Practical implementation of real-time fish classification from acoustic broadband echo sounder data- RealFishEcho progress report : Year 1-June 2017

The EU has by means of new policy restricted the discarding of fish at sea, including bycatch and slipping. As a result, the fishing industry now requires improved methods to identify fish species and size before the catch process begins. With the introduction of robust broadband echosounder (i.e. downward looking sonar) on the market, active acoustic data now have the potential for improved target discrimination for both type and size (i.e. determine fish species and size). The aim of this project is to develop methods for fish classification and size estimation using data from broadband echosounder and further implement them into a software for near-real time viewing. Such a software would help skippers to take better informed decisions while fishing. This project is running over three years (June 2016 to June 2019) in collaboration between Wageningen Marine Research (WMR), Redersvereniging voor de Zeevisserij (RVZ) and TNO. This document reports on the improvement of the methods used for fish species classificatio

Practical implementation of real-time fish classification from acoustic broadband echo sounder data - RealFishEcho progress report : Year 2 - June 201

The EU has by means of new policy restricted the discarding of fish at sea. As a result, the fishing industry now requires improved methods to identify fish species and size before the catch process begins. With the introduction of robust broadband echosounders (i.e. downward looking sonar) on the market, active acoustic data now have the potential for improved target discrimination for both type and size (i.e. determine fish species and size).The aim of this project is to develop methods for fish classification and size estimation based on data collected on board commercial vessel equipped with broadband echosounders. These methods will then be implemented into a software package for near-real time viewing. Such a software package would help skippers to take better-informed decisions while fishing.This project runs over three years (June 2016 to June 2019) in collaboration between Wageningen Marine Research (WMR), Redersvereniging voor de Zeevisserij (RVZ) and TNO. Progress made in the second year of the project is presented in this report.Through the course of the reporting period, substantial amount of data have been collected and analysis show promising results. A test version of the classification software is planned to be deployed in the next phase of the project

An echosounder view on the potential effects of impulsive noise pollution on pelagic fish around windfarms in the North Sea

Anthropogenic noise in the oceans is disturbing marine life. Among other groups, pelagic fish are likely to be affected by sound from human activities, but so far have received relatively little attention. Offshore wind farms have become numerous and will become even more abundant in the next decades. Wind farms can be interesting to pelagic fish due to food abundance or fisheries restrictions. At the same time, construction of wind farms involves high levels of anthropogenic noise, likely disturbing and/or deterring pelagic fish. Here, we investigated whether bottom-moored echosounders are a suitable tool for studying the effects of impulsive - intermittent, high-intensity - anthropogenic noise on pelagic fish around wind farms and we explored the possible nature of their responses. Three different wind farms along the Dutch and Belgian coast were examined, one with exposure to the passing by of an experimental seismic survey with a full-scale airgun array, one with pile driving activity in an adjacent wind farm construction site and one control site without exposure. Two bottom-moored echosounders were placed in each wind farm and recorded fish presence and behaviour before, during and after the exposures. The echosounders were successful in detecting variation in the number of fish schools and their behaviour. During the seismic survey exposure there were significantly fewer, but more cohesive, schools than before, whereas during pile driving fish swam shallower with more cohesive schools. However, the types and magnitudes of response patterns were also observed at the control site with no impulsive sound exposure. We therefore stress the need for thorough replication beyond single case studies, before we can conclude that impulsive sounds, from either seismic surveys or pile driving, are a disturbing factor for pelagic fish in otherwise attractive habitat around wind farms.Animal science

Comparison of length measurements of the blue whiting samples

Blue whiting (Micromesistius poutussou) form dense spawning aggregations along the Hebridean Shelf and Porcupine Bank, west of Scotland and Ireland, starting early spring until May. The International Council for the Exploration of the Seas (ICES) coordinated the international scientific acoustic survey targeting this spawning aggregation of the blue whiting which provide indices of abundance per age-class, which are an essential input data source for the assessment of this stock. The commercial fishing effort overlap with the survey in area and time. A first step towards the use of commercial length frequency data for survey index calculation is to investigate if there is any difference between survey and commercial length frequency data, and understand the origin of potential differences. In this study, the length frequency data collected by the self-sampling program on PFA vessels during the blue whiting fishing trips was compared with the survey measurements with a main focus on the 2017 and 2018 data. From different vessels contributing to the data set, only 4 vessels had adequate overlap in space and time in 2018, and 2 vessels in 2017. The results indicated that the mean length and the distributions are promising similar from two of the vessels contributing to this dataset in 2018. In addition, the third vessel showed very high similarity when the sampling dates are very close to the survey station while geographical distance is below 20 nautical miles. In 2017, the measurements from the two vessels had very close similarity to the survey measurements. As further supporting these close similarities, the mean length from a single survey samples (that were focus of the comparisons) remained within the 95% confidence interval of the measurements from the repeated hauls of PFA vessels in relatively close location. In 2018, one of the vessels contributing to the data did not have adequate similarity based on the statistical comparisons, however its samples also did not have very close overlap with survey samples in space and time compared to the other vessels

