Now showing items 1-20 of 1199

    • A Low-Complexity Mosaicing Algorithm for Stock Assessment of Seabed-Burrowing Species

      Corrigan, D.; Sooknanan, K.; Doyle, J.; Lordan, C.; Kokaram, A. (IEEE Xplore, 2018)
      This paper proposes an algorithm for mosaicing videos generated during stock assessment of seabed-burrowing species. In these surveys, video transects of the seabed are captured and the population is estimated by counting the number of burrows in the video. The mosaicing algorithm is designed to process a large amount of video data and summarize the relevant features for the survey in a single image. Hence, the algorithm is designed to be computationally inexpensive while maintaining a high degree of robustness. We adopt a registration algorithm that employs a simple translational motion model and generates a mapping to the mosaic coordinate system using a concatenation of frame-by-frame homographies. A temporal smoothness prior is used in a maximum a posteriori homography estimation algorithm to reduce noise in the motion parameters in images with small amounts of texture detail. A multiband blending scheme renders the mosaic and is optimized for the application requirements. Tests on a large data set show that the algorithm is robust enough to allow the use of mosaics as a medium for burrow counting. This will increase the verifiability of the stock assessments as well as generate a ground truth data set for the learning of an automated burrow counting algorithm.
    • International Blue Whiting Spawning Stock Survey (IBWSS) Spring 2018

      Marine Institute; Wageningen Marine Research; Institute of Marine Research; PINRO; Faroese Marine Research Institute; Marine Scotland Marine Laboratory; Johann Heinrich von Thünen-Institut; Danish Institute for Fisheries Research; Galway, Mayo Institute of technology; Irish Parks and Wildlife Service (Marine Institute, 2018)
      Coordination of the survey was initiated in the meeting of the Working Group on International Pelagic Surveys (WGIPS) and continued by correspondence until the start of the survey. During the survey effort was refined and adjusted by the survey coordinator (Norway) using real time observations. The survey design was based on methods described in ICES Survey design Manual (2015). Overall weather conditions were mixed with periods of poor and good weather. All vessels experienced some downtime due to poor weather conditions. The entire survey was completed within 20 days, below the 21 day target threshold.
    • Cruise report: Irish Anglerfish & Megrim Survey 2017

      Gerritsen, H.D.; Kelly, E.; Stokes, D.; O'Hea, B.; Ni Chonchuir, G. (Marine Institute, 2018)
      The 2017 Irish Anglerfish and Megrim Survey (IAMS) took place from 14th February to 7th March (area 7bcjk) and 8-17th April 2017 (area 6a) on RV Celtic Explorer. The main objective of the survey is to obtain biomass estimates for anglerfish (Lophius piscatorius and L. budegassa) and establish an abundance index for megrim (Lepidorhombus whiffiaginis and L. boscii) in areas 6a (south of 58°N) and 7 (west of 8°W). Secondary objectives are to collect data on the distribution and relative abundance of anglerfish, megrim and other commercially exploited species. The survey also collects maturity and other biological information for commercial fish species. The IAMS survey is coordinated with the Scottish Anglerfish and Megrim Survey (SIAMISS) and uses the same gear and fishing practices.
    • Cruise report: Irish Anglerfish & Megrim Survey 2016

      Gerritsen, H.D.; Kelly, E.; Stokes, D.; Ni Chonchuir, G.; Moore, S.J. (Marine Institute, 2018)
      The 2016 Irish Anglerfish and Megrim Survey (IAMS) took place from 4-24th January and 25th February to 6th March 2016 on RV Celtic Explorer. The main objective of the survey is to obtain biomass estimates for anglerfish (Lophius piscatorius and L. budegassa) in and establish an abundance index for megrim (Lepidorhombus whiffiaginis and L. boscii) in VIa (south of 58°N) and VII (west of 8°W). Secondary objectives are to collect data on the distribution and relative abundance of anglerfish, megrim and other commercially exploited species. The survey also collects maturity and other biological information for commercial fish species. The IAMS survey is coordinated with the Scottish Anglerfish and Megrim survey (SIAMISS) and uses the same gear and fishing practices.
    • Cruise report: Irish Beam trawl Ecosystem Survey 2017

