Faculty of Sciences

Department of Biology

Marine Biology Research group

The use of echosounder tools for fish detection in the North Sea

By

Yves De Blick

Promotors: Dr. Jan Reubens (UGent), dhr. Klaas Deneudt (VLIZ)

Mentors: Dr. Elisabeth Debusschere (VLIZ), dhr. Wim Versteeg (VLIZ)

Master’s dissertation submitted to obtain the degree of Master of Science in Biology– Global Change Ecology

Academic year 2015-2016

© All rights reserved. This thesis contains confidential information and confidential research results that are property to the UGent. The contents of this master thesis may under no circumstances be made public, nor complete or partial, without the explicit and preceding permission of the UGent representative, i.e. the supervisor. The thesis may under no circumstances be copied or duplicated in any form, unless permission granted in written form. Any violation of the confidential nature of this thesis may impose irreparable damage to the UGent. In case of a dispute that may arise within the context of this declaration, the Judicial Court of Gent only is competent to be notified.

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Contents Acknowledgements ................................................................................................................................. v

Summary ................................................................................................................................................ vi

Samenvatting ........................................................................................................................................ vii

Objectives .............................................................................................................................................. ix

Chapter 1 ................................................................................................................................................. 1

1. Introduction ................................................................................................................................ 1

2. General principles of hydroacoustics .......................................................................................... 3

A. Acoustic detections ................................................................................................................. 3

B. Targets .................................................................................................................................... 5

C. Echosounder frequencies ....................................................................................................... 6

3. Active sonar ................................................................................................................................ 8

A. Echosounder system ............................................................................................................... 8

B. Types of active sonar .............................................................................................................. 9

a. Single beam echosounder ................................................................................................... 9

b. Split-beam echosounder ................................................................................................... 10

c. Multibeam echosounder ................................................................................................... 11

d. Recreational versus scientific echosounder ...................................................................... 13

C. Limitations of the echosounder ............................................................................................ 14

a. Theoretical aspects ........................................................................................................... 14

b. In practice.......................................................................................................................... 15

D. Equipment available in Belgium and neighbouring countries .............................................. 17

Chapter 2 ............................................................................................................................................... 20

1. Practical issues for the use of an echosounder ........................................................................ 20

A. Installation ............................................................................................................................ 20

B. Calibration ............................................................................................................................. 23

C. Survey conditions .................................................................................................................. 25

2. Echosounder tools .................................................................................................................... 27

A. BioSonics DT-X split-beam echosounder .............................................................................. 27

a. General information .......................................................................................................... 27

b. Demonstration of the BioSonics DT-X split-beam echosounder ...................................... 28

B. IXBlue SeaPix 3D sonar .......................................................................................................... 31

a. General information .......................................................................................................... 31

b. Demonstration of the SeaPix IXBlue 3D sonar .................................................................. 33

C. Kongsberg EM2040 MBES ..................................................................................................... 34

a. General information:......................................................................................................... 34

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b. Demonstration of the Kongsberg EM2040 MBES ............................................................. 34

Chapter 3 - Echosounder data analysis ................................................................................................. 36

1. Material and methods .............................................................................................................. 36

A. Acoustic sampling ................................................................................................................. 36

B. Data visualization .................................................................................................................. 38

C. Data post-processing ............................................................................................................ 39

a. Exploration of software packages ..................................................................................... 39

BioSonics Visual Acquisition DT-X ......................................................................................... 39

QPS Fledermaus .................................................................................................................... 40

Echoview ............................................................................................................................... 45

b. Post-processing methods .................................................................................................. 49

Post-processing BioSonics data with Echoview .................................................................... 49

Post-processing Kongsberg data with Echoview .................................................................. 51

Spreadsheet calculations ...................................................................................................... 56

c. Statistics ............................................................................................................................ 58

2. Results ....................................................................................................................................... 59

A. Fish track counts ................................................................................................................... 59

B. Statistical analysis ................................................................................................................. 60

C. Influence of turbulence on the detected fish tracks............................................................. 62

Discussion.............................................................................................................................................. 66

Reflective properties of fish .............................................................................................................. 66

Fish track counts ............................................................................................................................... 66

Post-processing in the Echoview software package ......................................................................... 67

Echosounder tools and their demonstrations .................................................................................. 74

Conclusions ........................................................................................................................................... 76

Future perspectives .............................................................................................................................. 78

References ............................................................................................................................................ 79

Addendum ............................................................................................................................................ 84

1. Data tables ................................................................................................................................ 84

2. SAS-codes .................................................................................................................................. 93

3. Figures ....................................................................................................................................... 94

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Acknowledgements

I would like to use this opportunity to thank some people who made it possible for me to submit this master thesis as a whole. In particular:

Dr. Jan Reubens (Postdoctoral research fellow, UGent) and Klaas Deneudt (Project manager, Datacenter VLIZ) for creating this interesting and innovative topic. Performing an explorative study on the implementation of hydroacoustics in the marine fisheries research was a new world for me. This made it, in first place, very challenging but also rewarding to obtain all this new knowledge. From the beginning, Jan and Klaas kept an open dialogue with me to find, together, the best structure and implementation methods for this thesis. Wim Versteeg (Senior Marine technician, VLIZ) was soon brought in to introduce and assist me in the world of echosounders tools. Wim has been available for help and advice every day, since then. In the search of other experts in the use of hydroacoustics in marine fisheries research, Wim brought me in contact with Dr. Matthias Baeye (Directorate Natural Environment, KBIN) who was instantly enthusiastic to enlighten me some of the main assets. Further from home, I got great help from Briony Hutton (Product Manager) and Bernd Wechner (Partner Manager) representing Echoview Software Pty Ltd (formerly Myriax Software Pty Ltd, located in Hobart, Tasmania). They provided me with a free of charge full test license for the Echoview post-processing software package. Besides this, they were 24/7 (sometimes literally!) available for assistance in the use of their software products. Thanks to them, a more elaborate performance of data analysis in this thesis was possible. As the practical work made place for writing, Elisabeth Debusschere (Science Officer, Datacenter VLIZ) came on the scene as an excellent writing mentor. She dedicated a lot of her time to proofread and provide improvements to the structure of my thesis report. In my personal life, my family supported me ceaselessly, such as during the whole course of my study career. In particular, I would like to mention my girlfriend Lina for keeping me motivated at all times and showing her strong interest in the progress and findings of this thesis.

To all those people, I want to express my greatest gratitude and appreciation for helping me finish this master thesis with a feeling of gladness and satisfaction.

