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Prakasa, E., A. Rachman, D. R. Noerdjito, and R. Wardoyo. "Development of segmentation algorithm for determining planktonic objects from microscopic images." IOP Conference Series: Earth and Environmental Science 944, no. 1 (December 1, 2021): 012025. http://dx.doi.org/10.1088/1755-1315/944/1/012025.
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Abstract Plankton are free-floating organisms that live, grow, and move along with the ocean currents. This free-floating organism plays important roles as primary producers, they serve as a link to energy transfer, and a factor that regulates the biogeochemical cycles. Indonesia, with almost 60% of its territory covered by the ocean, harbours a wide variety of planktonic species. However, one of the issues within usual planktonic studies is the lack of a fast and accurate method for identifying and classifying the plankton type. Thus, the computer vision methods on microscopic images were proposed to deal with the problem. The classification follows two main steps, detecting plankton location and followed by plankton differentiation. The segmentation algorithm is required to limit the determination area. The present study describes the segmentation methods on fifteen plankton types. The U-Net based architecture was implemented to segment the plankton texture from other objects. The segmentation result was also compared with the manual assessment to compute the performance parameters. The accuracy, 0.970±0.025, gives the highest value whereas the smallest value is found in the precision parameter, 0.761±0.156.
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Campbell, R. W., P. L. Roberts, and J. Jaffe. "The Prince William Sound Plankton Camera: a profiling in situ observatory of plankton and particulates." ICES Journal of Marine Science 77, no. 4 (March 24, 2020): 1440–55. http://dx.doi.org/10.1093/icesjms/fsaa029.
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Abstract A novel plankton imager was developed and deployed aboard a profiling mooring in Prince William Sound in 2016–2018. The imager consisted of a 12-MP camera and a 0.137× telecentric lens, along with darkfield illumination produced by an in-line ring/condenser lens system. Just under 2.5 × 106 images were collected during 3 years of deployments. A subset of almost 2 × 104 images was manually identified into 43 unique classes, and a hybrid convolutional neural network classifier was developed and trained to identify the images. Classification accuracy varied among the different classes, and applying thresholds to the output of the neural network (interpretable as probabilities or classifier confidence), improved classification accuracy in non-ambiguous groups to between 80% and 100%.
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Shahani, Kamran, Hong Song, Syed Raza Mehdi, Awakash Sharma, Ghulam Tunio, Junaidullah Qureshi, Noor Kalhoro, and Nooruddin Khaskheli. "Design and Testing of an Underwater Microscope with Variable Objective Lens for the Study of Benthic Communities." Journal of Marine Science and Application 20, no. 1 (March 2021): 170–78. http://dx.doi.org/10.1007/s11804-020-00185-9.
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AbstractMonitoring the ecology and physiology of corals, sediments, planktons, and microplastic at a suitable spatial resolution is of great importance in oceanic scientific research. To meet this requirement, an underwater microscope with an electrically controlled variable lens was designed and tested. The captured microscopic images of corals, sediments, planktons, and microplastic revealed their physical, biological, and morphological characteristics. Further studies of the images also revealed the growth, degradation, and bleaching patterns of corals; the presence of plankton communities; and the types of microplastics. The imaging performance is majorly influenced by the choice of lenses, camera selection, and lighting method. Image dehazing, global saturation masks, and image histograms were used to extract the image features. Fundamental experimental proof was obtained with micro-scale images of corals, sediments, planktons, and microplastic at different magnifications. The designed underwater microscope can provide relevant new insights into the observation and detection of the future conditions of aquatic ecosystems.
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Karmini, Mimin, and H. Yuniarto. "BIOSTRATIGRAFI FORAMINIFERA KUARTER PADA BOR INTI MD 982152 DAN 982155 DARI SAMUDRA HINDIA." JURNAL GEOLOGI KELAUTAN 11, no. 2 (February 16, 2016): 55. http://dx.doi.org/10.32693/jgk.11.2.2013.231.
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Dari bor inti pada EKSPEDISI IMAGES, di Samudra Hindia, telah diteliti sebanyak 21 percontoh sedimen dari lokasi MD 982152, dan 29 buah dari lokasi MD 982155 untuk kepentingan biostratigrafi berdasarkan analisis foraminifera plankton dalam interval 1,5 meter.
Pada kedua penampang bor inti tersebut hanya dijumpai satu zona foraminifera plankton Kuarter, yaitu Zona Globorotalia truncatulinoides. Untuk MD 982152, zona ini bisa dibagi ke dalam dua subzona, yakni Subzona-subzona Globorotalia crassaformis hessi dan Globigerinella calida, sedangkan untuk MD 982155, zona tersebut bisa dibagi lagi ke dalam tiga subzona, yakni Subzona-subzona Globorotalia crassaformis hessi Globigerinella calida, dan Beella digitata.
Kejadian yang signifikan di kedua penampang itu adalah Datum Pemunculan Pertama dari Globigerinella calida dan Pemunculan Akhir dari Globorotalia crassaformis hessi. Pada MD 982155, dijumpai Pemunculan Pertama dari Beella digitata.
Kata kunci: foraminifera plankton, Kuarter, biostratigrafi, Samudra Hindia.
From IMAGES Expedition in Indian Ocean, 21 samples from MD 982152, and 29 samples from MD 982155 had been studied for the purpose of biostratigraphy based on planktonic foraminifera within 1,5 meter interval.
In both sections, only one Quaternary zone is found, namely Globorotalia truncatulinoides Zone. For MD 982152, that zone can be subdivided into two interval subzones e.g. Globorotalia crassaformis hessi and Globigerinella calida calida. However, in MD 982155 Globorotalia truncatulinoides Zone can be subdivided into three subzones namely, Globorotalia crassaformis hessi, Globigerinella calida calida, and Beella digitata Subzones.
The planktonic foraminifera event revealed in both sections are the First Appearance Datum (FAD) of Globigerinella calida calida and the Last Appearance (LAD) of Globorotalia crassaformis hessi. In MD 982155 the FAD of Beella digitata is found.
Keywords: planktonic foraminifera, Quaternary, biostratigraphy, Indian Ocean.
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Luo, T., K. Kramer, D. B. Goldgof, L. O. Hall, S. Samson, A. Remsen, and T. Hopkins. "Recognizing Plankton Images From the Shadow Image Particle Profiling Evaluation Recorder." IEEE Transactions on Systems, Man and Cybernetics, Part B (Cybernetics) 34, no. 4 (August 2004): 1753–62. http://dx.doi.org/10.1109/tsmcb.2004.830340.
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Cheng, Xuemin, Yong Ren, Kaichang Cheng, Jie Cao, and Qun Hao. "Method for Training Convolutional Neural Networks for In Situ Plankton Image Recognition and Classification Based on the Mechanisms of the Human Eye." Sensors 20, no. 9 (May 2, 2020): 2592. http://dx.doi.org/10.3390/s20092592.
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In this study, we propose a method for training convolutional neural networks to make them identify and classify images with higher classification accuracy. By combining the Cartesian and polar coordinate systems when describing the images, the method of recognition and classification for plankton images is discussed. The optimized classification and recognition networks are constructed. They are available for in situ plankton images, exploiting the advantages of both coordinate systems in the network training process. Fusing the two types of vectors and using them as the input for conventional machine learning models for classification, support vector machines (SVMs) are selected as the classifiers to combine these two features of vectors, coming from different image coordinate descriptions. The accuracy of the proposed model was markedly higher than those of the initial classical convolutional neural networks when using the in situ plankton image data, with the increases in classification accuracy and recall rate being 5.3% and 5.1% respectively. In addition, the proposed training method can improve the classification performance considerably when used on the public CIFAR-10 dataset.
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Schröder, Simon-Martin, Rainer Kiko, and Reinhard Koch. "MorphoCluster: Efficient Annotation of Plankton Images by Clustering." Sensors 20, no. 11 (May 28, 2020): 3060. http://dx.doi.org/10.3390/s20113060.
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In this work, we present MorphoCluster, a software tool for data-driven, fast, and accurate annotation of large image data sets. While already having surpassed the annotation rate of human experts, volume and complexity of marine data will continue to increase in the coming years. Still, this data requires interpretation. MorphoCluster augments the human ability to discover patterns and perform object classification in large amounts of data by embedding unsupervised clustering in an interactive process. By aggregating similar images into clusters, our novel approach to image annotation increases consistency, multiplies the throughput of an annotator, and allows experts to adapt the granularity of their sorting scheme to the structure in the data. By sorting a set of 1.2 M objects into 280 data-driven classes in 71 h (16 k objects per hour), with 90% of these classes having a precision of 0.889 or higher. This shows that MorphoCluster is at the same time fast, accurate, and consistent; provides a fine-grained and data-driven classification; and enables novelty detection.