      Gerritsen, H.D.; Moore, S.J. (Marine Institute, 2018)
      The second annual Irish Beam trawl Ecosystem (IBES) took place from 7-16th March 2017 on RV Celtic Explorer in the western Celtic sea. The main objective of the survey is to connect the Irish Anglerfish and Megrim Survey (IAMS) to the UK beam trawl surveys in the Celtic Sea, English Channel and Irish Sea, with the purpose of providing a swept-area biomass estimate for anglerfish (Lophius piscatorius and L. budegassa) in area VII. Secondary objectives are to collect data on the distribution and relative abundance of commercially exploited species as well as invertebrates and by-catch species, particularly vulnerable and indicator species. The survey also collects maturity and other biological information for commercial fish species in the western Celtic Sea. The IBES survey uses the same gear, methods and stratification as the CEFAS Q1 South-west Ecosystem Survey (Q1SWECOS). The IBES survey is formally coordinated by the ICES Working Group on Beam Trawl Surveys
    • Cruise Report: Irish Beam trawl Ecosystem Survey 2016

      Gerritsen, H.D. (Marine Institute, 2018)
      The first annual Irish Beam trawl Ecosystem (IBES) took place from 6-16th March 2016 on RV Celtic Explorer in the western Celtic sea. The main objective of the survey is to connect the Irish Anglerfish and Megrim Survey (IAMS) to the UK beam trawl surveys in the Celtic Sea, English Channel and Irish Sea, with the purpose of providing a swept-area biomass estimate for anglerfish (Lophius piscatorius and L. budegassa) in area VII. Secondary objectives are to collect data on the distribution and relative abundance of commercially exploited species as well as invertebrates and by-catch species, particularly vulnerable and indicator species. The survey also collects maturity and other biological information for commercial fish species in the western Celtic Sea. The IBES survey is coordinated with the CEFAS Q1 South-west Ecosystem Survey (Q1SWECOS) and uses the same gear and methods.
    • Creating a weekly Harmful Algal Bloom bulletin

      Leadbetter, A.; Silke, J.; Cusack, C. (Marine Institute, 2018)
      This document describes the procedural steps in creating an information product focused on toxic and harmful phytoplankton. The product is an online Harmful Algal Bloom (HAB) bulletin for aquaculturists, who can face serious operational challenges in the days after a HAB event. Data from satellite, numerical hydrodynamic models and In-situ ocean observations are organised and presented into visual information products. These products are enhanced through local expert evaluation and their interpretation is summarised in the bulletin. This document aims to provide both process overviews (the “what” of the Best Practice in producing the bulletins) and detail procedures (the “how” of the Best Practice”) so that the bulletins may be replicated in other geographic regions.
    • Shellfish Stocks and Fisheries Review 2016-2017: an assessment of selected stocks

      Marine Institute; Bord Iascaigh Mhara (Marine Institute, 2018)
      This review presents information on the status of selected shellfish stocks in Ireland. In addition, data on the fleet (<13 m) and landings for all species of shellfish (excluding Nephrops and mussels) are presented. The intention of this annual review is to present stock assessment and scientific advice for shellfisheries which may be subject to new management proposals or where scientific advice is required in relation to assessing the environmental impact of shellfisheries especially in areas designated under European Directives.
    • Reproductive Failure of Landlocked Atlantic Salmon from New York's Finger Lakes: Investigations into the Etiology and Epidemiology of the “Cayuga Syndrome”