Yves De Blick

Ghent University

May 2016

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Summary

More than 80 years ago, the use of sonar technology to detect fish underwater was demonstrated. Year after year, technological improvements were made and sonar became more frequently used in research and fisheries. With the development of calibration techniques, quantitative assessments became possible and non-invasive fisheries research could be performed. Species identification, abundance estimates, distribution patterns and fish behaviour are all part of the list of possibilities. Even though oceans and seas are interconnected, they all have their own characteristics. Many studies regarding the use of echosounder tools in fisheries research have been performed on many different locations across the Atlantic and Pacific Ocean and the North and Baltic Sea. Within the North Sea, however, the most southern part of the North Sea remains quite untouched. This sea is characterized by its high flow rates and often rough conditions. In the Belgian part of this southern North Sea (BPNS), the use of sonar is mainly focussed on bathymetry, in which seabed profiling and detection of bottom structures can be done. In the current state of global overexploitation of fish stocks, more accurate and extensive fish stock assessments are required. This is where sonar comes up as a possible tool to provide this additional insights. Many different sonar systems are available on the market and an exploration on their capabilities to detect fish in the BPNS was requested. In this thesis, three sonar tools have been studied regarding their performances by the use of the available literature, preceded by an extensive report on the general principles of sonar tools . In addition to this, water column recordings have been studied, which were collected during the demonstrations on these tools on the research vessel RV Simon Stevin. The goal was to investigate if fish can be detected and visualized and to interpret the results to formulate a conclusion which is relevant for biological fisheries research. These recordings have been processed by the use of software, which is specifically designed to process water column recordings from sonar tools. Several variables were obtained during the processing, which also were interpreted. The differences between the locations in the BPNS, which were sampled by the use of a sonar tool, immediately became clear. During every survey, different weather and sea conditions were applicable. Additional to this, the followed protocol, in terms of vessel speed during the recording and time duration of the recording, was not equal for all water column recordings. All the surveys were also performed during different seasons and different times of the day. This created severe implications for the further post-processing of these data. Nonetheless, the differences in detection capabilities between the two demonstrated sonar tools were examined and this difference was not proven by the analysis. Because of the wide variety in working methods in the post-processing software packages, these differences have been elaborately discussed as well, to provide certain guidelines for continuation of this work. Because of this, during the post-processing, sources of noise in the data were further examined. This which showed that turbulence appears to account for a substantial part of the total amount of detected targets. This was the case for both sonar tools. These turbulence zones were shown to be present in both surface layers and the layers above the seabed. The difficult settings in the post-processing software package and limited previous knowledge, made that the detected targets could not be confirmed to be fish purely. As a last part, the conclusion was made on the explorative study on the three compared sonar tools, in which is stated that the IXBlue SeaPix 3D sonar appears to be the most promising tool to use for fish detection. However, these findings are not assisted by data results, as no demonstration with this tool was done on the research vessel RV Simon Stevin.

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Samenvatting

Meer dan 80 jaar geleden is het gebruik van sonar technologie, om vissen te detecteren onder het wateroppervlak, gedemonstreerd. Sonar werd steeds frequenter gebruikt in onderzoek en visserij, door de technologische ontwikkelingen en verbeteringen die aangebracht werden. Na de ontwikkeling van calibratiemethoden werden kwantitatieve metingen mogelijk en kon visserijonderzoek op een niet-invasieve manier volbracht worden. De identificatie van soorten, het maken van abundantieschattingen en het bestuderen van verspreidingspatronen en het gedrag van vissen, behoren allemaal tot die mogelijkheden. Ondanks dat de meeste zeeën en oceanen in verbinding staan met elkaar, zijn deze toch gekenmerkt door een verscheidenheid aan eigenschappen. Verschillende studies zijn uitgevoerd op verschillende locaties in zowel de Atlantische en Pacifische Cceaan als in de Noordzee en Baltiche Zee. In de Noordzee is echter het zuidelijkste deel nog onontgonnen gebied voor het gebruik van sonar in visserijonderzoek. Deze zee is gekenmerkt door sterke stromingen en een woelig karakter. In het Belgische deel van de zuidelijke Noordzee wordt sonar vooral gebruikt in bathymetrische studies, waarbij zeebodemkaarten kunnen opgesteld worden en structuren in of op de zeebodem gedecteerd kunnen worden. Door de huidige wereldwijde overexploitatie van visbestanden, zijn uitgebreide en doortaste schattingen van de visbestanden vereist. Dit is waar sonar in beeld komt als een mogelijk werktuig om extra inzichten en kennis te verwerven. Er zijn veel verschillende sonartoestellen op de markt en dus was een exploratie naar de capaciteiten om vis te detecteren in het Belgische deel van de Noorzee vereist. In deze thesis zijn drie sonartoestellen bestudeerd aan de hand van de beschikbare literatuur, voorafgegaan door een uitgebreide bespreking van de algemene principes van sonar. Bijkomend zijn twee van deze toestellen uitgebreid bestudeerd aan de hand van opnames van de waterkolom, die verzameld zijn tijdens de demonstraties van deze toestellen op het onderzoeksschip RV Simon Stevin. Het doel was om na te gaan of vissen gedetecteerd en gevisualizeerd kunnen worden en deze resultaten te interpreteren zijn tot een relevant besluit voor biologisch visserijonderzoek. De waterkolom opnames zijn verwerkt door gebruik te maken van software, specifiek ontwikkeld voor het verwerken van waterkolom data van sonartoestellen. Verscheidene variabelen zijn bekomen door de verwerking, welke op hun beurt geïnterpreteerd zijn. De verschillen tussen de verschillende staalname locaties in het Belgisch deel van de Noordzee, in welke opnames met het sonartoestel uitgevoerd zijn, werden snel duidelijk. Gedurende de verschillende staalnames waren verschillende weersomstandigheden en zee condities van toepassing. Bijkomend was er geen vast protocol, met betrekking tot vaarsnelheid gedurende de meting en tijdsduur van de meting. Alle staalnames zijn ook uitgevoerd in verschillende seizoenen en op verschillende momenten gedurende de dag of nacht. Dit brengt implicaties met zich mee, die verdere verwerking van de data vermoeilijken. Toch is een vergelijkende studie uitgevoerd met betrekking tot de invloed van het verschil in sonartoestel op de detectie capaciteiten. Hieruit bleek dat deze verschillen niet statistisch bewezen kunnen worden. Omwille van de verscheidenheid in werkmethodes bij de verwerking van de data in de gespecialiseerde softwarepakketten, zijn de verschillende werkmethodes eveneens uitvoerig besproken met als doel enkele richtlijnen te vormen die gebruikt kunnen worden bij voortzetting van dit project. Uit deze studie is gebleken dat turbulentie een belangrijke vorm van storing vormt, daar deze een groot aandeel beschrijft in de bekomen hoeveelheid gedetecteerde vissen. Deze bron van storing is aangetoond zowel in de lagen net onder het oppervlak, als in de diepere lagen boven de zeebodem. Omwille van de gecompliceerde instellingen in de verwerkingssoftware kon er geen bevestiging gegeven worden dat alle gedetecteerde objecten weldegelijk vissen zijn.