Investigation of the use of the EK80 CW during acoustic surveys on board Tridens

Fisheries acoustic surveys are routinely conducted around the world, and particularly within the ICES community. For nearly 20 years, the Simrad EK60 system has been the most commonly used echosounder equipment, and it is now being superseded by the Simrad EK80 system (CW mode). The comparison of the two systems and the impact of the transition from one system to the next for routine acoustic surveys has been investigated by several institutes. This report specifically investigates the use of the EK80 CW on board the Dutch Research Vessel (RV) Tridens II. RV Tridens II is routinely used by Wageningen Marine Research for conducting acoustic surveys. Currently, while the EK80 system is also available on board, the EK60 is used for survey recordings. In order to bring a transition from the EK60 to the EK80 CW, this study investigated: 1. the consistency in calibration results for the EK80 CW since 2015. This is done by generating time series plots of historical EK80 CW calibration data collected on RV Tridens II. 2. the consistency between the EK60 and the EK80 CW with data collected ping to ping using a multiplexer during the herring acoustic surveys (HERAS) in 2017 and 2018. The EK60/EK80 CW results are also put in light of findings of another published study (Macaulay et al. 2018) based on data collected on RV Tridens II in 2016 during the blue whiting acoustic (IBWSS) survey. Calibration and EK60/EK80 CW results from HERAS 2018 reveal large discrepancies with the EK80 CW 38 kHz channel originating from July 2017. The EK60/EK80 CW results from HERAS 2018 also show smaller discrepancies for the 18 kHz channel, due to different areas of the acoustic ring down below the transducer and noise interferences of the EK80 CW. Nevertheless, the analysis of other frequency channels for both HERAS 2017 and 2018 data show a good agreement between the systems. In addition, the analysis of 18 kHz and 38 kHz channels for HERAS 2017 exemplify good consistency between the EK60 and the EK80 CW, suggesting an electrical problem is causing the discrepancies observed during HERAS 2018. Though the issue with the 18 kHz and 38 kHz channels on board RV Tridens II needs to be tackled prior to using the EK80 CW for routine surveys, this study together with previous studies suggest that results from the EK80 CW are comparable to those of the EK60. It is therefore recommended to switch to using the EK80 CW for routine acoustic surveys onboard RV Tridens II once the issue with the equipment malfunctioning is resolved

Analysis of ancillary acoustic data during acoustic trawl surveys

Acoustic trawl surveys are routinely conducted around the world. They consist on following pre-defined transects, imaging the water column acoustically using downward active acoustic systems (so called scientific echosounders) and conducting regular trawling. This type of survey is used to assess the state of marine species (most often fish) at a specific point in time. Whilst echosounder data and trawling information are the base of an acoustic trawl survey, various types of ancillary data can be collected to complement the survey. An important part of the processing of data collected during a fish species acoustic survey is the scrutinisation process. It consists on the categorization and allocation of echo traces into species or species groups. Through expert judgement of the analyst, this relies on acoustic (frequency components, school morphology, time of day, depth etc) and biological (fishing) information. This information is usually specific to each survey and each species. For difficult scrutinisation cases, ancillary data (e.g. additional acoustic data, video data) can significantly aid this process. In this report, the use of two type of ancillary acoustic data collected during the herring Acoustic Survey (HERAS) onboard Tridens II are investigated: the multi-beam echosounder data (MBES, ME70) and the multi-frequency data from the split-beam echosounders (EK60/EK80 Continuous Wave). First, MBES data from HERAS 2016 were analysed with the aim of: (1) building a database of 3D fish school descriptors for potential future use during HERAS survey scrutinisation, (2) comparing MBES data with single beam echosounder data (EK60) in the context of abundance estimation. The results of the comparison between the ME70 and the EK60 showed that results are in line though an increased coverage of the water column with the ME70 induces greater variability. Historical HERAS data were analysed in order to investigate acoustic fingerprints for herring during this survey. The HERAS surveys from 2015 to 2019 were reanalysed using LSSS (Large Scale Survey System) automatic routines for fish school detection. The fish school descriptors and acoustic fingerprints were then used for classification using a Neural Network (NN). The NN classifier yielded an accuracy for herring of ~70%