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Ohman, Mark D. "A sea of tentacles: optically discernible traits resolved from planktonic organisms in situ." ICES Journal of Marine Science 76, no. 7 (August 3, 2019): 1959–72. http://dx.doi.org/10.1093/icesjms/fsz184.
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Abstract Trait-based simplifications of plankton community structure require accurate assessment of trait values as expressed in situ. Yet planktonic organisms live suspended in a fluid medium and often bear elongate appendages, delicate feeding structures, and mucous houses that are badly damaged upon capture or removal from the fluid environment. Fixatives further distort organisms. In situ imaging of zooplankton from a fully autonomous Zooglider reveals a suite of trait characteristics that often differ markedly from those inferred from conventionally sampled plankton. In situ images show fragile feeding appendages in natural hunting postures, including reticulate networks of rhizopods, feeding tentacles of cnidarians, and tentilla of ctenophores; defensive spines and setae of copepods; intact mucous houses of appendicularians; and other structures that are not discernible in conventionally collected zooplankton. Postures characteristic of dormant copepods can be identified and the presence of egg sacs detected. Intact, elongate diatom chains that are much longer than measured in sampled specimens are resolvable in situ. The ability to image marine snow, as well as small-scale fluid deformations, reveals micro-habitat structure that may alter organismal behaviour. Trait-based representations of planktonic organisms in biogeochemical cycles need to consider naturally occurring traits expressed by freely suspended planktonic organisms in situ.
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Mcnair, Heather, Courtney Nicole Hammond, and Susanne Menden-Deuer. "Phytoplankton carbon and nitrogen biomass estimates are robust to volume measurement method and growth environment." Journal of Plankton Research 43, no. 2 (March 2021): 103–12. http://dx.doi.org/10.1093/plankt/fbab014.
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Abstract Phytoplankton biomass is routinely estimated using relationships between cell volume and carbon (C) and nitrogen (N) content that have been defined using diverse plankton that span orders of magnitude in size. Notably, volume has traditionally been estimated with geometric approximations of cell shape using cell dimensions from planar two-dimensional (2D) images, which requires assumptions about the third, depth dimension. Given advances in image processing, we examined how cell volumes determined from three-dimensional (3D), confocal images affected established relationships between phytoplankton cell volume and C and N content. Additionally, we determined that growth conditions could result in 30–40% variation in cellular N and C. 3D phytoplankton cell volume measurements were on average 15% greater than the geometric approximations from 2D images. Volume method variation was minimal compared to both intraspecific variation in volumes (~30%) and the 50-fold variation in elemental density among species. Consequently, C:vol and N:vol relationships were unaltered by volume measurement method and growth environment. Recent advances in instrumentation, including those for at sea and autonomous applications can be used to estimate plankton biomass directly. Going forward, we recommend instrumentation that permits species identification alongside size and shape characteristics for plankton biomass estimates.
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Luo, T., K. Kramer, D. B. Goldgof, L. O. Hall, S. Samson, A. Remsen, and T. Hopkins. "Errata to “Recognizing Plankton Images From the Shadow Image Particle Profiling Evaluation Recorder”." IEEE Transactions on Systems, Man and Cybernetics, Part B (Cybernetics) 34, no. 6 (December 2004): 2423. http://dx.doi.org/10.1109/tsmcb.2004.837353.
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Pérez-Enríquez, Ricardo, Alejandra Arciniega, Noé Díaz-Viloria, and Salvador E. Lluch-Cota. "Diversity of planktonic gastropods from western Baja California Peninsula assessed by 18S rDNA sequences." Revista Mexicana de Biodiversidad 94 (May 24, 2023): e944968. http://dx.doi.org/10.22201/ib.20078706e.2023.94.4968.
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The study of planktonic mollusks is a relevant element to understand the dynamics of the benthic communities under present and future environmental conditions. We present the description of the biodiversity of planktonic gastropods at 2 sampling sites on the Pacific coast of the Baja California Peninsula, Mexico. Organisms collected from plankton tows at 2 locations (Cabo Tosco, n = 89 and La Bocana, n = 213) were sequenced for a portion of the 18S rDNA gene. High diversity was registered, with 71 Molecular Operational Taxonomic Units (MOTUs), which contrasts with the low phenotypic diversity of stereoscopic images. Differences in community composition between and within sampling sites indicate that planktonic gastropod distribution is not random but probably modulated by micro-environmental processes such as currents or biological events. The presence of non-gastropod sequences within some shells (n = 6) suggests their use as carriers of eggs or larvae of other taxa.
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Blackburn, Nicholas, Åke Hagström, Johan Wikner, Rocio Cuadros-Hansson, and Peter Koefoed Bjørnsen. "Rapid Determination of Bacterial Abundance, Biovolume, Morphology, and Growth by Neural Network-Based Image Analysis." Applied and Environmental Microbiology 64, no. 9 (September 1, 1998): 3246–55. http://dx.doi.org/10.1128/aem.64.9.3246-3255.1998.
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ABSTRACT Annual bacterial plankton dynamics at several depths and locations in the Baltic Sea were studied by image analysis. Individual bacteria were classified by using an artificial neural network which also effectively identified nonbacterial objects. Cell counts and frequencies of dividing cells were determined, and the data obtained agreed well with visual observations and previously published values. Cell volumes were measured accurately by comparison with bead standards. The survey included 690 images from a total of 138 samples. Each image contained approximately 200 bacteria. The images were analyzed automatically at a rate of 100 images per h. Bacterial abundance exhibited coherent patterns with time and depth, and there were distinct subsurface peaks in the summer months. Four distinct morphological classes were resolved by the image analyzer, and the dynamics of each could be visualized. The bacterial growth rates estimated from frequencies of dividing cells were different from the bacterial growth rates estimated by the thymidine incorporation method. With minor modifications, the image analysis technique described here can be used to analyze other planktonic classes.
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Lang, Kaiqi, Hui Cai, and Xiaoping Wang. "A Plankton Detection Method Based on Neural Networks and Digital Holographic Imaging." Chemosensors 10, no. 6 (June 8, 2022): 217. http://dx.doi.org/10.3390/chemosensors10060217.
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Detecting marine plankton by means of digital holographic microscopy (DHM) has been successfully deployed in recent decades; however, in most previous studies, the identification of the position, shape, and size of plankton has been neglected, which may negate some of the advantages of DHM. Therefore, the procedure of image fusion has been added between the reconstruction of initial holograms and the final identification, which could help present all the images of plankton clearly in a volume of seawater. A new image fusion method called digital holographic microscopy-fully convolutional networks (DHM-FCN) is proposed, which is based on the improved fully convolutional networks (FCN). The DHM-FCN model runs 20 times faster than traditional image fusion methods and suppresses the noise in the holograms. All plankton in a 2 mm thick water body could be clearly represented in the fusion image. The edges of the plankton in the DHM-FCN fusion image are continuous and clear without speckle noise inside. The neural network model, YOLOv4, for plankton identification and localization, was established. A mean average precision (mAP) of 97.69% was obtained for five species, Alexandrium tamarense, Chattonella marina, Mesodinium rubrum, Scrippsiella trochoidea, and Prorocentrum lima. The results of this study could provide a fast image fusion method and a visual method to detect organisms in water.
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Swartzman, Gordon, Richard Brodeur, Jeffrey Napp, Danny Walsh, Roger Hewitt, David Demer, George Hunt, and Elizabeth Logerwell. "Relating spatial distributions of acoustically determined patches of fish and plankton: data viewing, image analysis, and spatial proximity." Canadian Journal of Fisheries and Aquatic Sciences 56, S1 (November 30, 1999): 188–98. http://dx.doi.org/10.1139/f99-206.
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We developed a point-and-click acoustic data viewer (FishViewer) for exploratory comparison of up to three acoustic survey transects (or three frequencies) at a time and other environmental and biological data (e.g., surface temperature and seabird abundance). FishViewer also contains image-processing tools (e.g., morphological and threshold filters) for distinguishing between fish shoals and plankton patches and for patch identification. These tools and methods are illustrated using survey data collected at three frequencies (38, 120, and 200 kHz) near the Pribilof Islands, Bering Sea, during September 1995. Data were also visualized by converting the patches identified in the acoustic images to polygons, showing the boundaries of each patch using a connected component algorithm. Proximity between these fish shoal and plankton patch polygons was examined statistically using an interval-based nonparametric regression model (generalized additive models) and a distance-based proximity measure. The methods presented for data refinement, visualization, and the establishment of fish-plankton patch proximity serve as a paradigm for scale-robust hypothesis formulation and testing of spatial patterns of fish and plankton.