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Als laatste deel is een conclusie opgesteld van de vergelijkende studie, die de drie verschillende sonartoestellen behandelt, waarbij de IXBlue SeaPix 3D sonar als meestbelovend en toepasbaar sonartoestel beschreven wordt. Deze conclusie kon echter niet bevestigd worden door dataresultaten, gezien het ontbreken van een demonstratie van dit sonartoestel op het onderzoeksschip RV Simon Stevin.

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Objectives

This thesis is aimed to be a comprehensive and elucidative document which can be used as a guide throughout the general processes of hydroacoustic in marine biological research in the Belgian part of the North Sea (BPNS). In particular, the implementation for fish detection is discussed. Some of the research questions that arose are:

• What is active sonar and how does it work? • How does sound propagate through water? • What are the different active sonar instrument types? • How can targets be detected by the use of active sonar instrument types? • How is an active sonar used during a survey? • What results can be obtained from acoustic recordings of the water column?

These questions gave rise to the three main objectives this thesis builds on, which are:

• A profound introduction to the general principles of hydroacoustics and overview of three different active sonar instrument types, being a single beam echosounder, split-beam echosounder and multibeam echosounder.

• A detailed description of three echosounder tools, their characteristics and their application to water column studies during demonstrations on board of the RV Simon Stevin.

• A data exploration, post-processing and analysis of different types of echosounder water column data, for detected fish targets.

Each objective is discussed in this thesis and assigned to a separate chapter.

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Chapter 1

1. Introduction

Sound is an important factor for animals in seas and oceans, for communication, predator-prey detection and sensing their surroundings (Cato, Noad, & McCauley, 2005). Some examples of the importance can be found in mating, prey (or predatory) and navigation behaviour (Hildebrand, 2009). Animals evolved to detect and or produce sounds. Some species even obtained the ability to use echolocation (Thomas, Moss, & Vater, 2004). When a produced soundwave hits a target, part of this soundwave will be reflected as an echo, which can be detected by the animal (Figure 1.1). This is an intriguing phenomenon that is used by not only water-living animals (Cetacean, whales and dolphins), but also land-living animals (Microchiroptera, bats) (Thomas et al., 2004). Underwater sound travels at a speed five times faster than through air. Besides this, sound can travel greater distances underwater than through air. Because of this feature, especially marine animals evolved to use sound for different purposes (Cato et al., 2005; Popper & Carson, 1998).

Echolocation in nature is a technique that humans adopted as sonar (Sound Navigation And Ranging), to detect objects in the water column which cannot be seen with the naked eye (Fernandes, Gerlotto, Holliday, Nakken, & Simmonds, 2002). All devices that can perform remote detection of an object in the water by the use of sound propagation, are gathered under the general term of sonar. A division can be made between two types of sonars. A passive sonar is a listening device. It detects sounds that are produced by objects in the water (Cato et al., 2005). Secondly, an active sonar is a device that produces sound waves and can detect echoes originating from hitting an object in the water. When an active sonar system transmits and receives acoustic sound waves simultaneously in a downward direction, this system is called an echosounder (John K Horne, 2000). Sonar was first introduced for military purposes and later adopted for civil uses, both scientific and commercial. The initial aim of this technology was to map bathymetry. Water column data was often filtered out as noise from the acoustic recording during the processing, to obtain the valuable seabed backscatter for hydrographic purposes. By mapping the seabed, characteristics of the seabed could be analysed, but also objects on the seabed such as submarine pipelines, plane- and shipwrecks or other objectscan be visualized (Hildebrand, 2009). Bathymetrical research became more important with increasing industrial development. A second application for echosounder tools is located within the new research field of hydroacoustics and aimed on fisheries studies (both for commercial and scientific purposes) (Fernandes et al., 2002). The acoustic tools can be used for abundance and distribution assessment and behavioural studies (Fernandes et al., 2002). The backscatter originating from targets such as single fish, fish schools, plankton, debris, gas bubbles, etc. can be analysed. Consequently, this hydroacoustic technique is identified as one of the most promising and suitable tools available to do the stock assessments in fisheries science (Koslow, 2009).

Figure 1.1, adapted from Sunardi et al, 2009. Schematic representation of sound reflection.

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Since our oceans and seas are in a critical stage of anthropogenic overexploitation, effective management strategies are necessary to maintain the biodiversity and size of fish stocks all over the world. To meet the requirements of the Ecosystem Approach for Fishery (EAF), stock assessments need to be performed based on accurate abundance and distribution data (Howell, 2008). For a long time, fisheries research in the North Sea depended solely on classical sampling methods, such as beam trawl and pelagic trawl surveys (Mackinson, van der Kooij, & Neville, 2005; Mayer, Li, & Melvin, 2002). These sampling methods are invasive and can impose technical flaws (Doray, Mahevas, & Trenkel, 2010). Certain areas with abundances of the target species can be inaccessible for trawling. Another reason is the possible imprecision in abundance estimates and aggregation structure, as the haul is made for a selective moment and location. The aggregation structures within this sampling transect cannot be determined from the catch numbers. In addition, fish behaviour (i.e. herding, diel vertical migrations, net avoidance, escapement) in response to the trawling is also important, since it can influence the catch numbers (Mcquinn, Simard, Stroud, Beaulieu, & Walsh, 2005)(Doray, Mahevas, et al., 2010). These gear-sampling biases can directly lead to a bias in size and species compositions of marine communities (Koslow, 2009). Classical net samplings do not provide a sufficient answer to determine the total number/biomasses of fish species present in a certain area. Nowadays, technological knowledge strongly improved and should be incorporated into this research. Hydroacoustic tools have been successfully adjusted for fish detection on demand of researchers worldwide. They provide non-selective data, where bias is minimized (Foote, 2006). It is cost effective and makes visualization of the water column real-time available. By using the former 'noise' data from the water column, information can be gathered for fish stock assessment, fish ecology and fisheries management. Besides these topics, error in trawl data and catchability of certain species can be studied (Graham, Jones, & Reid, 2004). However, hydroacoustics are not yet the standard method used in fisheries research due to a number of reasons. They impose a high initial cost and are associated with a steep learning curve because of complex settings during both sampling, analysis and software processing.

