Limnology and Oceanography: Methods最新文献

{"title":"Deep learning-based characterization of underwater methane bubbles using simple dual camera platform","authors":"Yann Marcon,&nbsp;Marie Stetzler,&nbsp;Bénédicte Ferré,&nbsp;Eberhard Kopiske,&nbsp;Gerhard Bohrmann","doi":"10.1002/lom3.10672","DOIUrl":"https://doi.org/10.1002/lom3.10672","url":null,"abstract":"<p>Seabed gas and oil emissions appear as bubble plumes ascending through the water column in various environments. Understanding bubble characteristics—size, rise speed—is important for estimating escape rates of fluids like methane, oil, and carbon dioxide. However, measuring underwater gas bubbles is challenging, often requiring expensive specialized equipment. This study presents a novel methodology using two calibrated consumer-grade cameras to estimate bubble size distribution, rise velocities, and corresponding gas or oil flow rates. Our approach, named BURST (Bubble Rise and Size Tracking), uses a trained neural network for automated bubble detection in diverse camera footage, effectively analyzing under varying lighting conditions and visibility, without requiring a uniform backlit background for bubble identification. Post-detection, bubbles are tracked and synchronized between the cameras, with three-dimensional triangulation used to deduce sizes and rise speeds, enabling flow rate calculations. We demonstrate the efficacy of our methodology through basin experiments capturing methane bubble plumes with controlled flow rates. Additionally, we successfully apply this methodology to existing footage from natural methane emission sites in the Hopendjupet seeps within the central Barents Sea, measuring methane flow rates of approximately 46 and 24 mmol CH₄ min⁻¹ at water depths of 327 and 341 m, respectively. These results underscore the practical applicability of BURST in complex underwater environments without disrupting natural bubble flow. By utilizing readily available equipment, BURST enables reliable bubble measurements in challenging real-world conditions, including the analysis of legacy footage not initially intended for bubble flow rate quantification. The BURST python script is available at https://github.com/BUbbleRST/BURST/.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"23 3","pages":"155-175"},"PeriodicalIF":2.1,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.10672","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143571196","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Underwater Zooplankton Enhancement Light Array (UZELA): A technology solution to enhance zooplankton abundance and coral feeding in bleached and non-bleached corals","authors":"Andréa G. Grottoli,&nbsp;Shannon L. Dixon,&nbsp;Ann Marie Hulver,&nbsp;Claire E. Bardin,&nbsp;Claire J. Lewis,&nbsp;Christopher R. Suchocki,&nbsp;R3D Consortium,&nbsp;Robert J. Toonen","doi":"10.1002/lom3.10669","DOIUrl":"https://doi.org/10.1002/lom3.10669","url":null,"abstract":"<p>Coral resilience to heat stress is higher in corals that eat more zooplankton. In addition, coral feeding on zooplankton increases as zooplankton concentrations increase. To leverage the advantage that zooplankton feeding has on coral resilience, we developed the Underwater Zooplankton Enhancement Light Array (UZELA). UZELA is a patented autonomous, submersible, and programmable underwater light that is deployable for 6 months on a single battery. With 1 h of operation per night, it locally concentrates naturally occurring zooplankton, providing corals with greater feeding opportunities. Field tests show that UZELA increases local zooplankton concentrations by sevenfold compared to adjacent non-UZELA controls and coral feeding rates by 10 to 50-fold in both healthy and bleached <i>Montipora capitata</i> and <i>Porites compressa</i> corals compared to conspecifics without UZELA. With the continuing decline of coral reefs, technologies that can enhance coral feeding could play a critical role in coral resilience for coral in restoration nurseries and on the reef.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"23 3","pages":"201-211"},"PeriodicalIF":2.1,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.10669","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143571298","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Inferring microalgae density and net ecosystem production on soft sediments using infrared imaging","authors":"Anthony R. Ives,&nbsp;Emily L. Adler,&nbsp;K. Riley Book,&nbsp;Jamieson C. Botsch,&nbsp;Árni Einarsson,&nbsp;Ian S. Hart,&nbsp;Colin H. Ives,&nbsp;Ian Jin,&nbsp;Amanda R. McCormick,&nbsp;Joseph S. Phillips","doi":"10.1002/lom3.10671","DOIUrl":"https://doi.org/10.1002/lom3.10671","url":null,"abstract":"<p>Measuring microalgae density in soft-sediment benthos has challenges for even the most sophisticated methods. If the goal is to assess the photosynthetic potential of epipelon, then microalgae should be sampled only at the surface of the benthos to the depth of light penetration. Furthermore, microalgae density may show spatial and temporal variability that can only be captured by using many point samples and nondestructive sampling. Here, we use simple near-infrared (NIR) imagery to assess surface density of microalgae in soft underwater sediments and to infer their