos J, Pedersen ML, Ulusoy B, Weinell CE, Pedersen HC, Petersen PM, Dam-Johansen K, Pedersen C. A Tunable Hyperspectral Imager for Detection and Quantification of Marine Biofouling on Coated Surfaces. SENSORS (BASEL, SWITZERLAND) 2022; 22:7074. [PMID: 36146436 PMCID: PMC9505677 DOI: 10.3390/s22187074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/31/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Fouling control coatings (FCCs) are used to prevent the accumulation of marine biofouling on, e.g., ship hulls, which causes increased fuel consumption and the global spread of non-indigenous species. The standards for performance evaluations of FCCs rely on visual inspections, which induce a degree of subjectivity. The use of RGB images for objective evaluations has already received interest from several authors, but the limited acquired information restricts detailed analyses class-wise. This study demonstrates that hyperspectral imaging (HSI) expands the specificity of biofouling assessments of FCCs by capturing distinguishing spectral features. We developed a staring-type hyperspectral imager using a liquid crystal tunable filter as the wavelength selective element. A novel light-emitting diode illumination system with high and uniform irradiance was designed to compensate for the low-filter transmittance. A spectral library was created from reflectance-calibrated optical signatures of representative biofouling species and coated panels. We trained a neural network on the annotated library to assign a class to each pixel. The model was evaluated on an artificially generated target, and global accuracy of 95% was estimated. The classifier was tested on coated panels (exposed at the CoaST Maritime Test Centre) with visible intergrown biofouling. The segmentation results were used to determine the coverage percentage per class. Although a detailed taxonomic description might be complex due to spectral similarities among groups, these results demonstrate the feasibility of HSI for repeatable and quantifiable biofouling detection on coated surfaces.
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Affiliation(s)
- Joaquim Santos
- Department of Electrical and Photonics Engineering (DTU Electro), Technical University of Denmark, 4000 Roskilde, Denmark
| | - Morten Lysdahlgaard Pedersen
- CoaST, Department of Chemical and Biochemical Engineering (DTU Chemical Engineering), Technical University of Denmark, 2800 Kongens Lyngby, Denmark
- Sino-Danish Center for Education and Research, Beijing 100093, China
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Burak Ulusoy
- CoaST, Department of Chemical and Biochemical Engineering (DTU Chemical Engineering), Technical University of Denmark, 2800 Kongens Lyngby, Denmark
- Sino-Danish Center for Education and Research, Beijing 100093, China
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Claus Erik Weinell
- CoaST, Department of Chemical and Biochemical Engineering (DTU Chemical Engineering), Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Henrik Chresten Pedersen
- Department of Electrical and Photonics Engineering (DTU Electro), Technical University of Denmark, 4000 Roskilde, Denmark
| | - Paul Michael Petersen
- Department of Electrical and Photonics Engineering (DTU Electro), Technical University of Denmark, 4000 Roskilde, Denmark
| | - Kim Dam-Johansen
- CoaST, Department of Chemical and Biochemical Engineering (DTU Chemical Engineering), Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Christian Pedersen
- Department of Electrical and Photonics Engineering (DTU Electro), Technical University of Denmark, 4000 Roskilde, Denmark
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Underwater Hyperspectral Imaging (UHI): A Review of Systems and Applications for Proximal Seafloor Ecosystem Studies. REMOTE SENSING 2021. [DOI: 10.3390/rs13173451] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
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.