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2. General principles of hydroacoustics

A. Acoustic detections As a sound wave propagates, it spreads out spherically from the moment it is transmitted by the transducer (figure 1.2). The intensity of the wave decreases following the inverse square-law (I = I0 / R², in which R is the range) (Simmonds & MacLennan, 2006).

When a sound wave hits an object, some of the energy is absorbed while the rest is scattered. This means that a secondary wave is created that spreads out away from the target. This spreading is however different for targets of different sizes. Acoustic scattering from fishes can be divided into four regions, being the Rayleigh scattering, resonant, transition and geometric region (figure 1.3) (Simmonds & MacLennan, 2006).

Figure 1.2, taken from Simmonds and MacLennan, 2006: spherical spreading of a transmitted sound wave.

Figure 1.3, taken from Johannesson, K. A. et al, 1983: Four acoustic scattering regions. The x-axis describes the ratio of target length (L) over the wavelength of the incident sound wave (λ). On the y-axis is the sound intensity of the scattered wave (σ).

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When a target is very small (length = L) compared to the wavelength (λ), the target acts as a point source and scatters the secondary sound wave in all directions. This is a scattering in the Rayleigh region (J. K. Horne, 2000; Simmonds & MacLennan, 2006). When the target length increases or the wavelength decreases, the ratio L/λ will increase. When this ratio becomes equal to 1, the scattering will be in the resonance region. The intensity of the scattered wave increases and the target vibrates in resonance with the frequency of the sound wave. With an increasing L/λ ratio, the sound scattering is in the transition region. This region is the intermediate region between the resonance and geometric region (see figure 1.4). The geometric region is applicable when the target length exceeds the wavelength strongly (L/ λ >> 10) . In this situation, the target acts like a wall (figure 1.4) (J. K. Horne, 2000; Johannesson & Mitson, 1983; Medwin, 2005; Simmonds & MacLennan, 2006).

During the travel of the sound wave through the water column, a certain amount of acoustic energy gets lost due to absorption. The sound wave propagates through the medium by means of acoustic energy transfer between the successive molecules. The acoustic energy causes the molecules to vibrate and transfer this energy forward (Simmonds & MacLennan, 2006). For the molecules to overcome the resistance to move, a certain amount of the energy is converted into heat and not transferred onto the successive molecule. Some of the energy is thus absorbed by the medium. Certain elements in seawater absorb additional energy and convert it to heat, compared to fresh water. This makes sound absorption in seawater greater than in fresh water (DOSITS.org, n.d.; Simmonds & MacLennan, 2006).

Objects in the water column that are not assigned as targets for the study, are all described as a source of reverberation (Simmonds & MacLennan, 2006). These classification as unwanted targets is subjective and based on the study aims. When large targets are the desired targets and small targets cause the reverberation, the use of a low frequency is advised. By using a frequency that ensonifies (lit.: fills with sound) in the resonance and geometric scattering regions, the target of interest will scatter geometrically and be detected. The reverberation echoes are in the Rayleigh region and thus very small and won’t be detected (figure 1.3) (Medwin, 2005).

Figure 1.4, adapted from Medwin, H., 2005: Illustration of sound scattering in the three main scattering regions (Rayleigh scattering, resonant and geometric).

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B. Targets

Many targets can be detected by using sound waves. Not only fish and plankton are included within the target category, but also coral reefs (Roberts, Brown, Long, & Bates, 2005), submerged vegetation (Sabol, Melton, Chamberlain, Doering, & Haunert, 2002) and seabed structure(Anderson, Van Holliday, Kloser, Reid, & Simard, 2008). However, this thesis focusses on targets that are relevant within the field of marine biological research in the Belgian part of the North Sea (BPNS). The two main groups that receive priority for assessment are fishes and plankton. Any structure in the water column with a certain density will create a reflection of the incident sound wave (Simmonds & MacLennan, 2006). Many fish species have a swim bladder for buoyancy while swimming (Foote, 1980). This is a gas-filled structure that creates a strong backscatter, due to the large density contrast between gas and the fluid medium (Jørgensen, 2003; Simmonds & MacLennan, 2006). Generally, a swim bladder has an elongated shape with an irregular surface. The shape of this swim bladder is highly variable and thus species with different swim bladder shape lead to a different strength of the backscattered soundwave (Jørgensen, 2003).

As explained in ’BOX 1: Target tilt angle’, the tilt angle of the reflective organ influences the strength of the reflected signal, which will be measured by the receiver of the echosounder. A swim bladder is mostly positioned in a dorsal-caudal orientation, but differences exist between different fish species (figure 1.6). Besides this, the target tilt angle of the fish itself creates an addition to the angle of the reflective organ within the body, which should be taken into account (figure 1.5).

For gadoids it has been proven that the swim bladder is the main reflective organ and responsible for 90 – 95% of total amount of backscattered sound intensity, even though the volume of the swim bladder in marine fish is barely 5% of the total fish volume (Foote, 1980; Johannesson & Mitson, 1983). Fish without a swim bladder create a weaker backscatter due to reflection of the incident (transmitted) wave front on the fish flesh, blood and bone. Consequently, the target strength will be weaker than for a similar sized fish with a swim bladder (Foote, 1980).

BOX 1: Target tilt angle With fish as target, the strength of the reflection of the acoustic wave is strongly influenced by the tilt angle of the body. This is the angle between the long axis of the body and the incident wave front. When for example, a fish is swimming with the head down, it describes a negative tilt angle. When the fish head is up, the tilt angle is positive (figure 1.5).

Figure 1.5, taken from Simmonds and MacLennan, 2006: Illustration of tilt angles

When an incident wave front hits the target, the secondary reflected wave will change when the tilt angle changes. This is in first place because the reflective surface, as seen from the transducer, is reduced with an increasing tilt. Secondly, interference of the wavelets can occur when the target is not parallel to the incident wave front. When the target has a positive or negative tilt, the wavelets at different parts of the target can be out of phase and the summed amplitude is reduced (Simmonds & MacLennan, 2006).

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The second target group are the zooplankton species which contain internal lipid globules and or gas bubbles in their external floating structures, have a contrasting density to the surrounding water. These can create a noticeable backscatter (Simmonds & MacLennan, 2006). There is, however, a high diversity in morphology of zooplankton species. Different groups based on morphological characteristics, being fluid-like (decapod shrimp, euphausiid, salp), hard elastic shelled (gastropod), and gas-bearing (siphonophore), have been analysed and compared regarding their acoustics echo levels. The results showed that all groups show different echo levels (Stanton, Chu, & Wiebe, 1996).