photosynthetic capacity. In lab studies, NIR imagery gives estimates of epipelon density that are strongly correlated with standard chlorophyll <i>a</i> (Chl <i>a</i>) assays using pigment extraction and fluorometry (<span></span><math>\u0000 <mrow>\u0000 <msubsup>\u0000 <mi>R</mi>\u0000 <mi>adj</mi>\u0000 <mn>2</mn>\u0000 </msubsup>\u0000 </mrow></math>  = 0.70), but NIR imagery is better able to separate experimental treatments. In analyses of sediment samples from a lake, NIR imagery gives estimates of epipelon Chl <i>a</i> density that are strongly correlated to net ecosystem production (NEP). Near-infrared imagery also gives a fine-grained assessment of the spatial distribution of epipelon that helps to explain the relationship between epipelon density and NEP. Finally, images from an underwater NIR camera over the course of a wind disturbance event give estimates of the relative density of microalgae that is buried and is likely to be, at least temporarily, photosynthetically inactive. These results show that NIR imagery provides an easy and nondestructive method for sampling surface densities of microalgae which is particularly suitable for remote field locations and for educational settings in which students can generate results with cheap and robust equipment.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"23 3","pages":"176-190"},"PeriodicalIF":2.1,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.10671","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143571295","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development and laboratory assessment of a subsea particle image velocimetry system for bubble and turbulence measurements in marine seeps","authors":"Xuchen Ying,&nbsp;Mustahsin Reasad,&nbsp;Binbin Wang","doi":"10.1002/lom3.10670","DOIUrl":"https://doi.org/10.1002/lom3.10670","url":null,"abstract":"<p>We present the development and laboratory evaluation of RPiPIV, an underwater particle image velocimetry (PIV) system controlled by a Raspberry Pi. Designed specifically to measure bubble characteristics and bubble-induced flow in natural hydrocarbon seeps, RPiPIV comprises three primary pressure enclosures, housing a consumer-grade laser for particle illumination, a Gig-E camera for image capture, a Raspberry Pi for system control, and essential supporting electronics for voltage conversion, battery management, and remote connection. Operating on 24–36 V DC power, the RPiPIV system can be deployed tethered onto a remotely operated vehicle or self-contained for extended duration measurements. Comparing the RPiPIV and a laboratory high-speed camera system, we conducted assessments of bubble imaging in a bubble stream and PIV measurements in a water jet, bubble-chain flow, and single-orifice bubble plume. Laboratory assessments revealed that bubble diameter estimates differed by approximately 5%. In PIV measurements, mean axial velocities exhibited differences of approximately 5%, while turbulent normal and shear stresses showed variances within 10–30%. Dissipation rates of turbulence kinetic energy differed by approximately 60%. These findings underscore the system's potential for reliably quantifying complex multiphase flow characteristics in deep-sea environments.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"23 3","pages":"139-154"},"PeriodicalIF":2.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.10670","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143571207","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Size matters: Perspective and angle-correction improves accuracy in noninvasive image-based body size measurements","authors":"T. Bøhn,&nbsp;E. Watts,&nbsp;R. Primicerio,&nbsp;P. Bjørn,&nbsp;J. F. Strøm","doi":"10.1002/lom3.10667","DOIUrl":"https://doi.org/10.1002/lom3.10667","url":null,"abstract":"<p>River management should secure conservation of biodiversity and sustainable use of aquatic resources. Conservation of fish populations requires time-series data on the number of fish present and the size-structure. The number of fish and species composition can be resolved by video-surveillance, but detailed measurements of body size often come from more intrusive methods such as fish traps and electrofishing that impose additive stress or mortality on individuals. We have developed and tested a nonintrusive method for video-surveillance which enables estimation of fish length, of anadromous Arctic char (<i>Salvelinus alpinus</i>) in a subarctic river. We use pixel counts in images of fish that swim through a tunnel, to measure the size of the fish, and calibrate our measurements with two parallel laser lines (100 mm apart) that are visible on the fish, both from the side and from above, facilitated by a 45° mirror. We demonstrate how the accuracy in body length measurements depends on camera perspective, fish angle, body curvature and swimming speed, and evaluate this with three independent observers. Our results show that the typically used side-view camera (lateral view) underestimated the fish on average by 10.7%, but that accuracy could be significantly improved by including: (1) angle-correction (for non-perpendicular fish positioning), (2) by measuring the fish from above (dorsal view), and (3) by including the body curvature of actively swimming fish. Our method represents a cost-efficient approach for monitoring size-structure in vulnerable populations that is of management concern and where intrusive monitoring should be avoided.