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Moberg, Emily A., and Heidi M. Sosik. "Distance maps to estimate cell volume from two-dimensional plankton images." Limnology and Oceanography: Methods 10, no. 4 (April 2012): 278–88. http://dx.doi.org/10.4319/lom.2012.10.278.
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Pereira, G. C., A. R. Figueiredo, and N. F. F. Ebecken. "Using in situ flow cytometry images of ciliates and dinoflagellates for aquatic system monitoring." Brazilian Journal of Biology 78, no. 2 (August 17, 2017): 240–47. http://dx.doi.org/10.1590/1519-6984.05016.
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Abstract Short-period variability in plankton communities is poorly documented, especially for variations occurring in specific groups in the assemblage because traditional analysis is laborious and time-consuming. Moreover, it does not allow the high sampling frequency required for decision making. To overcome this limitation, we tested the submersible CytoSub flow cytometer. This device was anchored at a distance of approximately 10 metres from the low tide line at a depth of 1.5 metres for 12 hours to monitor the plankton at a site in the biological reserve of Barra da Tijuca beach, Rio de Janeiro. Data analysis was performed with two-dimensional scatter plots, individual pulse shapes and micro images acquisition. High-frequency monitoring results of two interesting groups are shown. The abundance and carbon biomass of ciliates were relatively stable, whereas those from dinoflagellates were highly variable along the day. The linear regression of biovolume measures between classical microscopy and in situ flow cytometry demonstrate high degree of adjustment. Despite the success of the trial and the promising results obtained, the large volume of images generated by the method also creates a need to develop pattern recognition models for automatic classification of in situ cytometric images.
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Sun, H., P. W. Benzie, N. Burns, D. C. Hendry, M. A. Player, and J. Watson. "Underwater digital holography for studies of marine plankton." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 366, no. 1871 (January 25, 2008): 1789–806. http://dx.doi.org/10.1098/rsta.2007.2187.
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Conventional and digital holographies are proving to be increasingly important for studies of marine zooplankton and other underwater biological applications. This paper reports on the use of a subsea digital holographic camera (eHoloCam) for the analysis and identification of marine organisms and other subsea particles. Unlike recording on a photographic film, a digital hologram (e-hologram) is recorded on an electronic sensor and reconstructed numerically in a computer by simulating the propagation of the optical field in space. By comparison with other imaging techniques, an e-hologram has several advantages such as three-dimensional spatial reconstruction, non-intrusive and non-destructive interrogation of the recording sampling volume and the ability to record holographic videos. The basis of much work in optics lies in Maxwell's electromagnetic theory and holography is no exception: we report here on two of the numerical reconstruction algorithms we have used to reconstruct holograms obtained using eHoloCam and how their starting point lies in Maxwell's equations. Derivation of the angular spectrum algorithm for plane waves is provided as an exact method for the in-line numerical reconstruction of digital holograms. The Fresnel numerical reconstruction algorithm is derived from the angular spectrum method. In-line holograms are numerically processed before and after reconstruction to remove periodic noise from captured images and to increase image contrast. The ability of the Fresnel integration reconstruction algorithm to extend the reconstructed volume beyond the recording sensor dimensions is also shown with a 50% extension of the reconstruction area. Finally, we present some images obtained from recent deployments of eHoloCam in the North Sea and Faeroes Channel.
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Wilborn, Rachel E., Christopher N. Rooper, Pam Goddard, Kresimir Williams, and Rick Towler. "A novel design for sampling benthic zooplankton communities in disparate Gulf of Alaska habitats using an autonomous deep-water plankton pump." Journal of Plankton Research 42, no. 4 (June 27, 2020): 457–66. http://dx.doi.org/10.1093/plankt/fbaa030.
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Abstract Deep-water larval fish and zooplankton utilize structurally complex, cold-water coral and sponge (CWCS) habitats as refuges, nurseries and feeding grounds. Fine-scale sampling of these habitats for larval fish and zooplankton has proven difficult. This study implemented a newly designed, autonomous, noninvasive plankton pump sampler that collected large mesozooplankton within 1 m of the seafloor. It was successfully deployed in the western Gulf of Alaska between the Shumagin Islands (~158°W) and Samalga Pass (−170°W), and collected in situ zooplankton from diverse benthic communities (coral, sponge and bare substrates) at depths in excess of 100 m. Key design parameters of the plankton pump were its ability to be deployed from ships of opportunity, be untethered from the vessel during sampling and be deployed and retrieved in high-relief, rocky areas where CWCS are typically present. The plankton pump remains stationary while collecting from the water column, rests within 1 m of the seafloor and captures images of the surrounding habitat and substrate. This plankton pump design is a low-cost, highly portable solution for assessing the role of benthic habitat in the life cycle of mesozooplankton, a linkage that has been relatively underexplored due to the difficulty in obtaining near-bottom samples.
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Cheng, Xuemin, Kaichang Cheng, and Hongsheng Bi. "Dynamic Downscaling Segmentation for Noisy, Low-Contrast in Situ Underwater Plankton Images." IEEE Access 8 (2020): 111012–26. http://dx.doi.org/10.1109/access.2020.3001613.
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Jiao, Qingliang, Ming Liu, Pengyu Li, Liquan Dong, Mei Hui, Lingqin Kong, and Yuejin Zhao. "Underwater Image Restoration via Non-Convex Non-Smooth Variation and Thermal Exchange Optimization." Journal of Marine Science and Engineering 9, no. 6 (May 25, 2021): 570. http://dx.doi.org/10.3390/jmse9060570.
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The quality of underwater images is an important problem for resource detection. However, the light scattering and plankton in water can impact the quality of underwater images. In this paper, a novel underwater image restoration based on non-convex, non-smooth variation and thermal exchange optimization is proposed. Firstly, the underwater dark channel prior is used to estimate the rough transmission map. Secondly, the rough transmission map is refined by the proposed adaptive non-convex non-smooth variation. Then, Thermal Exchange Optimization is applied to compensate for the red channel of underwater images. Finally, the restored image can be estimated via the image formation model. The results show that the proposed algorithm can output high-quality images, according to qualitative and quantitative analysis.
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Rosa, Judson, Thiago Matos, Débora da Silva, Carolina Reis, Cristina Dias, Tatiana Konno, and Lohengrin Fernandes. "Seasonal Changes in the Size Distribution of Copepods Is Affected by Coastal Upwelling." Diversity 15, no. 5 (May 9, 2023): 637. http://dx.doi.org/10.3390/d15050637.
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Water temperature controls the physiology, growth rate, distribution, and behavior of most plankton populations in the sea and thus affects the energy transfer in marine ecosystems. The present study focuses on the influence of seasonal changes in sea surface temperature on phytoplankton and the size distribution of copepods in the Arraial do Cabo Upwelling System (Brazil), where a wind-driven coastal upwelling can lead to multiple distinct bottom-up cascade effects on the food web. To address the potential effect of the seasonal changes, environmental data were obtained and the abundance of plankton determined from monthly samples collected in triplicate from 2010 to 2014. The samples were analyzed on a Benchtop FlowCAM (FC), and copepods (<1000 µm) were classified according to their Ellipses Equivalent Major Axis using image analysis software ImageJ (IJ). For IJ analysis, a batch-processing macro was built to open all FC raw images and then crop each copepod individually into a single picture. Using these images, prosome and urosome lengths were manually measured with the straight-line tool in IJ. With the combinations of measurements obtained in the IJ adjusted as FC measurements, we established a new, faster, and more effective way to measure copepods. With the copepod size classification, we found that there is a cycle in copepod size combined with the upwelling cycle that is related to temperature rather than to phytoplankton growth. Copepod abundance as a whole peaked during the autumn, winter, and spring seasons. The method performed here proved that FC is an effective tool for classifying copepod sizes and detecting seasonal variation.
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Li, Xiu, Rujiao Long, Jiangpeng Yan, Kun Jin, and Jihae Lee. "TANet: A Tiny Plankton Classification Network for Mobile Devices." Mobile Information Systems 2019 (April 3, 2019): 1–8. http://dx.doi.org/10.1155/2019/6536925.
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This paper is devoted to a lightweight convolutional neural network based on the attention mechanism called the tiny attention network (TANet). The TANet consists of three main parts termed as a reduction module, self-attention operation, and group convolution. The reduction module alleviates information loss caused by the pooling operation. The new parameter-free self-attention operation makes the model to focus on learning important parts of images. The group convolution achieves model compression and multibranch fusion. Using the main parts, the proposed network enables efficient plankton classification on mobile devices. The performance of the proposed network is evaluated on the Plankton dataset collected by Oregon State University’s Hatfield Marine Science Center. The results show that TANet outperforms other deep models in speed (31.8 ms per image), size (648 kB, the size of the hard disk space occupied by the model), and accuracy (Top-1 76.5%, Top-5 96.3%).