C. Echosounder frequencies A range of frequencies can be deployed for acoustic surveys. Depending on the study aim, a certain frequency is chosen from a range, most probably, between 38 kHz and 1.8 MHz. Multiple frequencies can be combined and transmitted simultaneously (EIFAC/CEN workshop experts, 2014). High frequencies have short wavelengths (λ) and because of this, smaller animal can be detected than by using lower frequencies. At 200 kHz, both fish and plankton species can be detected and distinguished. At 38 kHz fish can be detected, but this frequency is less suitable to detect plankton species (Parker-Stetter, Rudstam, Sullivan, & Warner, 2009). Absorption of sound in water increases rapidly with increasing frequency (Simmonds & MacLennan, 2006). An echosounder tool which uses a high frequency, is thus limited to a shorter range than those using a low frequency. To counter this limitation, the beam width can be reduced to improve the detection range. The beam width is inversely proportional to the frequency. For example the beam width at 400 kHz is 10% from the beam width at 40 kHz. (Simmonds & MacLennan, 2006).

Figure 1.6, taken from Gauthier and Horne, 2004, Acoustic characteristics of forage fish species in the Gulf of Alaska and Bering Sea.: Swimbladder shape and orientation of different fish species.

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Each study aim has its optimal working frequency range (figure 1.7). Measuring fish at depths of several kilometres, for example, is optimally done with low frequencies of 10 kHz or lower. When the study area is shallow and the target species are plankton near the surface, a high frequency ranging from 100 to 5 MHz is suitable. For detecting fish on continental shelves with depths up to 400 m, a frequency range of 30-200 kHz is most often applied (Simmonds & MacLennan, 2006). In general, the most desirable frequency for fisheries assessment are intermediate frequencies from the range of 38, 70 or 120 kHz (Parker-Stetter et al., 2009).

Figure 1.7, taken from Simmonds and MacLennan, 2006: Categorisation of echosounder frequencies into detectable target groups. Each target group is delineated by frequency (kHz) on the x-axis. On the y-axis, both the typical sampled volume (m³) and maximum range (m) are plotted in relation to the echosounder frequencies (kHz).

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3. Active sonar

A. Echosounder system A transmitter produces electrical energy at a certain predefined frequency. Next, the transducer converts this electrical signal into acoustical energy which leads to sound propagation through the water. The acoustical beam is directional and of a certain beam width (Simmonds & MacLennan, 2006). A typical fisheries echosounder has a beam width between 5 and 15°. Subsequently, this acoustic sound wave travels through the water column. On its way it can encounter objects, which scatter or reflect the signal. Some of this scattered energy will arrive back at the transducer and be detected. This is the backscattered sound, or the echo. The receiving unit within the transducer detects the acoustic backscatter and translates this back into an electrical signal which can be interpreted by the system and stored (J. K. Horne, 2000; Simmonds & MacLennan, 2006). The simplest echosounders provide most often only information regarding location of aggregations of fish. These tools are highly efficient and cost-effective for the use in fisheries. However, quantitative measurements are often not possible (Mcinnes, Khoosal, Murrell, Merkle, & Lacerda, 2015). This is due to the lack of calibration of the echosounder tool, which will be tackled in chapter 2 (figure 1.8).

Figure 1.8, taken from Sunardi, J. et al, 2009: Schematic representation of echosounding for fish detection.

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B. Types of active sonar

Three active sonar tools are discussed in this topic, being the single beam, split-beam and multibeam echosounder. In adition, the distiction is made between recreational and scientific echosounder tools.

a. Single beam echosounder

Single beam echosounders are a standard used instrument for seabed detection in hydrography (Anderson et al., 2008). The transmitter of a single beam echosounder sends out pulses from the transducer downwards or upwards, depending on the sampling method (SIMRAD, 2015a). However, as the name already makes clear, just one beam is formed in which the pulse is transmitted. When a target reflects the pulse, an echo is sent back to the receiver. The receiver is composed out of numerous elements, which detect the echo and calculates the depth. It is, however, not possible to distinguish the detection position between these elements. Because of this, the exact target position and direction cannot be determined (figure 1.9) (Simmonds & MacLennan, 2006).

This echosounder is traditionally composed out of a transducer, a general purpose transceiver (GPT), a signal hub and a work station. Some single beam echosounder have the opportunity to operate multiple transducers and or multiple frequencies simultaneously. The Kongsberg EA600 single beam echosounder can operate one or two transceiver unit, each operating one or two transducers. This echosounder can operate at frequencies, ranging from 12 to 710 kHz (Kongsberg_Maritime, 2015a). The Simrad EK15 single beam echosounder can operate up to 15 transceiver units, each operating one transducer. By combining multiple transducer modules, multiple single beams can be transmitted and received simultaneously. Because of this, a larger voume of water can be ensonified. When more transceiver units are installed, an Ethernet switch box is added to the system as a hub to connect with the processing unit. This Simrad EK15, however, can operate at only one frequency, being 200 kHz (SIMRAD, 2015a). The detection depth can vary strongly between different single beam echosounder tools. For example, the Kongsberg EA600 has a depth range from very shallow up to 10000 m. This is because of the wide range of 10 different single beam frequencies, from which two can be operated at the same time (Kongsberg_Maritime, 2015a). The Simrad EK15 has only one operating frequency and is limited to a maximal depth range of 200 m.

The output data files are raw files (.raw file format), which can be read by third party post-processing software, such as Echoview and Sonar5. These raw files can provide a raw acoustic variable and raw line variables for post-processing(SIMRAD, 2015a). The acoustic variable is the volume backscattering strength (Sv), which expresses the reflection properties of the medium. This is not assigned to a certain point value, but represents the reflection properties of the ensonified water volume on the incident wave front. Examples for which Sv is used as analysis variable are fish and plankton density estimation. The unit of Sv is m²*m-³.

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b. Split-beam echosounder

A split-beam echosounder is characterized by the division of the transducer in four quadrants of transmitter elements. The transducer transmits a pulse with all elements and receives it with the four quadrants separately (Parker-Stetter et al., 2009). This way, the position and direction of the target within the beam can be determined. A split-beam echosounder provides a location of the target in three dimension (x and y coordinates within the beam and depth), while a single beam echosounder only provides a location in one dimension, being the depth of the target within the beam (figure 1.9).

The symmetry of the quadrants is not fixed for all split-beam echosounders. For example, the Simrad EK60 split-beam echosounders (which is now succeeded by the Simrad EK80 split-beam echosounder) has four symmetrical transducer quadrants. The Biosonics DT200 split-beam echosounder has one larger quadrant that is used for determining the echo amplitude, while the other three smaller quadrants are used to determine the difference in angle between the target and the main central axis (Simmonds & MacLennan, 2006).

Similar to the single beam echosounder, detection specifications differ between the different split-beam echosounder tools. For example, the HTI model 244 multi-frequency split-beam echosounder can operate up to 16 transducers of up to 5 different frequencies within the range of 35 kHz to 1 MHz (HTI_Sonar, 2012).