      Fisher, J.P.; Spitsbergen, J.M.; Rodman, G.; symula, j. (American Fisheries Society, 1995)
      We describe a disease syndrome that afflicts larval, landlocked Atlantic salmon Salmo salar from Cayuga Lake, one of central New York's Finger Lakes. Mortality associated with the “Cayuga syndrome” is 98–100%. Death usually occurs between 650 and 850 centigrade degreedays after fertilization, approximately 2–4 weeks before yolk resorption is complete. Although there is minor temporal variation in the onset of the Cayuga syndrome in progeny from individual females, all sac fry eventually succumb. Incubation of embryos and sac fry under constant, ambient, or reduced temperature regimens slightly alters the degree-day timing of syndrome onset, but does not improve survival. Based on mortality rate, manifestation of the Cayuga syndrome has not changed in the past 10 years, even though incubation waters of varying chemistry and temperature have been used. Mortality of the negative control stocks used for these studies never exceeded 10% from hatching to first feeding. Findings from reciprocal crossbreeding experiments indicate the problem is associated with ova only. A noninfectious etiology is indicated by the lack of consistently identifiable fish pathogens from syndrome-afflicted sac fry and by the failure to transmit the condition horizontally. Suspect contaminants were eliminated as potential causative factors. Epidemiological studies on the viability of other Finger Lakes stocks indicate that Atlantic salmon from Keuka and Seneca lakes are also afflicted (100% mortality). yet those from Skaneateles Lake are not. The cause of this syndrome appears to be nutritional.
    • Atlantic Herring and Horse Mackerel in 6aS/7b; Industry Acoustic Survey Cruise Report

      O’Malley, M.; Clarke, M.; Smith, T.; Mullins, E. (Marine Institute, 2018)
      An acoustic survey of Atlantic herring Clupea harengus and horse mackerel Trachurus trachurus was conducted in ICES areas 6aS/7b in Nov 2017 using the pair trawl vessels MFV Eilean Croine S238 and MFV Sparkling Star D437. This survey is the second in a time series that is hoped will be developed into a long-term index of spawning/pre-spawning herring and horse mackerel in 6aS/7b, for use in stock assessments in the future. The survey design was based on the predicted distribution of herring and horse mackerel in this area during this time. In total 1,482nmi of cruise track was completed using 27 transects and related to a total area coverage of approximately 2,200 nmi². Parallel transect spacing was set at 7.5nmi for the wider area, and 3.5nmi for Donegal Bay. Coverage extended from inshore coastal areas to the 200 m contour in the west and north. A mini survey was carried out in Lough Swilly using a zig-zag design. A Simrad ES-38B (38 kHz) split-beam transducer mounted on a towed body was calibrated before the survey near Rathmullan Pier in Lough Swilly, Co. Donegal. Very strong herring marks (e.g. > 2nmi long, 200m wide and ~18m deep) were evident in Lough Swilly, an area where boats in the monitoring fishery were concentrating effort. There was also a series of strong herring marks in Bruckless Bay and Inver Bay in discreet areas. There were very few herring marks offshore. A total of four hauls were taken for biological analysis. Biological samples from the monitoring fishery were used to augment the samples from the survey. Samples were taken from boats fishing in Lough Swilly, Bruckless Bay and Inver Bay as close spatially and temporally as possible to the survey in these areas. Herring were dominated by 3-wr fish in all hauls. The 3-wr age class constituted 32% of the overall numbers. Horse mackerel were distributed throughout the survey area, but particularly throughout the area to the north and west of Tory Island. Horse mackerel length distribution was dominated by a mode at 24cm, with a smaller mode at 30cm. This corresponded to a dominance of 3-wr fish (~67%) in all of the samples. The total stock biomass (TSB) estimate of herring for the combined 6aS/7b area was 40,646 tonnes (Lough Swilly = 12,098 tonnes, Donegal Bay = 23,157 tonnes, and the remaining NW area = 5,391 tonnes). This is considered to be a minimum estimate of herring in the 6aS/7b survey area at the time of the survey. The TSB estimate of horse mackerel for the total surveyed area in 6aS/7b area was 68,079 tonnes, considered to be a minimum estimate of horse mackerel in the 6aS/7b survey area at the time of the survey. The CV estimates on biomass and abundance are high (~0.50 for herring and ~ 0.62 for horse mackerel) for the survey in 2017. For herring, this is mostly caused by the over-reliance on a few acoustic marks of herring in Lough Swilly and Bruckless/Inver Bays in particular. For horse mackerel, this is most likely caused by and over-reliance of two transects in particular. Horse mackerel are a widely distributed stock, therefore the stock was not contained by this survey.
    • The Irish Maritime Transport Economist Volume 14