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A. I., Sukhinov, and Panasenko N. D. "COMPARATIVE INVESTIGATION OF NEURAL AND LOCALLY BINARY ALGORITHMS FOR IMAGE IDENTIFICATION OF PLANKTON POPULATIONS." Computational Mathematics and Information Technologies 1, no. 2 (October 1, 2022): 70–80. http://dx.doi.org/10.23947/2587-8999-2022-1-2-70-80.
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The work is devoted to the «neural network-lbp» method of processing satellite images of multispectral water coastal systems for identification of phytoplankton populations of spotted structure: determination of their boundaries, distribution of color gradations and, based on this, determination of the distribution of phytoplankton concentrations inside the spots and the location of the center of mass. The efficiency and effectiveness of the proposed neural network-lbp method is investigated in comparison with the method based on the use of a three-layer neural network. For the analysis, a test set of images is involved – flat shapes with rather complex boundaries, which will allow us to quantify the quality of the algorithms being compared. The results of the work show an increase in recognition accuracy by 1.5-3% when using the proposed method.
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Luo, Jia. "Principal Component Analysis–Based Feature Recognition Technology for Marine Plankton Images in IoT Systems." Journal of Testing and Evaluation 52, no. 3 (March 21, 2024): 20230079. http://dx.doi.org/10.1520/jte20230079.
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A. I., Sukhinov, Protsenko S.V., and Panasenko N. D. "MATHEMATICAL MODELING AND ECOLOGICAL DESIGN OF THE MARINE SYSTEMS TAKING INTO ACCOUNT MULTI-SCALE TURBULENCE USING REMOTE SENSING DATA." Computational Mathematics and Information Technologies 1, no. 3 (December 31, 2022): 104–13. http://dx.doi.org/10.23947/2587-8999-2022-1-3-104-113.
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The paper considers a mathematical model of biological kinetics and geochemical cycles based on a system of convection-diffusion equations with nonlinear coefficients, supplemented by a spatially inhomogeneous three-dimensional mathematical model of wave hydrodynamics of a shallow reservoir, with a refined coefficient of turbulent vertical exchange. The task of monitoring the water surface in order to detect phytoplankton spots involves the creation and verification of effective methods for clustering these objects on the surface of reservoirs, in particular, restoring their boundaries based on remote sensing data. The article uses multispectral satellite images as sounding data. Based on the obtained images of plankton populations, the initial conditions for mathematical models of biogeochemical cycles can be determined, on the basis of which prognostic calculations are performed.
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Hossain Bhuiyan, Mohammad Azmal, Md Rasikul Islam, Sam Shariar Islam, Abu Kowser, and Moniruzzaman Khondker. "Floristic Composition of Plankton in Shitalakhsya River, Narayanganj, Dhaka." Dhaka University Journal of Biological Sciences 31, no. 1 (February 10, 2022): 45–57. http://dx.doi.org/10.3329/dujbs.v31i1.57915.
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Information of phytoplankton flora of polluted river ecosystems of Bangladesh are scanty. The present study was undertaken to explore the phytoplankton flora at Dakshin Rupshi Station of the river Shitalakhsya, Narayanganj, Dhaka. The study was carried out from May 2017 to March 2018 by collecting pelagic plankton samples bimonthly. A total of 53 species under 36 genera were identified, of which 51 species have been illustrated through photomicrographic images and listing. Two species of phytoplankton namely, Pyrobotrys incurva Arnoldi and Phacus ranula Pochmann were identified from the river water but could not be produced here. The recorded algal divisions of phytoplankton are Cyanophyta (6), Chlorophyta (19), Euglenophyta (13), Chrysophyta (13) and Pyrrhophyta (2). The standing crops presented by each division are: 463.5, 428.33, 199.67, 664.33 and 26.25×103 ind/l by Cyanophyta, Chlorophyta, Euglenophyta, Chrysophyta and Pyrrhophyta, respectively. The trend in contributing the number of species is Chlorophyta > Euglenophyta and Chrysophyta > Cyanophyta > Pyrrhophyta. For standing crop, the trend is Chrysophyta > Cyanophyta > Chlorophyta > Euglenophyta > Pyrrhophyta. Pollutant loading from the urban sources actually cuts the penetration of light into the upper part of the river water and thus creating a shrinking environment for the survival of phytoplankton. The present floristic study of phytoplankton of the River Shitalakhsya adds knowledge to the species composition and their systematic position which would be helpful for any further floristic study of phytoplankton on the river ecosystems of Bangladesh. Dhaka Univ. J. Biol. Sci. 31(1): 45-57, 2022 (January)
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Scott, James, Sophie Pitois, Hayden Close, Nevena Almeida, Phil Culverhouse, Julian Tilbury, and Gill Malin. "In situ automated imaging, using the Plankton Imager, captures temporal variations in mesozooplankton using the Celtic Sea as a case study." Journal of Plankton Research 43, no. 2 (March 2021): 300–313. http://dx.doi.org/10.1093/plankt/fbab018.
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Abstract The Plankton Imager (PI) is an underway semi-automated, high-speed imaging instrument, which takes images of all passing particles and classifies the mesozooplankton present. We used data (temperature, salinity and mesozooplankton abundance) collected in the Celtic Sea in spring and autumn from 2016 to 2019 to assess the ability of the PI to describe temporal changes in the mesozooplankton community and to capture the seasonality of individual taxa. The description obtained using the PI identified both seasonal and interannual changes in the mesozooplankton community. Variation was higher between years than seasons due to the large variation in the community between years in autumn, attributed to the breaking down of summer stratification. The spring community was consistent between years. The seasonality of taxa broadly adhered to those presented in the literature. This demonstrates the PI as a robust method to describe the mesozooplankton community. Finally, the potential future applications and how to make best use of the PI are discussed.
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Sukhinov, Alexander, Natalia Panasenko, and Aleksey Simorin. "Algorithms and programs based on neural networks and local binary patterns approaches for monitoring plankton populations in sea systems." E3S Web of Conferences 363 (2022): 02027. http://dx.doi.org/10.1051/e3sconf/202236302027.
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The work is devoted to the method of multispectral space images analyzing of aquatic coastal systems for identifying phytoplankton populations of complicated structures: determining their boundaries, distributing color gradations and, based on this, determining the distribution of phytoplankton concentrations within patches and the location of the "mass" center. A combination of local binary patterns (LBP) and neuralnetworks methods is considered. Due to these characteristics it is possible, basing on a series of processed images of the same water area for different time points (dates), to determine the changing rate in the spots boundaries and their concentrations, the shift of the mass center which are influenced by the aquatic environment movement and the processes of phytoplankton growth and death. The results of the work allow us to determine the Azov Sea state. Experimental data of the program are given in confirmation part.
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Grujčić, Vesna, Sami Saarenpää, John Sundh, Bengt Sennblad, Benjamin Norgren, Meike Latz, Stefania Giacomello, Rachel A. Foster, and Anders F. Andersson. "Towards high-throughput parallel imaging and single-cell transcriptomics of microbial eukaryotic plankton." PLOS ONE 19, no. 1 (January 19, 2024): e0296672. http://dx.doi.org/10.1371/journal.pone.0296672.
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Single-cell transcriptomics has the potential to provide novel insights into poorly studied microbial eukaryotes. Although several such technologies are available and benchmarked on mammalian cells, few have been tested on protists. Here, we applied a microarray single-cell sequencing (MASC-seq) technology, that generates microscope images of cells in parallel with capturing their transcriptomes, on three species representing important plankton groups with different cell structures; the ciliate Tetrahymena thermophila, the diatom Phaeodactylum tricornutum, and the dinoflagellate Heterocapsa sp. Both the cell fixation and permeabilization steps were adjusted. For the ciliate and dinoflagellate, the number of transcripts of microarray spots with single cells were significantly higher than for background spots, and the overall expression patterns were correlated with that of bulk RNA, while for the much smaller diatom cells, it was not possible to separate single-cell transcripts from background. The MASC-seq method holds promise for investigating "microbial dark matter”, although further optimizations are necessary to increase the signal-to-noise ratio.
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Huber, Brian T., Maria Rose Petrizzo, and Kenneth G. MacLeod. "Planktonic Foraminiferal Endemism at Southern High Latitudes Following the Terminal Cretaceous Extinction." Journal of Foraminiferal Research 50, no. 4 (October 1, 2020): 382–402. http://dx.doi.org/10.2113/gsjfr.50.4.382.