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"23 3","pages":"191-200"},"PeriodicalIF":2.1,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.10667","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143571325","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quantifying invasion dynamics: Quantitative polymerase chain reaction vs. droplet digital polymerase chain reaction in monitoring the alien invasive bloody-red shrimp Hemimysis anomala and its interaction with perch in Lake Geneva","authors":"Sirine Melliti,&nbsp;Marine Vautier,&nbsp;Cécile Chardon,&nbsp;Stéphan Jacquet","doi":"10.1002/lom3.10666","DOIUrl":"https://doi.org/10.1002/lom3.10666","url":null,"abstract":"<p>Invasive alien species constitute a major threat to aquatic systems due to their potential impact on endemic biodiversity, ecosystem functioning, infrastructure, and possible sanitary issues. It is therefore crucial to obtain information on their presence, abundance, and distribution. The bloody-red shrimp <i>Hemimysis anomala</i>, which originated from the Ponto-Caspian area, has recently settled in Western European lakes, including Lake Geneva. Although divers have frequently reported the presence and development of this small crustacean over the last decade, no monitoring has yet been proposed. During a period of 2.5 yr, we tested and optimized an environmental deoxyribonucleic acid approach by comparing two polymerase chain reaction techniques, quantitative and digital droplet polymerase chain reaction, to assess the presence, abundance, and dynamics of the animal as well as that of a potential predator, the perch (<i>Perca fluviatilis</i>). We show and discuss the efficiency of the methods and reveal for the first time the seasonal dynamics of <i>Hemimysis anomala</i> at a selected site in Lake Geneva. We highlight, in agreement with diving observations, that the animal's abundance is high in winter and declines rapidly in early spring, concomitantly with temperature increase and perch presence.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"23 3","pages":"212-222"},"PeriodicalIF":2.1,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143571356","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A computer vision-based approach for estimating carbon fluxes from sinking particles in the ocean","authors":"Vinícius J. Amaral,&nbsp;Colleen A. Durkin","doi":"10.1002/lom3.10665","DOIUrl":"https://doi.org/10.1002/lom3.10665","url":null,"abstract":"<p>The gravitational settling of organic particles in the ocean drives long-term sequestration of carbon from surface waters to the deep ocean. Quantifying the magnitude of carbon sequestration flux at high spatiotemporal resolution is critical for monitoring the ocean's ability to sequester carbon as ecological conditions change. Here, we propose a computer vision-based method for classifying images of sinking marine particles and using allometric relationships to estimate the amount of carbon that the particles transport to the deep ocean. We show that our method reduces the amount of time required by a human image annotator by at least 90% while producing ecologically informed estimates of carbon flux that are comparable to estimates based on purely manual review and chemical bulk carbon measurements. This method utilizes a human-in-the-loop domain adaptation approach to leverage images collected from previous sampling campaigns in classifying images from novel campaigns in the future. If used in conjunction with autonomous imaging platforms deployed throughout the world's oceans, this method has the potential to provide estimates of carbon sequestration fluxes at high spatiotemporal resolution while facilitating an understanding of the ecological pathways that are most important in driving these fluxes.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"23 2","pages":"117-130"},"PeriodicalIF":2.1,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.10665","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143389457","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Otoliths, bones, teeth, and more: Development of a new polishing wheel for calcified structures","authors":"Nicholas Strait,&nbsp;David Taylor,&nbsp;Rebecca Forney,&nbsp;Jacob Amos,&nbsp;Jessica Miller","doi":"10.1002/lom3.10662","DOIUrl":"https://doi.org/10.1002/lom3.10662","url":null,"abstract":"<p>Biochronological information stored in the calcified structures of organisms provide fundamental organismal, environmental, and ecological data. Bones, teeth, statoliths, corals, and otoliths are widely used to answer a myriad of questions related to trophic position, migration, age and growth, environmental variation, and historical climate. Many calcified structures, particularly the ear stones of fishes (otoliths), are small (50 <i>μ</i>m to 5 mm) and require precise preparation methods, which vary depending on the structure and research question but commonly include embedding, sectioning, and polishing prior to structural or chemical analysis. Globally, management agencies rely on the precise polishing of millions of otoliths each year