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Verhaegen G, Cimoli E, Lindsay D. Life beneath the ice: jellyfish and ctenophores from the Ross Sea, Antarctica, with an image-based training set for machine learning. Biodivers Data J 2021; 9:e69374. [PMID: 34475799 PMCID: PMC8382665 DOI: 10.3897/bdj.9.e69374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 08/03/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Southern Ocean ecosystems are currently experiencing increased environmental changes and anthropogenic pressures, urging scientists to report on their biodiversity and biogeography. Two major taxonomically diverse and trophically important gelatinous zooplankton groups that have, however, stayed largely understudied until now are the cnidarian jellyfish and ctenophores. This data scarcity is predominantly due to many of these fragile, soft-bodied organisms being easily fragmented and/or destroyed with traditional net sampling methods. Progress in alternative survey methods including, for instance, optics-based methods is slowly starting to overcome these obstacles. As video annotation by human observers is both time-consuming and financially costly, machine-learning techniques should be developed for the analysis of in situ /in aqua image-based datasets. This requires taxonomically accurate training sets for correct species identification and the present paper is the first to provide such data. NEW INFORMATION In this study, we twice conducted three week-long in situ optics-based surveys of jellyfish and ctenophores found under the ice in the McMurdo Sound, Antarctica. Our study constitutes the first optics-based survey of gelatinous zooplankton in the Ross Sea and the first study to use in situ / in aqua observations to describe taxonomic and some trophic and behavioural characteristics of gelatinous zooplankton from the Southern Ocean. Despite the small geographic and temporal scales of our study, we provided new undescribed morphological traits for all observed gelatinous zooplankton species (eight cnidarian and four ctenophore species). Three ctenophores and one leptomedusa likely represent undescribed species. Furthermore, along with the photography and videography, we prepared a Common Objects in Context (COCO) dataset, so that this study is the first to provide a taxonomist-ratified image training set for future machine-learning algorithm development concerning Southern Ocean gelatinous zooplankton species.
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Affiliation(s)
- Gerlien Verhaegen
- Advanced Science-Technology Research (ASTER) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, JapanAdvanced Science-Technology Research (ASTER) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)YokosukaJapan
| | - Emiliano Cimoli
- Institute for Marine and Antarctic Studies, College of Sciences and Engineering, University of Tasmania, Hobart, AustraliaInstitute for Marine and Antarctic Studies, College of Sciences and Engineering, University of TasmaniaHobartAustralia
- Discipline of Geography and Spatial Sciences, School of Technology, Environments and Design, College of Sciences and Engineering, University of Tasmania, Hobart, AustraliaDiscipline of Geography and Spatial Sciences, School of Technology, Environments and Design, College of Sciences and Engineering, University of TasmaniaHobartAustralia
| | - Dhugal Lindsay
- Advanced Science-Technology Research (ASTER) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, JapanAdvanced Science-Technology Research (ASTER) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)YokosukaJapan
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Rapid changes in spectral composition after darkness influences nitric oxide, glucose and hydrogen peroxide production in the Antarctic diatom Fragilariopsis cylindrus. Polar Biol 2021. [DOI: 10.1007/s00300-021-02867-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Rapid Quantification of Microalgae Growth with Hyperspectral Camera and Vegetation Indices. PLANTS 2021; 10:plants10020341. [PMID: 33578920 PMCID: PMC7916729 DOI: 10.3390/plants10020341] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/05/2021] [Accepted: 02/06/2021] [Indexed: 11/17/2022]
Abstract
Spectral cameras are traditionally used in remote sensing of microalgae, but increasingly also in laboratory-scale applications, to study and monitor algae biomass in cultures. Practical and cost-efficient protocols for collecting and analyzing hyperspectral data are currently needed. The purpose of this study was to test a commercial, easy-to-use hyperspectral camera to monitor the growth of different algae strains in liquid samples. Indices calculated from wavebands from transmission imaging were compared against algae abundance and wet biomass obtained from an electronic cell counter, chlorophyll a concentration, and chlorophyll fluorescence. A ratio of selected wavebands containing near-infrared and red turned out to be a powerful index because it was simple to calculate and interpret, yet it yielded strong correlations to abundances strain-specifically (0.85 < r < 0.96, p < 0.001). When all the indices formulated as A/B, A/(A + B) or (A − B)/(A + B), where A and B were wavebands of the spectral camera, were scrutinized, good correlations were found amongst them for biomass of each strain (0.66 < r < 0.98, p < 0.001). Comparison of near-infrared/red index to chlorophyll a concentration demonstrated that small-celled strains had higher chlorophyll absorbance compared to strains with larger cells. The comparison of spectral imaging to chlorophyll fluorescence was done for one strain of green algae and yielded strong correlations (near-infrared/red, r = 0.97, p < 0.001). Consequently, we described a simple imaging setup and information extraction based on vegetation indices that could be used to monitor algae cultures.