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Abstract Austral planktonic foraminiferal assemblages from immediately above the Cretaceous/Paleogene (K/Pg) boundary at Ocean Drilling Program Hole 690C (Maud Rise, Weddell Sea) and International Ocean Drilling Program Hole U1514C (southeast Indian Ocean) show a much different record of post-extinction recovery than anywhere outside the circum-Antarctic region. Species of Woodringina and Parvularugoglobigerina, genera with well-documented evolutionary successions within the early Danian P0 and Pα biozones at tropical/subtropical and mid-latitude localities, are absent from southern high latitude sequences. This study proposes new criteria for biostratigraphic correlation of the lowermost Danian Antarctic Paleocene AP0 and AP1 Zones using stratophenetic observations from Scanning Electron Microscope images of lower Danian planktonic foraminifera at deep-sea sites in the southern South Atlantic and southern Indian Ocean. The small but distinctive species Turborotalita nikolasi (Koutsoukos) is a highly reliable index species for the lowermost Danian as it consistently occurs immediately above the K/Pg boundary at multiple southern high latitude sites, which is consistent with its distribution at middle and low latitudes. Also useful for cross-latitude correlation is Parasubbotina neanika n. sp., which first appears within the lowermost Danian worldwide. The geographic distribution of the New Zealand species Antarcticella pauciloculata (Jenkins) and Zeauvigerina waiparaensis (Jenkins), as well as Eoglobigerina maudrisensis n. sp. from just above the K/Pg in the southern South Atlantic and southern Indian Ocean, helps define the extent of the Austral Biogeographic Province and provides evidence for marine communication via marine seaways across Antarctica. While An. pauciloculata was previously considered a benthic species, new stable isotope evidence demonstrates that it lived a planktonic mode of life. It is possible this species evolved from a benthic ancestor and that the benthic to planktonic transition occurred through an intermediate tychopelagic lifestyle at a time when calcareous plankton were less abundant as a result of the terminal Cretaceous mass extinction.
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Haigh, S. P., K. L. Denman, and W. W. Hsieh. "Simulation of the planktonic ecosystem response to pre- and post-1976 forcing in an isopycnic model of the North Pacific." Canadian Journal of Fisheries and Aquatic Sciences 58, no. 4 (April 1, 2001): 703–22. http://dx.doi.org/10.1139/f01-010.
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To investigate the hypothesis that the 1976 "regime shift" in North Pacific fish populations resulted from climatic change propagating up the fisheries food web, we have embedded a four-component planktonic ecosystem model in an ocean general circulation model. The Miami isopycnic model (MICOM) has been implemented on a 2° grid over the domain from 18°S to 61°N, with a KrausTurner-type mixed layer model overlaying 10 isopycnal layers. An initial baseline run with forcing for the period 19521988 reasonably reproduces the spatial patterns and seasonal changes in SeaWiFS images. Estimates of annual net and export production compare well with contemporary observations of primary and export production at Ocean Station Papa in the subarctic North Pacific but are low by a factor of 810 at station ALOHA near Hawaii. Two subsequent runs with forcing for the periods 19521975 and 19771988 show the main gyres to strengthen after 1976 with large areas of increased mixed layer depth. In the light-limited subarctic, limited areas of shallower spring mixed layer produced increased phytoplankton biomass, whereas in the nutrient-limited subtropical gyre, increased nutrients (or migration of the subarctic front and the equatorial current system into the gyre) after 1976 correlated with increased plankton biomass.
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Watanabe, Yasunori, Jun Sakai, Yuta Mitobe, and Yasuo Niida. "BIOLUMINESCENCE IMAGING FOR MEASURING FLUID SHEAR DISTRUBUTIONS." Coastal Engineering Proceedings 1, no. 33 (December 15, 2012): 31. http://dx.doi.org/10.9753/icce.v33.waves.31.
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The dinoflagellate Pyrocystis lunula emits light in response to water motion. The statistical features of the bioluminescence, emitted by P. lunula, owing to shear stress in oscillatory boundary layer flows over ripped bed were studied in this paper with the aim to develop a new imaging technique for measuring fluid strain rate and shear using plankton that emit light in response to mechanical stimulation. The flash intensity has been found to correlate with fluid strain rate estimated from fluid velocity over ripples. Thus the instantaneous planar distribution of the fluid shear can be estimated from video images of the bioluminescence in a fluid region by using the empirical relation determined in this study.
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Abeynayaka, Amila, Fujio Kojima, Yoshikazu Miwa, Nobuhiro Ito, Yasuo Nihei, Yu Fukunaga, Yuga Yashima, and Norihiro Itsubo. "Rapid Sampling of Suspended and Floating Microplastics in Challenging Riverine and Coastal Water Environments in Japan." Water 12, no. 7 (July 3, 2020): 1903. http://dx.doi.org/10.3390/w12071903.
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Environmental sampling plays an important role in quantitative and qualitative investigation of plastic pollution. Rivers are a major source, carrying plastic litter into the oceans. Microplastic sampling in riverine and coastal environments is often a challenging task due to limited access, time taken, costs, human resources, etc. Our present study evaluated the performance of newly developed sampling devices (Albatross Mark 5 and 6 (AM-5 and AM-6)) that were suitable to collect floating and suspended microplastic samples in challenging freshwater and coastal environments (95 locations). Our observations indicated a similar magnitude of microplastic concentrations with AM-5 and AM-6 sampling compared to conventional plankton nets. The sampling duration, originally 10–60 min (by plankton net), was reduced to 3 min (AM-5 and AM-6) for sampling water volumes of approximately 10 m3. The developed AM-6 device was used to collect samples from riverine and coastal environments in Japan. The microplastic particle polymer composition (using Fourier transform infrared spectrophotometry (FT-IR)), size, and shape (microscopic images) were investigated. The observations showed a statistically significant particle size reduction from the riverine to coastal areas. The dominant polymer types detected were polyethylene (PE) and polypropylene (PP). The observations were complied with the coastal microplastic observations that were reported for previous studies in Japanese water environments.
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Wang, Yan-Guo, Li-Chun Tseng, Xiao-Yin Chen, Rou-Xin Sun, Peng Xiang, Bing-Peng Xing, Chun-Guang Wang, and Jiang-Shiou Hwang. "Cold Dome Affects Mesozooplankton Communities during the Southwest Monsoon Period in the Southeast East China Sea." Journal of Marine Science and Engineering 11, no. 3 (February 26, 2023): 508. http://dx.doi.org/10.3390/jmse11030508.
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In order to better understand the cold dome influence on zooplankton community structure, zooplankton samples were collected during the southwest monsoon prevailing period from the southeast waters of the East China Sea. To reduce the bias caused by different sampling months, the samples were collected in June 2018 and in June 2019. An obvious cold dome activity was proven by images of remote sensing satellites during the June 2018 cruise. In contrast, the research area was much affected by open sea high temperature and water masses during the June 2019 cruise. Significant differences in water conditions were demonstrated by surface seawater temperature, salinity, and dissolved oxygen concentrations between the two cruises. Nevertheless, no significant differences were observed concerning mesozooplankton in general, copepods, large crustaceans, other crustaceans, and pelagic molluscs between the June 2018 and June 2019 cruises. However, the mean abundance of gelatinous plankton was significantly different with 1213.08 ± 850.46 (ind./m3) and 2955.93 ± 1904.42 (ind./m3) in June 2018 and June 2019, respectively. Noteworthy, a significantly lower mean abundance of meroplankton, with 60.78 ± 47.32 (ind./m3), was identified in June 2018 compared to 464.45 ± 292.80 (ind./m3) in June 2019. Pearson’s correlation analysis also showed a highly positive correlation of gelatinous plankton and meroplankton with sea surface temperature (p < 0.01). The variation of salinity showed a significant negative correlation with gelatinous plankton abundance (p < 0.05), and a highly significant negative correlation with the abundance of meroplankton (p < 0.01). Only the abundance of meroplankton showed a positive correlation with dissolved oxygen concentrations (p < 0.05). The copepod communities were separated in two groups which were consistent with sampling cruises in 2018 and 2019. Based on the specificity and occupancy of copepods, Macrosetella gracilis, Oithona rigida, Cosmocalanus darwinii, Paracalanus parvus, and Calocalanus pavo were selected as indicator species for the cold dome effect in the study area during June 2018, whereas the indicator species of warm water impact in the open sea were Calanopia elliptica, Subeucalanus pileatus, Paracalanus aculeatus, and Acrocalanus gibber during the June 2019 cruise.
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Lubsanova, E. L. "Digital maps of hydrobionts and surface waters quality, the Baikal natural territory." Geodesy and Cartography 967, no. 1 (February 20, 2021): 2–12. http://dx.doi.org/10.22389/0016-7126-2021-967-1-2-12.