      Irish Maritime Development Office (Marine Institute, 2017)
    • Sensitive Ecosystem Assessment and ROV Exploration of Reef Survey Report 2017

      O’Sullivan, D.; Leahy, Y.; Guinan, J.; Shipboard Scientific Party (Marine Institute, 2018)
      A requirement exists to quantify the abundance and distribution of offshore biogenic and geogenic reef habitats in Irish waters to fulfil Ireland’s legal mandate and to generate baseline data from which appropriate monitoring systems can be established. To address this an extensive offshore reef survey of Ireland’s Northwest Continental margin was commissioned by the National Parks and Wildlife Service (NPWS), funded by the European Maritime and Fisheries Fund (EMFF), and coordinated and led by INFOMAR (Integrated Mapping for the Sustainable Development of Ireland’s Marine Resources) and Ireland’s Marine Institute. The objectives of the survey were to implement the EMFF’s Marine Biodiversity Scheme - Natura Fisheries by mapping offshore reef habitats with a view to protecting them from deterioration due to fishing pressures. The reef project aligns with sub-article 6.2 of the Habitats Directive (EC 92/43/EEC) which requires member states to take measures to avoid deterioration of protected habitats. A survey, Sensitive Ecosystem Assessment and ROV Exploration of Reef (SeaRover), took place in July 2017 aboard the ILV Granuaile equipped with the Marine Institute’s remotely operated vehicle (ROV) Holland 1 and a multidisciplinary team of scientists to observe seabed features and biological associations along the northwest continental shelf. The Holland 1 employs high-definition (HD) camera, various composite video feeds and a robotic arm to facilitate sample collection. The primary scientific objective was to map the distribution and abundance of geogenic and biogenic reef habitat along the northwest shelf edge of Ireland’s continental slope with HD video. Secondary objectives included the collection of biological samples for genetic and population analysis and the collection of sediment cores for ground-truthing seabed mapping data and analysis of micro-plastics within deep-water sediment.
    • Celtic Sea Herring Acoustic Survey Cruise Report 2017, 15-04 November 2017

      O'Donnell, C.; O'Malley, M.; Lynch, D.; Lyons, K.; Keogh, N.; O’Driscoll, D. (Marine Institute, 2017)
      In the southwest of Ireland and the Celtic Sea (ICES Divisions VIIaS, g & j), herring are an important commercial species to the pelagic and polyvalent fleet. For a period in the 1970s and1980s, larval surveys were conducted for herring in this area. However, since 1989, acoustic surveys have been carried out, and currently are the only tuning indices available for this stock. In the Celtic Sea and VIIj, herring acoustic surveys have been carried out since 1989. Since 2004 the survey has been fixed in October and carried out onboard the RV Celtic Explorer. The geographical confines of the annual 21 day survey have been modified in recent years to include areas to the south of the main winter spawning grounds in an effort to identify the whereabouts of winter spawning fish before the annual inshore spawning migration. Spatial resolution of acoustic transects has been increased over the entire south coast survey area. The acoustic component of the survey has been further complemented since 2004 by detailed hydrographic, marine mammal and seabird surveys.
    • The Stock Book 2017 : Annual Review of Fish Stocks in 2017 with Management Advice for 2018