A split-beam echosounder provides raw files (.raw file format) as output data, which can provide two important variables that are relevant for fish detection. The first variable is, similar to the output of a single beam echosounder, the Sv (volume backscattering strenth) value. As a second variable, the target strength (TS) is provided, with decibel (dB) as unit. TS describes the reflection properties of a single target in the water column and can be calculated because the exact location of the target within the beam is determined. This is not the case for single beam echosounders, for which the TS thus cannot be provided. However, statistical estimations exist to overcome this shortcome (Manik, Mamun, & Hestirianoto, 2014). The TS is equal to 10 times the logarithm of the backscattering cross-section (σbs), which is the reflected intensity (IR)(or backscatter intensity (Ibs)) divided by the incident intensity (Iinc). In a formula this is σbs= IR / Iinc .The unit of the backscattering cross-section is m². This variable is mostly used for single target detection and fish tracking. The target length can be calculated from TS, which in case of fish can be linked to the size of the swimbladder or body. TS can also be used to calculate fish densities if the TS of the ensonified fish species is known (Echoview_support, n.d.-b; Mcinnes et al., 2015). The only difference with Sv is that TS represents the reflection properties of the area of a target, rather than reflection properties of the ensonified water volume (Echoview_support, n.d.-b; Oslo_University, n.d.).

Figure 1.9, adapted from Parker-Stetter, S. et al., 2009: Difference in detection dimensions for single and split-beam echosounders.

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c. Multibeam echosounder

For most echosounders, an increasing ensonifying depth range causes the spatial resolution to decrease strongly. This limitation is overcome by the introduction of a multibeam echosounder (MBES) which is composed out of a fan of beams with a narrow individual beam width (0.5 – 2°) (Gerlotto, Soria, & Fréon, 1999).

Secondly, because of this fan of numerous beams, the swatch coverage increases substantially. With a same sampling transect, a much larger volume of water can be ensonified than with the use of a single or split-beam echosounder. This is both time saving and economically interesting because of the reduction in survey duration (L3_Communications, 2000a). For example, the Simrad ME70 MBES is composed out of 45 beams, which creates a coverage swath up to 150°, while for a standard split-beam echosounder, this is limited to a swath of 7-12°, (Mosca et al., 2015)

In most MBES systems, the transducer and receiver are positioned perpendicular, in the so-called Mills Cross (figure 1.10). This technique was designed to enhance the location capabilities of a MBES system. If the transducer and receiver would be aligned parallel, it wouldn’t be possible to specify precisely the position of the target on the ensonified strip (figure 1.10 a). When the transducer and receiver are positioned perpendicular to each other, there is only a small intersection where the ensonified strip of the transducer and the receiving strip of the receiver cross (figure 1.10 b). This means that only objects on that intersect can give an echo originating from that certain transmitted ping. This increases the precision of the measured location. Because a multibeam echosounder has multiple beams, multiple ensonified intersections will be positioned next to each other and forming a wide ensonified transect in which detailed location of the echo along the strip is possible (figure 1.10 c).

MBES are traditionally used for bathymetric studies, for which calibration methods exist (QPS, n.d.). In 2006, Foote, K. G. et al. adapted acoustic calibration methods which allow the performance of quantitative measurement from MBES water column data. This enables the use of MBES systems in both bathymetry and scientific fisheries and other ecological research (Foote, 2006). Some examples of scientific calibrated MBES are Simrad ME70 MBES, Simrad MS70 MBES and IXBlue SeaPix MBES (Mosca et al., 2015; Ona, Mazauric, & Andersen, 2009).

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Figure 1.10, taken from L3_Communications, 2000: The Mills Cross Technique. (a) transducer and receiver array are parallel and form an ensonified strip on the seabed. (b) transducer and receiver positioned perpendicular to each other, forming a Mills Cross. The intersect forms a smaller ensonified strip of the seabed. (c) Mills Cross with multiple steered beams.

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d. Recreational versus scientific echosounder

Fisheries echosounders are used for both scientific and commercial goals. Recreational echosounders are characterised by a simple setup in which most often the only output is a live coloured display in which detected targets are visualised. This is a non-quantitative output, as recreational echosounders are not calibrated. The standard performances of these echosounders cannot be checked. Hence, accurate density and biomass estimations are not possible. Scientific echosounders, on the other hand, are calibrated. This calibration is most often performed by using a standard target with a known acoustic target strength. This calibration allows a quantitative interpretation of the received signal. In addition, these scientific echosounder are more complex and in addition allow the storage of the gathered data from the received signals for further processing (Mcinnes et al., 2015).

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C. Limitations of the echosounder

a. Theoretical aspects

Not all zones of the water column are similarly detectable. There are two important zones, which limit detection of targets, being the blind zone and the dead zone (figure 1.11) (Scalabrin, Marfia, & Boucher, 2009).

The theoretical blind zone is near the surface, where limitations of the acoustic near-field inhibit detection (figure 1.12) (Simmonds & MacLennan, 2006).

Figure 1.12, taken from Simmonds and MacLennan, 2006: Acoustic soundwave energy propagation: (1) The reduction of intensity of a point-source with the increase in range, follows the inverse-square law. (2) Due to near-field effect, the intensity near the transducer is limited and highly variable.

Figure 1.11: Illustration of the blind zone and dead zone of an echosounder, transmitting one beam.

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The near-field is characterized by a large variability in sound intensity within a short range from the sound source (Hansen, 1994). As there is no constant relationship between the sound wave intensity and the sound source, interpretation of the backscattered sound waves is difficult (Parker-Stetter et al., 2009). From a certain range, the sound wave is in the far field, which is characterized by a linear relationship between the sound wave intensity and the sound source. In the far field, the sound intensity decreases by 6 dB when the distance to the sound source doubles (figure 1.12) (Hansen, 1994).

The second undetectable zone for the echosounder is the theoretical dead zone, which is located just above the seabed (figure 1.13) (Mello & Rose, 2009).