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The author provides information on a developed method of geoinformation mapping hydrobionts in order to automatize digital cartographic images formation with spatial-andtemporal distribution of species and long-term trends of freezing surface waters’quality changes at studying relationships in the functioning of hydrobiological communities. The features of technique with the description of technical stages for creating databases and constituent elements of geoinformation software by the example of designing a regional geoservice with interactive plankton-and-benthos-aquatic-organisms’ maps in the Baikal natural territory are presented. Signs mapping the classes of water pollution by hydrobiological indicators on points available for recognition by colour-blind people are offered to be applied in cartographic material. They are easily reproduced on objects near surface streams in cases of water pollution for warning the population.
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Afanasyev, D. F., S. V. Bondarev, D. V. Khrenkin, and L. A. Zhivoglyadova. "EXPERIENCE IN ORGANIZING THE REMOTE COLLABORATION OF HYDROBIOLOGISTS AND CREATING A DATABASE OF DIGITAL IMAGES OF PLANKTON AND BENTHOS." Aquatic Bioresources & Environment 3, no. 1 (2020): 121–24. http://dx.doi.org/10.47921/2619-1024_2020_3_1_121.
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Tarquis, A. M., A. Platonov, A. Matulka, J. Grau, E. Sekula, M. Diez, and J. M. Redondo. "Application of multifractal analysis to the study of SAR features and oil spills on the ocean surface." Nonlinear Processes in Geophysics 21, no. 2 (March 28, 2014): 439–50. http://dx.doi.org/10.5194/npg-21-439-2014.
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Abstract. The use of synthetic aperture radar (SAR) to investigate the ocean surface provides a wealth of useful information that is very seldom used to its full potential. Here we will discuss the application of multifractal techniques to detect oil spills and the dynamic state of the sea regarding turbulent diffusion. We present different techniques in order to relate the shape of the multifractal spectral functions and the maximum fractal dimension to the behaviour of the ocean surface. We compare eddy and sheared dominated flows with convective driven flows and discuss the different features and observation methods. We also compare the scaling of different oil spills detected by means of SAR images. Recent spills and weathered ones are selected and compared to investigate their behaviour in different spatial and temporal ranges. We calculate the partition function based on the grey intensity value of each SAR pixel deriving several types of multifractal spectra as a function of spill residence time estimated for each image. Image manipulations are seen to reduce the speckle noise and thus distinguish much better the texture of the oil spill images. The results are used to discuss how eddy diffusivity may be estimated and used in a description of the ocean surface using a simple turbulence kinematic simulation model to predict the shape of oil spills. Differences in the multifractal spectrum among SAR images may detect the slicks due to plankton and also provide information on the age of the oil spills, on the Lagrangian turbulent structure and on ocean surface diffusivity.
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Dyomin, Victor, Alexandra Davydova, Nikolay Kirillov, and Igor Polovtsev. "Features of the Application of Coherent Noise Suppression Methods in the Digital Holography of Particles." Applied Sciences 13, no. 15 (July 27, 2023): 8685. http://dx.doi.org/10.3390/app13158685.
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The paper studies the influence of coherent noises on the quality of images of particles reconstructed from digital holograms. Standard indicators (for example, signal-to-noise ratio) and such indicators as the boundary contrast and boundary intensity jump previously proposed by the authors are used to quantify the image quality. With the use of these parameters, for examples of some known methods of suppressing coherent noises in a holographic image (eliminating the mutual influence of virtual and real images in in-line holography, and time averaging), the features and ranges of applicability of such correction were determined. It was shown that the use of the complex field amplitude reconstruction method based on the Gerchberg–Saxton algorithm and the spatial-frequency method improves the quality of determining the particle image boundary (by boundary intensity jump) starting from the distance between a hologram and a particle, which is about twice the Rayleigh distance. In physical experiments with model particles, averaging methods were studied to suppress non-stationary coherent noises (speckles). It was also shown that averaging over three digital holograms or over three holographic images is sufficient to provide a quality of particle image boundary suitable for particle recognition. In the case of multiple scattering, when it is necessary to impose a limit on the working volume length (depth of scene) of the holographic camera, the paper provides estimates that allow selecting the optimal working volume length. The estimates were made using the example of a submersible digital holographic camera for plankton studies.
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Kudryavtsev, Valery I. "Possibilities of laser location for remote monitoring of marine organisms (analytic review)." Izvestiya TINRO 176, no. 1 (March 30, 2014): 261–87. http://dx.doi.org/10.26428/1606-9919-2014-176-27-33.
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Possibilities of lidar detection of fish and plankton are overviewed on cited results of nature experiments in the sea. Volume-backscattering coefficients for the lidar with wave-length 532 nm and the acoustic sonar are compared for schools of some fish species. Examples of effective detecting of fish schools and assessment of their abundance by lidar are demonstrated for cases of sardine and anchovy at California coast, capelin and herring in the North Pacific, mullet at the west coast of Florida, juvenile mackerel in the coastal Atlantic waters of southern Europe, menhaden in the Chesapeake Bay, and others. In some experiments, the per-kilometer costs of airborne lidar surveys are estimated as 10 % or less as compared to ship-based sampling. Besides, the lidar surveys take a shorter time and their results are not distorted by avoidance behavior of fish caused by ship and sampling gear noises. Experimental surveys of thin scattering layers (probably formed by plankton) made by NOAA fish lidar are overviewed, as well, including the first tests of the system in the South California Bay in April 1997, the tests in the North-West Atlantic at Iberian coast in August-September 1998, in the Gulf of Alaska in July-September 2001 and May-August 2002, in the Norwegian Sea in July 2002, in the North-East Pacific at the coast of Oregon and Washington in July 2003, and in the Gulf of Alaska in July 2003. Some aspects of future development for improvement of school-detecting capabilities of lidar are discussed, as additional scanning for 2D-images and adding of second receiver co-polarized with the laser light for better identification of fish species and other scatterers in the sea.
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Lončarić, Neven. "Planktic Foraminiferal Content in a Mature Agulhas Eddy from the SE Atlantic: Any Influence on Foraminiferal Export Fluxes?" Geologia Croatica 59, no. 1 (2006): 41–50. http://dx.doi.org/10.4154/gc.2006.03.
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The Agulhas eddies, large-scale rings of warm salty water, occasionallyintrude into the Benguela Current system from the Indian Ocean and progress northwards across the Cape Basin and the Walvis Ridge. This inter-ocean exchange of heat and salt along the Cape of Good Hope is considered to play a crucial role for the global thermohaline circulation. Yet, the modern faunal composition of mature eddies from the northern Cape Basin and Walvis Ridge was uninvestigated in spite of the global importance of the Agulhas inflow, preventing firm micropalaeontological study of the palaeoceanographic variability of the ocean exchange in this area.This paper describes the composition of the modern planktic foraminiferal assemblages collected from a mature Agulhas eddy when it entered into the northern Benguela Current system. The effect of the eddy’s gradual decay on the foraminiferal communities in the upper water column is specifically examined, using plankton tow and CTD-rosette profiles, obtained within and outside the ring. In addition,exported foraminiferal fluxes beneath the eddy were investigated in order to determine their impact on the accumulation assemblages as recorded in sediment traps moored near the sea floor and in the core-top sediment from a box corer.The examined mature eddy “W” was clearly evident on the satellitealtimetry images by its elevated surface. It was distinguished from the surrounding ocean by a slightly higher salinity, deeper surface mixed layer and higher planktic foraminiferal standing stocks. Similarto planktic foraminiferal fauna in freshly formed eddies from the Agulhas retroflection, species such as Globigerinoides trilobus s.l., Globigerinoides ruber, Orbulina universa, Globigerinella siphoni-fera and Globorotalia scitula dominated in the ring “W” assemblages. However, Globorotalia menardii, a species previously believed to be characteristic for the Agulhas leakage into the S. Atlantic, was virtuallyabsent in the eddy “W” fauna. Also Globorotaloides hexagona, a species endemic in Indian Ocean waters, was not found in the water column, in the export flux or underlying sediment. The February to July foraminiferal flux patterns recorded by the sediment traps mirror the February standing stocks from the water column. Here in contrast, the core-top results show dominance of intermediate/cold water speciesthat originate from the seasonal spring bloom. This signal prevailsin sediment to the extent that any potential Agulhas eddy signaturein the sediment was overprinted.
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Wang, Yanjuan, Junsheng Wang, Tianqi Wang, and Chengxiao Wang. "Simultaneous Detection of Viability and Concentration of Microalgae Cells Based on Chlorophyll Fluorescence and Bright Field Dual Imaging." Micromachines 12, no. 8 (July 29, 2021): 896. http://dx.doi.org/10.3390/mi12080896.