Improvement of greater argentine stock assessment

An ongoing commercial market sampling for the Dutch greater argentine fishery is carried out by WMR in collaboration with the pelagic fishing fleet of the Netherlands. Start of this sampling programme goes back to year 1990. The aim of this programme is to achieve a haul-level sampling each year, stratified in area and time within the targeted ICES division. Later, market sampling data is pooled with respect to the quarter and the ICES divisions and the inferred age structure to is allocated to the catch, a classical ALK is generated from the collected age-length data which describes the probability of age given length (Fridriksson 1934). The sample sizes in this long time series can be relatively low in some years and the coverage can be relatively limited in space and time. The additional data sets, collected outside of this program, such as length composition data collected by self-sampling of PFA, maybe useful for filling some of these gaps and improve the level of accuracy of the estimations. However, this approach requires - A detailed understanding of the characteristics of the data set and the patterns in the market sampling time series. - A careful comparison between the datasets while assessing the quality and consistency of the measurements - Adoption of an unbiased method to incorporate age structure information from one dataset to the other. In the first section of the report, the characteristics of the two datasets are explained such as the sampling strategy, sample processing, sample size as well as the demographic changes over the years. Secondly the results of the comparison between the two datasets are presented. The initial aim was to focus on the samples from the two different sampling programs overlapping in space and time. However the level of overlap was not as close as expected. Nevertheless the closest samples in space and time selected and compared. It was found that the resemblance between the datasets did not show a pattern that can be explained with the distance or time between the samples. This is most likely due to stochasticity of the length distributions. A secondary problem that was tackled with was the lack of age information in the PFA data sets. Although length distributions can be an indirect indicator of the age structure a cohort estimation can not be acquired from the length distribution due to slow growth and long life span of the species. One solution would be inferring such missing ages using the available age/length information. Currently, classical age/length keys are commonly used to extrapolate otolith readings to length composition. Unfortunately the classical ALK obtained with data from one year/area cannot be applied to another year/area, because the underlying structure of the population may change due to variation in recruitment, survival or growth. An alternative is the use of an inverse key, which describes the probability of length given age, and has the benefit that this probability is not affected by variation in recruitment and survival. An inverse key can be applied to other years or areas, but under the assumption that size at age does not vary between years or areas. Another alternative is the combined forward-inverse key (hereafter called ‘combined key’) which combines the forward and inverse key into one approach (Hoenig et al. 2002). It uses Bayes’ rule to implement the forward and inverse key into one maximum likelihood framework through the probability of length at age. In this work, we applied the combined key using an R package implementation ( ‘ALKr’) by Murta et al. (2016). For this exercise, we used market age/length samples to build a combined key for greater greater argentine and compared it with the results obtained by the classical ALK. We further used the constructed combined key to estimate the age composition for the catch of samples by the PFA based on their length measurements. The resulting combined key is a promising solution for estimating the age composition in the PFA self-sampling data set, from which the length composition could be used as an input. However before that it is necessary to ensure that the this length composition time series is free from systematic biases with reasonable accuracy. Therefore a comprehensive check was carried out for the PFA length frequency data while using the market sampling dataset as a reference. The results are presented in this report. Lastly stock assessment tests were performed for the greater argentine by with and without incorporation of the PFA data, and the results are discussed

Practical implementation of real-time fish classification from acoustic broadband echo sounder data - RealFishEcho progress report : Year 2 - June 201

The EU has by means of new policy restricted the discarding of fish at sea. As a result, the fishing industry now requires improved methods to identify fish species and size before the catch process begins. With the introduction of robust broadband echosounders (i.e. downward looking sonar) on the market, active acoustic data now have the potential for improved target discrimination for both type and size (i.e. determine fish species and size).The aim of this project is to develop methods for fish classification and size estimation based on data collected on board commercial vessel equipped with broadband echosounders. These methods will then be implemented into a software package for near-real time viewing. Such a software package would help skippers to take better-informed decisions while fishing.This project runs over three years (June 2016 to June 2019) in collaboration between Wageningen Marine Research (WMR), Redersvereniging voor de Zeevisserij (RVZ) and TNO. Progress made in the second year of the project is presented in this report.Through the course of the reporting period, substantial amount of data have been collected and analysis show promising results. A test version of the classification software is planned to be deployed in the next phase of the project