to obtain vital demographic data, such as age and growth. However, this process is time consuming, labor intensive, and ergonomically strenuous. Since the early 1970s, there has been limited advancement in preparation methods with many still using manual approaches or costly, and at times inefficient, equipment. Therefore, we designed and fabricated an affordable, adjustable speed, multi-wheel polisher, which can be powered with alternating or direct current. Sample preparation time is reduced, and sample consistency is notably improved compared to manual approaches. While specifically designed for consistent and relatively rapid preparation of otolith thin sections, the polisher is readily adaptable to a variety of applications. Designs and manufacturing for these wheels are publicly available through the iLab at Oregon State University.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"23 2","pages":"131-137"},"PeriodicalIF":2.1,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.10662","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143389458","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bringing heatwaves into the lab: A low-cost, open-source, and automated system to simulate realistic warming events in an experimental setting","authors":"Amelia L. Ritger,&nbsp;Gretchen E. Hofmann","doi":"10.1002/lom3.10663","DOIUrl":"https://doi.org/10.1002/lom3.10663","url":null,"abstract":"<p>Aquatic ecosystems face increasing threats from heatwaves driven by anthropogenic climate change, necessitating continued research to understand and manage the ecological consequences. Experimental studies are essential for understanding the impacts of heatwaves in aquatic systems; however, traditional experimental methods often fail to capture real-world complexity. Here, we present a method for simulating aquatic heatwaves that match the dynamic nature of real-world heatwave events in an experimental setting. Our method allows researchers to re-create heatwaves that have happened in the past or produce entirely new heatwave scenarios based on future projections. A Raspberry Pi serves as the foundation of our autonomous, customizable temperature control system, leveraging a low-cost and open-source platform for adaptability and accessibility. We demonstrate system functionality for laboratory experiments by first simulating a hypothetical marine heatwave scenario with defined temperature parameters and then replicating a real-world marine heatwave that occurred in the Santa Barbara Channel, California, in 2015. The average difference between desired and observed temperatures was 0.023°C for the basic heatwave simulation and less than 0.001°C for the real-world heatwave simulation, with standard deviations of 0.04°C and 0.01°C, respectively. Our novel method facilitates broader access to high-quality and affordable tools to study extreme climate events. By adopting a more realistic experimental approach, scientists can conduct more informative aquatic heatwaves studies.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"23 2","pages":"87-96"},"PeriodicalIF":2.1,"publicationDate":"2024-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.10663","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143389427","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CoralCT: A platform for transparent and collaborative analyses of growth parameters in coral skeletal cores","authors":"Thomas M. DeCarlo,&nbsp;Allyndaire Whelehan,&nbsp;Brighton Hedger,&nbsp;Devyn Perry,&nbsp;Maya Pompel,&nbsp;Oliwia Jasnos,&nbsp;Avi Strange","doi":"10.1002/lom3.10661","DOIUrl":"https://doi.org/10.1002/lom3.10661","url":null,"abstract":"<p>We present CoralCT, a software application for analysis of annual extension, density, and calcification in coral skeletal cores. CoralCT can be used to analyze computed tomography (CT) scans or X-ray images of skeletal cores through a process in which observers interact with images of a core to define the locations of annual density bands. The application streamlines this process by organizing the observer-defined banding patterns and automatically measuring growth parameters. Analyses can be conducted in two or three dimensions, and observers have the option to utilize an automatic band-detection feature. CoralCT is linked to a server that stores the raw CT and X-ray image data, as well as output growth rate data for hundreds of cores. Overall, this server-based system enables broad collaborations on coral core analysis with standardized methods and—crucially—creates a pathway for implementing multiobserver analysis. We assess the method by comparing multiple techniques for measuring annual extension and density, including a corallite-tracing approach, medical imaging software, two-dimensional vs. three-dimensional analyses, and between multiple observers. We recommend that CoralCT be used not only as a measurement tool but also as a platform for data archiving and conducting open, collaborative science.</p>","PeriodicalId":18145,"journal":{"name":"Limnology and Oceanography: Methods","volume":"23 2","pages":"97-116"},"PeriodicalIF":2.1,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.10661","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143389258","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}