      Marine Institute (Marine Institute, 2017)
      The Stock Book is the principal annual publication of the Marine Institute's Fisheries Ecosystems Advisory Services (FEAS). Its purpose is to provide the latest impartial scientific advice on the commercially exploited fish stocks of interest to Ireland. The Stock Book is used by the Department of Agriculture, Food and the Marine - (DAFM) at the Total Allowable Catch (TAC) negotiations with the EU in December and throughout the year at fisheries management meetings.
    • Explorers planning guide for primary school teachers: ocean literacy and engagement

      Dromgool-Regan, Cushla; Burke, Noirin; Allard, Brendan (Marine Institute, 2017)
      The Explorers Education Programme™ aims to build on Ireland’s marine and maritime heritage by increasing awareness of the value, opportunities and social benefits of our ocean wealth and identity. This ocean literacy and engagement guide provides ocean facts, evaluation tools and ideas for the classroom.
    • Aran, Galway Bay and Slyne Head Nephrops Grounds (FU17) 2017 UWTV Survey Report and catch options for 2018

      Lordan, C.; Doyle, J.; Butler, R.; Sugrue, S.; Allsop, C.; O'Connor, S.; Vacherot, J.P. (Marine Institute, 2017)
      This report provides the main results and findings of the fifteenth annual underwater television on the Aran, Galway Bay and Slyne head Nephrops grounds, ICES assessment area; Functional Unit 17. The survey was multi-disciplinary in nature collecting UWTV, fishing, CTD and other ecosystem data. In 2017 a total of 40 UWTV stations were successfully completed, 31 on the Aran Grounds, 5 on Galway Bay and 4 on Slyne Head patches. The mean burrow density observed in 2017, adjusted for edge effect, was medium at 0.29 burrows/m². The final krigged burrow abundance estimate for the Aran Grounds was 343 million burrows with a CV (or relative standard error) of 3 %. The final abundance estimate for Galway Bay and Slyne Head was 25 and 11 million burrows with CVs of 7% and 3% respectively. The total abundance estimates have fluctuated considerably over the time series. The 2016 combined abundance estimate was 32% lower than in 2015 and at 379 million and is below the MSY Btrigger (540 million). Using the 2017 abundance estimate and updated stock data implies catch of 551 tonnes and landings of 513 tonnes in 2018 when MSY approach is applied (assuming that discard rates and fishery selection patterns do not change from the average of 2014–2016). Virgilaria mirabilis was the only sea-pen species observed on the UWTV footage. Trawl marks were present at 20% of the Aran stations surveyed.
    • Porcupine Bank Nephrops Grounds (FU16) 2017 UWTV Survey Report and catch options for 2018

      Lordan, C.; Doyle, J.; Butler, R.; Sugrue, S.; Allsop, C.; O’Connor, S.; Vacherot, J.P. (Marine Institute, 2017)
      This report provides the results of the fifth underwater television on the ‘Porcupine Bank Nephrops grounds’ ICES assessment area; Functional Unit 16. The survey was multi-disciplinary in nature collecting UWTV, CTD and other ecosystem data. In total 63 UWTV stations were successfully completed in a randomised 6 nautical mile isometric grid covering the full spatial extent of the stock. The mean burrow density observed in 2017, adjusted for edge effect, was 0.12 burrows/m². The final krigged abundance estimate was 850 million burrows with a relative standard error of 5% and an estimated stock area of 7,134 km2. The 2017 abundance estimate was 11% lower than in 2016. Using the 2017 estimate of abundance and updated stock data implies catch of 2,734 tonnes and landings of 2,734 tonnes in 2017 when MSY approach is applied (assuming that all catch is landed). The three species of sea-pen; Virgularia mirabilis, Funiculina quadrangularis and Pennatula phosphorea, were all observed during the survey. The deepwater sea-pen Kophobelemnon stelliferum was also observed and its presence/absence mapped from the available time-series. Trawl marks were also observed on 43% of the stations surveyed.
    • Western Irish Sea Nephrops Grounds (FU15) 2017 UWTV Survey Report and catch options for 2018