The transducer transmits beam pulses of which the cross-section describes a spherical shape. At the moment the central leading edge of the pulse, which is on the acoustic axis, hits the flat seabed surface, targets at different locations in this pulse section can be integrated in a different way (Ona & Mitson, 1996). Targets that are located below the spherical edge of the pulse will not be detected. As can be seen on figure 1.13, targets 2 and 3 would thus not be detected by the echosounder. They are located in the volume outside of the spherical volume and thus shaping the acoustic dead zone (figure 1.11) (Ona & Mitson, 1996). The spherical shape of the pulse also creates a seabed offset (dotted line), which is at the range of the outer edge of the pulse (figure 1.13). Target 1 is located on the same depth as target 2 and 3, but it is the only one of those three which is located within the spherical pulse section. This target will thus be detected before the pulse hits the seabed and be integrated as a target on the echogram. However, because it is positioned below the seabed offset it is not possible to separate the location of this target from the seabed (figure 1.13). The zone between the seabed and the seabed offset is therefore also included the total acoustic dead zone (figure 1.11) (Ona & Mitson, 1996).

b. In practice Water flow disturbance due to vessel movement and waves create air-bubbles in the water column which create a strong backscatter echo (figure 1.14). This interference inhibits a good detection and interpretation within the turbulence zone (Melvin & Cochrane, 2015). The total blind zone is, thus, composed out of the theoretical blind zone and possible turbulence zones. In extreme conditions, this surface acoustic blind zone has been shown to extend even up to 15 meters depth (Scalabrin et al., 2009). It should be, however, mentioned that the range of the near-field is on average only two

Figure 1.13, taken from Ona et al, 1996.: Cross-section of a transmitted pulse, showing the acoustic dead zone. Central in the beam is the acoustic axis. 7 targets are located in different zones of the cross-section.

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wavelengths (Gracey and associates, n.d.). This means that the contribution of the theoretical blind zone to the total blind zone is rather limited, in case of turbulence.

Single beam and split-beam echosounders transmit sound waves in one beam. For these echosounder tools, the theoretical dead zone is applicable (figure 1.11). A multibeam echosounder (MBES), however, has a fan of numerous beams, composing a spherical shape (Gerlotto et al., 1999). Each beam has a theoretical dead zone (figure 1.15). On a flat seabed, most often the centre beam will detect the seabed first. From this detection, the seabed depth range is selected. Because of the spherical shape of the beam fan, a part of the ensonified water column is outside the spherical volume and thus not integrated (Simmonds & MacLennan, 2006; Trenkel, Mazauric, & Berger, 2008). For MBES systems, the total acoustic dead zone includes the theoretical dead zones and the ensonified volume outside the spherical volume (figure 1.15).

Figure 1.14: print screen from Echoview software: Surface turbulence zone extending up to 3 meters depth. The unspecified dB pings variable and Sv pings variable are synchronised and thus showing the same ping cross-section.

Figure 1.15, illustration of the blind zone and dead zone for a MBES, composed out of numerous beams. The blind zone is the sum of all the blind zones from the individual beams. The dead zone is the sum of the theoretical dead zone for each beam and the total volume outside of the spherical shape of the beam fan.

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D. Equipment available in Belgium and neighbouring countries

VLOOT dab, which operates through the Flemish Government (figure 1.16), is owner of the Research Vessel (RV) Simon Stevin. This vessel performs coastal and oceanographic research. All the scientific assets are coordinated and organised by the Flemish Marine Institute (VLIZ). On board of the vessel is a hull-mounted Kongsberg EM2040 (200 kHz & 400 kHz) MBES. This echosounder, currently mainly used for bathymetric research, is tested for performance in water column detections, which is tackled in chapter 3 (MUMM, 2006; ODNature, n.d.; VLIZ, n.d.).

The Kongsberg EM2040 MBES is a four unit system, containing a transmit transducer, a receive transmitter, a processing unit and a workstation. Depending on the aim of the study, the used frequency can be selected within the range of 200 kHz to 400 kHz, in steps of 10 kHz. The angular coverage is 200°. Both continuous wave (CW) as frequency modulated (FM) pulses can be transmitted (see BOX 2). To obtain the maximum range and a high resolution, FM chirp is used (Kongsberg_Maritime, 2015b).

Table 1.1 and 1.2 provide information regarding the depth ranges and pulse lengths for the different operation modes of this echosounder tool.

Table 1.1, taken from Kongsberg Maritime, Kongsberg EM 2040: Overview of depth ranges for different operation modes.

Table 1.2, taken from Kongsberg Maritime, Kongsberg EM 2040: Overview of pulse lengths for different operation modes.

BOX 2: Pulse types

Echosounder tools can transmit two different pulse types, being the continuous wave (CW) pulse and the frequency modulated (FM) pulse.

A CW pulse is a transmit pulse with one single frequency. It has a fixed pulse length, single frequency and amplitude (Echoview_support, n.d.-a).

The second pulse type is an FM pulse. The most common type of an FM pulse is a chirp. It has a fixed pulse length and amplitude. It is a sweep signal, containing a band of frequencies which change over time at a constant amplitude. The rate at which the frequencies change is called the chirp rate (Echoview_support, n.d.-a).

Figure 1.16, taken by Wikimedia: Flemish flag

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The Belgian (figure 1.17) Federal government, through the subdivision of the Federal Science Policy Office is owner of the RV A962 Belgica. This military vessel is also used as oceanographic research vessel and performs research under coordination and organisation of the Royal Belgian Institute of Natural Sciences (KBIN). On board of the vessel is a hull-mounted Kongsberg EM3002D (300 kHz) MBES.

This Kongsberg EM3002D is a four unit system, containing two sonar heads, a processing unit and a workstation. This MBES uses frequencies from within the 300 kHz band, which includes 293, 300 and 307 kHz. The Pulse length at this frequency is 150 µs. The detection depth ranges from 1 m up to 200 m depths. This tool is most suitable for seabed mapping. The seabed coverage is claimed to be maximal, even at vessel speeds up to 10 knots (kn). Stabilisation systems include pitch and roll stabilisation and heave compensation (Howell, 2008; Kongsberg_Maritime, 2015c). Table 1.3 provides information regarding the number of soundings per ping and the maximum angular coverage of this

Kongsberg EM3002D MBES.

The French (figure 1.18) Research Institute for Exploitation of the Sea (IFREMER) has a well-developed knowledge and leading role in Europe in fisheries research, by the use of hydroacoustics. They operate pelagic acoustic surveys mainly in the Bay of Biscay and the Gulf of Lion. In cooperation with the echosounder building company Simrad (fisheries research products of Kongsberg), IFREMER developed the first calibrated MBES for fisheries research. This Simrad ME70 MBES was first installed on the RV Thalassa. In 2014, a second one was installed on the RV L’Europe. This echosounder was claimed to be the only available multibeam echosounder system on the market that could simultaneously collect calibrated quantitative data from the water column and bathymetry data from the seabed.

This Simrad ME70 MBES is a four unit system, containing a transmit transducer (800 elements), a receive transmitter, a processing unit and a workstation. It has an adjustable acoustic fan, containing 3 to 45 beams in fan plus two reference beams. All beams can be both configured as part of the multibeam fan or as split-beams. The total swath width is 140° and the athwartship centre of the fan can be adjusted 45° in both directions. This MBES uses a frequency range from 70 to 120 kHz (SIMRAD, 2015b).