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Cimoli E, Lucieer V, Meiners KM, Chennu A, Castrisios K, Ryan KG, Lund-Hansen LC, Martin A, Kennedy F, Lucieer A. Mapping the in situ microspatial distribution of ice algal biomass through hyperspectral imaging of sea-ice cores. Sci Rep 2020; 10:21848. [PMID: 33318636 PMCID: PMC7736878 DOI: 10.1038/s41598-020-79084-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/24/2020] [Indexed: 12/04/2022] Open
Abstract
Ice-associated microalgae make a significant seasonal contribution to primary production and biogeochemical cycling in polar regions. However, the distribution of algal cells is driven by strong physicochemical gradients which lead to a degree of microspatial variability in the microbial biomass that is significant, but difficult to quantify. We address this methodological gap by employing a field-deployable hyperspectral scanning and photogrammetric approach to study sea-ice cores. The optical set-up facilitated unsupervised mapping of the vertical and horizontal distribution of phototrophic biomass in sea-ice cores at mm-scale resolution (using chlorophyll a [Chl a] as proxy), and enabled the development of novel spectral indices to be tested against extracted Chl a (R2 ≤ 0.84). The modelled bio-optical relationships were applied to hyperspectral imagery captured both in situ (using an under-ice sliding platform) and ex situ (on the extracted cores) to quantitatively map Chl a in mg m−2 at high-resolution (≤ 2.4 mm). The optical quantification of Chl a on a per-pixel basis represents a step-change in characterising microspatial variation in the distribution of ice-associated algae. This study highlights the need to increase the resolution at which we monitor under-ice biophysical systems, and the emerging capability of hyperspectral imaging technologies to deliver on this research goal.
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Affiliation(s)
- Emiliano Cimoli
- Institute for Marine and Antarctic Studies, College of Sciences and Engineering, University of Tasmania, Private Bag 129, Hobart, TAS, 7001, Australia.
| | - Vanessa Lucieer
- Institute for Marine and Antarctic Studies, College of Sciences and Engineering, University of Tasmania, Private Bag 129, Hobart, TAS, 7001, Australia
| | - Klaus M Meiners
- Australian Antarctic Division, Department of Agriculture, Water and the Environment, Kingston, TAS, 7050, Australia.,Australian Antarctic Program Partnership, Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, 7001, Australia
| | - Arjun Chennu
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359, Bremen, Germany.,Leibinz Center for Marine Tropical Research, Fahrenheitstrasse 6, 28359, Bremen, Germany
| | - Katerina Castrisios
- Institute for Marine and Antarctic Studies, College of Sciences and Engineering, University of Tasmania, Private Bag 129, Hobart, TAS, 7001, Australia
| | - Ken G Ryan
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Lars Chresten Lund-Hansen
- Aquatic Biology, Department of Bioscience, Aarhus University, Ole Worms Allé 1, Building 1134, 8000, Aarhus C, Denmark.,Arctic Research Centre, Aarhus University, Ny Munkegade 116, Building 1540, 8000, Aarhus C, Denmark
| | - Andrew Martin
- Institute for Marine and Antarctic Studies, College of Sciences and Engineering, University of Tasmania, Private Bag 129, Hobart, TAS, 7001, Australia
| | - Fraser Kennedy
- Institute for Marine and Antarctic Studies, College of Sciences and Engineering, University of Tasmania, Private Bag 129, Hobart, TAS, 7001, Australia
| | - Arko Lucieer
- Discipline of Geography and Spatial Sciences, School of Technology, Environments and Design, College of Sciences and Engineering, University of Tasmania, Private Bag 76, Hobart, TAS, 7001, Australia
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Underwater Hyperspectral Imaging Technology and Its Applications for Detecting and Mapping the Seafloor: A Review. SENSORS 2020; 20:s20174962. [PMID: 32887344 PMCID: PMC7506868 DOI: 10.3390/s20174962] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/20/2020] [Accepted: 08/31/2020] [Indexed: 11/17/2022]
Abstract
Common methods of ocean remote sensing and seafloor surveying are mainly carried out by airborne and spaceborne hyperspectral imagers. However, the water column hinders the propagation of sunlight to deeper areas, thus limiting the scope of observation. As an emerging technology, underwater hyperspectral imaging (UHI) is an extension of hyperspectral imaging technology in air conditions, and is undergoing rapid development for applications in shallow and deep-sea environments. It is a close-range, high-resolution approach for detecting and mapping the seafloor. In this paper, we focus on the concepts of UHI technology, covering imaging systems and the correction methods of eliminating the water column’s influence. The current applications of UHI, such as deep-sea mineral exploration, benthic habitat mapping, and underwater archaeology, are highlighted to show the potential of this technology. This review can provide an introduction and overview for those working in the field and offer a reference for those searching for literature on UHI technology.
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