      Clements, A.; Doyle, J.; Lordan, C.; Lundy, M.; McCorriston, P.; McArdle, J.; McCausland, I.; Burns, G.; Schön, P.J. (Marine Institute, 2017)
      This report provides the main results and findings of the 15th annual underwater television survey on the ‘Irish sea west Nephrops grounds’ ICES assessment area, Functional Unit 15. The survey was multi-disciplinary in nature collecting UWTV and other ecosystem data. The 2017 design consisted of a randomised isometric grid of 100 stations at 4.5 nautical mile intervals out over the full known extent the stock. The resulting krigged burrow abundance estimate was 5.3 billion burrows. This was a similar result of that obtained in 2006, and 4% higher than the abundance in 2016. In contrast to 2016 the spatial distribution of burrows appears more homogenous across the survey area. Overall densities are high and abundance remains stable, well above MSY Btrigger. Reducing the number of stations compared to 2011 has not affected the accuracy of the survey estimate to date. The CV (or relative standard error) of 3% is in line with previous estimates and well below the upper limit of 20% recommended by SGNEPS 2012. Total catches and landings options at various different fishing mortalities were calculated and fishing at Fmsy in 2017 implies a total catch option at Fmsy (=Fmax) of 11,807 tonnes which results in landings of no more than 9,630 tonnes. The only sea-pen species observed in 2017 was Virgularia mirabilis and this was found at 16% of stations ranging from occasional to common, with high densities observed in the south-west of the ground. Trawl marks were noted at 36% of the UWTV stations.
    • FU19 Nephrops Grounds 2017 UWTV Survey and catch options for 2018

      Doyle, J.; Fitzgerald, R.; O’Brien, S.; Ryan, G.; McGeady, R.; Lordan, C. (Marine Institute, 2017)
      This report provides the main results of the eighth underwater television survey of the various Nephrops patches in Functional Unit 19. The survey was multi-disciplinary in nature collecting UWTV, CTD, multi-beam and other ecosystem data. In 2017 a total 41 UWTV stations were successfully completed. The mean density estimates varied considerably across the different patches. The 2017 raised abundance estimate was a 25% increase from the 2016 estimate and at 499 million burrows is above the MSY Btrigger (430 million). Using the 2017 estimate of abundance and updated stock data implies catch of 1,192 tonnes and landings of 889 tonnes in 2018 when MSY approach is applied (assuming that discard rates and fishery selection patterns do not change from the average of 2014–2016). Two species of sea pen were observed; Virgularia mirabilis and Pennatula phosphorea which have been observed on previous surveys of FU19. Trawl marks were observed at 10% of the stations surveyed.
    • The “Smalls” Nephrops Grounds (FU22) 2017 UWTV Survey Report and catch options for 2018

      O’Brien, S.; Blaszkowski, M.; Butler, R.; Fee, D.; Hernon, P.; Santana, C.; Lordan, C.; Doyle, J. (Marine Institute, 2017)
      This report provides the main results and findings of the twelfth annual underwater television survey on the ‘Smalls grounds’ ICES assessment area; Functional Unit 22. The survey was multi-disciplinary in nature collecting UWTV, CTD and other ecosystem data. A total of 40 UWTV stations were surveyed successfully (good quality video footage) carried out over an isometric grid at 4.5nmi or 8.3km intervals. The precision, with a CV of 5%, was well below the upper limit of 20% recommended by SGNEPS 2012. The 2017 abundance estimate was 16% higher than in 2016 and at 1600 million is above the new MSY Btrigger (990 million). Using the 2017 estimate of abundance and updated stock data implies catch of 4,332 tonnes and landings of 3,784 tonnes in 2018 when MSY approach is applied (assuming that discard rates and fishery selection patterns do not change from the average of 2014–2016). Only one species of sea-pen Virgilaria mirabilis was recorded as present at the stations surveyed. Trawl marks were observed at 59% of the stations surveyed. Ten beam trawl tows were carried out providing important data on the benthic communities and size structure of the Nephrops population.