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Ship ballast water contains high concentration of plankton, bacteria, and other microorganisms. If the huge amount of ballast water is discharged without being inactivated, it will definitely spell disaster to the marine environment. Microalgae is the most common species exiting in ballast water, so the detection of the concentration and viability of microalgae is a very important issue. The traditional methods of detecting microalgae in ballast water were costly and need the help of bulky equipment. Herein, a novel method based on microalgae cell intracellular chlorophyll fluorescence (CF) imaging combines with cell bright field (BF) microscopy was proposed. The geometric features of microalgae cells were obtained by BF image, and the cell viability was obtained by CF image. The two images were fused through the classic image registration algorithm to achieve simultaneous detection of the viability and concentration of microalgae cells. Furthermore, a low-cost, miniaturized CF/BF microscopy imaging prototype system based on the above principles was designed. In order to verify the effectiveness of the proposed method, four typical microalgae in ballast water (Platymonas, Pyramimonas sp., Chrysophyta, and Prorocentrum lima) were selected as the samples. The experimental results show that the self-developed prototype can quickly and accurately determine the concentration and the viability of microalgae cells in ship ballast water based on the dual images of BF and CF, and the detection accuracy is equivalent to that of commercial microscope. It was the first time to simultaneously detect the viability and concentration of microalgae cells in ship ballast water using the method that combining the fluorescence and bright field images; moreover, a miniaturized microscopic imaging prototype was developed. Those findings expected to contribute to the microalgae detection and ship ballast water management.
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Goodwin, Morten, Kim Tallaksen Halvorsen, Lei Jiao, Kristian Muri Knausgård, Angela Helen Martin, Marta Moyano, Rebekah A. Oomen, Jeppe Have Rasmussen, Tonje Knutsen Sørdalen, and Susanna Huneide Thorbjørnsen. "Unlocking the potential of deep learning for marine ecology: overview, applications, and outlook." ICES Journal of Marine Science 79, no. 2 (January 14, 2022): 319–36. http://dx.doi.org/10.1093/icesjms/fsab255.
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Abstract The deep learning (DL) revolution is touching all scientific disciplines and corners of our lives as a means of harnessing the power of big data. Marine ecology is no exception. New methods provide analysis of data from sensors, cameras, and acoustic recorders, even in real time, in ways that are reproducible and rapid. Off-the-shelf algorithms find, count, and classify species from digital images or video and detect cryptic patterns in noisy data. These endeavours require collaboration across ecological and data science disciplines, which can be challenging to initiate. To promote the use of DL towards ecosystem-based management of the sea, this paper aims to bridge the gap between marine ecologists and computer scientists. We provide insight into popular DL approaches for ecological data analysis, focusing on supervised learning techniques with deep neural networks, and illustrate challenges and opportunities through established and emerging applications of DL to marine ecology. We present case studies on plankton, fish, marine mammals, pollution, and nutrient cycling that involve object detection, classification, tracking, and segmentation of visualized data. We conclude with a broad outlook of the field’s opportunities and challenges, including potential technological advances and issues with managing complex data sets.
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Nocera, Ariadna C., Eloísa M. Giménez, Mariano J. Diez, María Valeria Retana, and Gesche Winkler. "Krill diel vertical migration in Southern Patagonia." Journal of Plankton Research 43, no. 4 (July 2021): 610–23. http://dx.doi.org/10.1093/plankt/fbab047.
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Abstract Diel vertical migration (DVM) of krill was studied throughout 36 h at a fixed station (46.05°S, 66.19°W; 98-m depth) located in the center of the San Jorge Gulf, Southern Patagonia area, during February 2014. Using an echosounder system, combined with an autonomous Video Plankton Recorder (Auto-VPR) and Jacknet samplings, we describe the migration pattern, the associated biomass and the macrozooplankton species involved. The net sampling and the Auto-VPR images allowed us to identify the krill species detected in the echosounder signals, which corresponded to Euphausia lucens, Euphausia vallentini and Nematoscelis megalops. The krill community followed a “normal pattern” of DVM, ascending at dusk (~18:30 h) and descending at dawn (~06:30 h), forming a dense layer near the bottom during the day. Krill vertical migration speed was estimated from the echogram data at ~ 1 cm s−1 (1 body length per s for 1-cm-long animal), and the integrated mean biomass was 57.8 g m−2. This study provides a description of temporal and spatial patterns of krill vertical distribution, which should be taken into account when studying the complexity of the SJG ecosystem dynamics and carbon flux.
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Bennke, Christin M., Greta Reintjes, Martha Schattenhofer, Andreas Ellrott, Jörg Wulf, Michael Zeder, and Bernhard M. Fuchs. "Modification of a High-Throughput Automatic Microbial Cell Enumeration System for Shipboard Analyses." Applied and Environmental Microbiology 82, no. 11 (March 25, 2016): 3289–96. http://dx.doi.org/10.1128/aem.03931-15.
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ABSTRACTIn the age of ever-increasing “-omics” studies, the accurate and statistically robust determination of microbial cell numbers within often-complex samples remains a key task in microbial ecology. Microscopic quantification is still the only method to enumerate specific subgroups of microbial clades within complex communities by, for example, fluorescencein situhybridization (FISH). In this study, we improved an existing automatic image acquisition and cell enumeration system and adapted it for usage at high seas on board an oceanographic research ship. The system was evaluated by testing settings such as minimal pixel area and image exposure times ashore under stable laboratory conditions before being brought on board and tested under various wind and wave conditions. The system was robust enough to produce high-quality images even with ship heaves of up to 3 m and pitch and roll angles of up to 6.3°. On board the research ship, on average, 25% of the images acquired from plankton samples on filter membranes could be used for cell enumeration. Automated enumeration was highly correlated with manual counts (r2> 0.9). Even the smallest of microbial cells in the open ocean, members of the alphaproteobacterial SAR11 clade, could be confidently detected and enumerated. The automated image acquisition and cell enumeration system developed here enables an accurate and reproducible determination of microbial cell counts in planktonic samples and allows insight into the abundance and distribution of specific microorganisms already on board within a few hours.IMPORTANCEIn this research article, we report on a new system and software pipeline, which allows for an easy and quick image acquisition and the subsequent enumeration of cells in the acquired images. We put this pipeline through vigorous testing and compared it to manual microscopy counts of microbial cells on membrane filters. Furthermore, we tested this system at sea on board a marine research vessel and counted bacteria on board within a few hours after the retrieval of water samples. The imaging and counting system described here has been successfully applied to a number of laboratory-based studies and allowed the quantification of thousands of samples and FISH preparations (see, e.g., H. Teeling, B. M. Fuchs, D. Becher, C. Klockow, A. Gardebrecht, C. M. Bennke, M. Kassabgy, S. Huang, A. J. Mann, J. Waldmann, M. Weber, A. Klindworth, A. Otto, J. Lange, J. Bernhardt, C. Reinsch, M. Hecker, J. Peplies, F. D. Bockelmann, U. Callies, G. Gerdts, A. Wichels, K. H. Wiltshire, F. O. Glöckner, T. Schweder, and R. Amann, Science 336:608–611, 2012,http://dx.doi.org/10.1126/science.1218344). We adjusted the standard image acquisition software to withstand ship movements. This system will allow for more targeted sampling of the microbial community, leading to a better understanding of the role of microorganisms in the global oceans.
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Farach-Espinoza, Edgardo Basilio, Juana López-Martínez, Ricardo García-Morales, Manuel Otilio Nevárez-Martínez, Daniel Bernardo Lluch-Cota, and Sofia Ortega-García. "Temporal Variability of Oceanic Mesoscale Events in the Gulf of California." Remote Sensing 13, no. 9 (May 2, 2021): 1774. http://dx.doi.org/10.3390/rs13091774.
Full textAbstract:
Oceanic mesoscale events such as eddies, coastal upwelling, filaments and fronts created by water mass intrusion present properties allowing them to concentrate, transport and disperse salt, nutrients and plankton, among other important constituents in the ocean. The use of satellite images enables the continuous monitoring of the ocean dynamics at different temporal and spatial scales, aiding the study of its variability. This study focuses on the identification of these mesoscale events in the Gulf of California (GC) by means of sea surface temperature (SST) and chlorophyll a (Chl a) fronts (edge) detection by processing 5-day satellite images from the 1998–2019 period. The annual occurrence or frequency and duration of each event was identified; the interannual variability was evaluated and underlying correlations with the Multivariate El Niño Index (MEI) and the Pacific Decadal Index (PDOI) were assessed via Principal Component Analysis. Most events showed a seasonal variability due to the seasonal behavior of forcing agents (i.e., Pacific Ocean and winds) that stimulate their formation or presence in the GC; seasonality was more evident in the northern region than in the southern region. The interannual variability of their frequency or duration was associated with strong and intense El Niño and La Niña conditions (positive or negative MEI values) together with positive or negative phases of the PDOI. The use of SST and Chl a satellite images with a 5-day temporal resolution allowed to better identify and quantify the annual frequency and duration of each mesoscale event. It allowed to detect a seasonal behavior of these events in the northern region, followed by the central region. The southern region, due to the interaction of different water masses with unique characteristics, exhibited a less evident seasonality in the frequency of eddies, and no apparent association between their interannual frequency and duration with the MEI and PDOI. Constantly monitoring these oceanic events and their variability will help in the understanding of how the different regions of this large marine ecosystem respond to these variations in the long term.
