Marine Institute Open Access Repository

Welcome to the Marine Institute Open Access Repository

The Marine Institute Open Access Repository facilitates full text access to the publications of the Marine Institute in accordance with copyright permissions. The aim of the Repository is to collect, preserve and provide open access to the publications of the Marine Institute, including the research publications supported by National and European funded marine research programmes.



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  • National survey of sea lice (Lepeophtheirus salmonis Krøyer and Caligus elongatus Nordmann) on fish farms in Ireland - 2017

    O'Donohoe, P.; Kane, F.; Kelly, S.; McDermott, T.; D'Arcy, J.; Casserly, J.; Downes, J.K.; Jackson, D. (Marine Insitute, 2018)
    Farmed stocks of Atlantic salmon in Ireland are inspected on 14 occasions throughout the year to monitor sea lice levels as part of a national programme.
  • Summary Report on 2016 Residue Monitoring of Irish Farmed Finfish and 2016 Border Inspection Post Fishery Product Testing undertaken at the Marine Institute

    Marine Institute (Marine Institute, 2018)
    On behalf of the Department of Agriculture, Food and Marine (DAFM), the Marine Institute carries out monitoring of chemical residues in finfish for aquaculture sector. This monitoring is set out in the annual National Residue Control Plan, which is approved by the European Commission, and is an important component of the DAFM food safety controls and is implemented under a service contract with the Food Safety Authority of Ireland. Since 1999, the Marine Institute has implemented the National Residues Monitoring Programme for aquaculture. This is carried out on behalf of the Sea Fisheries Protection Authority, which is the responsible organisation for residue controls on farmed finfish. The outcome for residues levels in farmed finfish during 2016 remains one of consistently low occurrence. In 2016, in excess of 691 tests and a total of 1,933 measurements were carried out on 136 samples (i.e. 126 target samples & 10 suspect samples) of farmed finfish for a range of chemical substances, including banned and unauthorised substances, various authorised veterinary treatments and environmental contaminants.
  • 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.

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