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Marzuki, Ismail, and Irham Pratama Putra. "Investigation of Microplastic Exposure to Marine Fish in the Marine Tourism Area of Makassar City." Indo. J. Chem. Res. 10, no. 1 (May 30, 2022): 38–46. http://dx.doi.org/10.30598/ijcr.2022.10-ism.
Full textAbstract:
Plastic waste pollution in the marine environment triggers the formation of microplastics dissolved in seawater. Microplastics are one of the nutrients for plankton and phytoplankton. Through the food chain, microplastics can accumulate in the bodies of marine biota, until they finally reach the human body. The purpose of this research is to investigate and determine the microplastic group in fish in Makassar City KWB destinations. The method applied is maceration extraction using 70% C2H5OH for 3 days, then extracted with N-Hexane. The non-polar extracts identified the microplastic components using FTIR spectroscopy and analyzed the types of microplastics based on their absorption spectrum images. The results of the study were that all fish samples coded PS.B.1, PS.B.2, PS.B.3, were contaminated with secondary microplastics. Types of microplastics were identified, namely PP, PVC, PE, PS, PET and PC. The microplastic contaminants are thought to be the result of community activities. The public needs to be aware of the potential for microplastic accumulation in the bodies of marine fish that are consumed. Managers of Makassar City KWB destinations are advised to apply a pattern of supervision to the community to care about waste and educate the implementation of plastic waste recycling management
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Schmarje, Lars, Johannes Brünger, Monty Santarossa, Simon-Martin Schröder, Rainer Kiko, and Reinhard Koch. "Fuzzy Overclustering: Semi-Supervised Classification of Fuzzy Labels with Overclustering and Inverse Cross-Entropy." Sensors 21, no. 19 (October 7, 2021): 6661. http://dx.doi.org/10.3390/s21196661.
Full textAbstract:
Deep learning has been successfully applied to many classification problems including underwater challenges. However, a long-standing issue with deep learning is the need for large and consistently labeled datasets. Although current approaches in semi-supervised learning can decrease the required amount of annotated data by a factor of 10 or even more, this line of research still uses distinct classes. For underwater classification, and uncurated real-world datasets in general, clean class boundaries can often not be given due to a limited information content in the images and transitional stages of the depicted objects. This leads to different experts having different opinions and thus producing fuzzy labels which could also be considered ambiguous or divergent. We propose a novel framework for handling semi-supervised classifications of such fuzzy labels. It is based on the idea of overclustering to detect substructures in these fuzzy labels. We propose a novel loss to improve the overclustering capability of our framework and show the benefit of overclustering for fuzzy labels. We show that our framework is superior to previous state-of-the-art semi-supervised methods when applied to real-world plankton data with fuzzy labels. Moreover, we acquire 5 to 10% more consistent predictions of substructures.
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Schlezinger, David R., Craig D. Taylor, and Brian L. Howes. "Assessment of Zooplankton Injury and Mortality Associated With Underwater Turbines for Tidal Energy Production." Marine Technology Society Journal 47, no. 4 (July 1, 2013): 142–50. http://dx.doi.org/10.4031/mtsj.47.4.5.
Full textAbstract:
AbstractCollaborative work between the UMASS-Marine Renewable Energy Center, the Town of Edgartown, and the Coastal Systems Program is focused on developing the tidal energy potential of Muskeget Channel. We have undertaken detailed oceanographic and environmental surveys to optimize in-stream turbine power generation and to quantify potential environmental effects. In 2011 and 2012, tidal turbine demonstration projects were conducted in Muskeget Channel to determine the combined effects of blade strikes, shear stress, turbulence, and cavitation on zooplankton. Single turbines may minimally impact zooplankton populations; however, full-scale projects may potentially alter zooplankton populations forming the base of coastal food webs. Static plankton tows were performed up- and downstream of the operating turbine axis. Integral flow meters allowed adjustment of tow duration to optimize zooplankton density in the concentrate. Samples were held at in situ temperatures, and sequential photomicrographs and video images were taken to determine particle density, size distribution, and the number of live organisms in samples taken up and down gradient of the operating tidal turbines within 3 h of collection. Statistical analysis showed no significant difference in the total number or size distribution of motile zooplankters, indicating tidal turbine operation did not cause significant mortality and suggested that impacts of commercial size tidal energy projects upon zooplankton populations in Muskeget Channel may be negligible.
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Lombard, F., L. Labeyrie, E. Michel, L. Bopp, E. Cortijo, S. Retailleau, H. Howa, and F. Jorissen. "Modelling planktic foraminifer growth and distribution using an ecophysiological multi-species approach." Biogeosciences 8, no. 4 (April 8, 2011): 853–73. http://dx.doi.org/10.5194/bg-8-853-2011.
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Abstract. We present an eco-physiological model reproducing the growth of eight foraminifer species (Neogloboquadrina pachyderma, Neogloboquadrina incompta, Neogloboquadrina dutertrei, Globigerina bulloides, Globigerinoides ruber, Globigerinoides sacculifer, Globigerinella siphonifera and Orbulina universa). By using the main physiological rates of foraminifers (nutrition, respiration, symbiotic photosynthesis), this model estimates their growth as a function of temperature, light availability, and food concentration. Model parameters are directly derived or calibrated from experimental observations and only the influence of food concentration (estimated via Chlorophyll-a concentration) was calibrated against field observations. Growth rates estimated from the model show positive correlation with observed abundance from plankton net data suggesting close coupling between individual growth and population abundance. This observation was used to directly estimate potential abundance from the model-derived growth. Using satellite data, the model simulate the dominant foraminifer species with a 70.5% efficiency when compared to a data set of 576 field observations worldwide. Using outputs of a biogeochemical model of the global ocean (PISCES) instead of satellite images as forcing variables gives also good results, but with lower efficiency (58.9%). Compared to core tops observations, the model also correctly reproduces the relative worldwide abundance and the diversity of the eight species when using either satellite data either PISCES results. This model allows prediction of the season and water depth at which each species has its maximum abundance potential. This offers promising perspectives for both an improved quantification of paleoceanographic reconstructions and for a better understanding of the foraminiferal role in the marine carbon cycle.
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Lombard, F., L. Labeyrie, E. Michel, L. Bopp, E. Cortijo, S. Retailleau, H. Howa, and F. Jorissen. "Simulating the growth and distribution of planktic foraminifer using an ecophysiological multi-species model." Biogeosciences Discussions 8, no. 1 (January 4, 2011): 1–49. http://dx.doi.org/10.5194/bgd-8-1-2011.
Full textAbstract:
Abstract. We present an eco-physiological model reproducing the growth of eight foraminifer species (Neogloboquadrina pachyderma, Neogloboquadrina incompta, Neogloboquadrina dutertrei, Globigerina bulloides, Globigerinoides ruber, Globigerinoides sacculifer, Globigerinella siphonifera and Orbulina universa). By using the main physiological rates of foraminifers (nutrition, respiration, symbiotic photosynthesis), this model estimates their growth as a function of temperature, light availability, and food concentration. Model parameters are directly derived or calibrated from experimental observations and only the influence of food concentration (estimated via chl-a concentration) was calibrated against field observations. Growth rates estimated from the model show positive correlation with observed abundance from plankton net data suggesting close coupling between individual and assemblage growth rates. This observation was used to directly estimate potential abundance from the model-derived growth. Using satellite data, the model simulate the dominant foraminifer with a 70.5% efficiency when compared to a data set of 576 field observations worldwide. Using outputs of a biogeochemical model of the global ocean (PISCES) instead of satellite images as forcing variables gives also good results, but with lower efficiency (58.9%). The model also correctly reproduces the relative worldwide abundance and the diversity of the eight species when compared to core tops observations both using satellite and PISCES data. This model allows prediction of the season and water depth at which each species has its highest growth potential. This offers promising perspectives for both an improved quantification of paleoceanographic reconstructions and for a better understanding of the foraminiferal role in the marine carbon cycle.