EM 3002D Dual sonar headNumber of soundings per ping 508 soundings/pingMaximum angular coverage 200°

Table 1.3, adapted from Kongsberg Maritime, Kongsberg EM 3002D: Overview of number of soundings per ping and the maximum angular coverage of the multibeam echosounder system.

Figure 1.17, taken by Wikimedia: Belgian flag

Figure 1.18, taken by Wikimedia: French flag

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Table 1.4 provides information regarding the pulse lengths of the Simrad ME70 for the lower and upper frequency limit. For each frequency, the pulse lengths are given for both the CW and FM mode.

In addition to the Simrad ME70, the RV Thalassa is equipped a Simrad EK60 split-beam echosounder. This is a modular echosounder with a basic assemblage consisting of four units, being a transmit transducer, a receive transmitter, a processing unit and a workstation. However, up to seven echosounder frequencies can be operated simultaneously, from within the range from 18 to 710 kHz. Any combination of transmit transducer and receive transmitter can be assembled (SIMRAD, n.d.). The Simrad EK60 split-beam echosounder, owned by IFREMER, can operate at five frequencies, being 18, 38, 70, 120 and 200 kHz, with a beam angles of 7°. Both echosounder tools are hull mounted in the vessel keel, at 6 m below the surface (Doray, Masse, & Petitgas, 2010).

The German (figure 1.19) Geomar – Helmholtz Centre for Ocean Research has professional experience in gas flux studies and seabed dynamics. The hydroacoustic tools used for this research, are a Simrad EK60 scientific split-beam echosounder, which is already discussed in the previous part and a L3-ELAC SeaBeam 1050/1180 MBES.

The L3-ELAC SeaBeam 1050/1180 MBES operates at a frequency of 180 kHz. The fan is composed out of 126 individual beams and covers 153°. The pulse length is selectable from 0.15, 0.3 or 1.3 ms. The resolution is 1.5° and ping speed is limited up to 25 pings per second. The maximal swath coverage is 900 m width and the maximal measuring depth is 600 m. The maximal vessel speed for a continuous seabed coverage is 16 kn (L3_Communications, 2000b).

The Royal Netherlands Institute for Sea Research (NIOZ) is the national oceanographic institution for the Netherlands (figure 1.20). They have performed hydroacoustic studies by the use of echosounder tools. The expertise of the NIOZ is, however, focused on bathymetric mapping and bubble detection and not on fish stock and community assessment.Their acoustic team works in cooperation with the German Geomar research centre (pers. comm. with Prof. Dr. Jens Greinert, Department of Marine Geology and Chemical Oceanography of the NIOZ).

The Institute for Marine Resources & Ecosystem Studies (IMARES) is the main institution of the Netherlands for applied marine ecological research. They have performed hydroacoustic studies, as a part of the ICES coordinated international hydroacoustic survey for blue whiting. In this study, a Simrad EK60 split-beam echosounder was used, which operated at both 38 and 120 kHz simultaneously (Fässler, 2011). Currently, they use the successor of the Simrad EK60 split-beam echosounder, being the Simrad EK80 split-beam echosounder.

SIMRAD ME70CW FM CW FM

Pulse lengths 64 µs 128 µs 5.12 ms 5.12 ms

70 kHz 120 kHz

Table 1.4, adapted from SIMRAD: Simrad ME70: Pulse lengths for the lower and upper frequency limit, and for both CW and FM mode.

Figure 1.19, taken by Wikimedia: German flag

Figure 1.20, taken by Wikimedia: Dutch flag

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Chapter 2

1. Practical issues for the use of an echosounder

A. Installation

To operate an acoustic survey, the transducer has to be installed on the most optimal place to answer the requirements of the study aim. There are different mounting possibilities to fix the transducer to a research vessel. The most-common ones are fixed to a towed body, pole mount, sonar tube or hull mounted (Parker-Stetter et al., 2009).

The first option is a towed body. This is a structure on which the transducer is installed that can be towed with a vessel. The towed body is designed to float at a certain depth in the water column, depending on the manufacturer of this structure and requirements of the survey (figure 2.1).

Advantages (Parker-Stetter et al., 2009):

- Not directly fixed to the vessel, so easily installed and removed.

- Less interference from gas-bubbles originating from the vessel movement, in the acoustic detection.

- Transducer can be brought closer to the target of interest (see BOX 3). - Some towed bodies have automatic stabilizing fins, which can compensate for roll and pitch

movement. -

Disadvantages (Parker-Stetter et al., 2009):

- Induced risk on usage issues in rough weather conditions due to risk on cable breakage. - Subsequently stability of the transducer can be jeopardized, in rough weather conditions. - In some cases, not possible to combine a trawl survey and an acoustic survey in which the

echosounder is fixed on a towed body.

Figure 2.1, taken from Parker-Stetter, S. L. et al., 2009: Illustration of a towed body.

BOX 3: Targets at greater depths.

The depth range of deep-sea species is often not a part of the depth range of most echosounder tools. For example, black scabbardfish (Aphanopus carbo) occurs at depths up to 1700 m (Gordo, 2009), while a 38 kHz Simrad EK60 split-beam echosounder has a maximum detection range of 1000 m depth. This limitation can be overcome by fixing the transducer on a deep towed body. This could also be applicable to the detection of micronekton in the mesopelagic zone (600-1200 m depth). As mentioned in chapter 1.2.C, high frequencies, used to detect small targets have a limitation in detection range. Therefore, the transducer could be lowered to reduce the distance between the transducer and the targets and increase the detection capabilities (Moline, Benoit-Bird, O’Gorman, & Robbins, 2015).

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As a second option, the pole-mounted installation is examined. Here, the transducer is mounted to a pole, which can be fixed to the vessel (figure 2.2).

Advantages (Parker-Stetter et al., 2009):

- An improved stability of the transducer, compared to a transducer fixed on a towed body. - Mounting position can be along the complete periphery of the vessel, depending on the

location of the interference sources such as bow-induced waves and engine turbulence bubbles.

Disadvantages (Parker-Stetter et al., 2009):

- Susceptible for pitch and or roll movement of the vessel. - Mounting construction can present an obstacle on the vessel.

Next, the sonar tube deployment is another installation option. The transducer is, similar to the previous option, fixed to a pole. Here, this pole can be lowered in a tube which runs through the body of the vessel, from the deck to the bottom of the vessel.

Advantages (Parker-Stetter et al., 2009):

- The transducer can be positioned at the most stable location on the vessel, which reduces vessel movement induced interference in the echosounder performance.

- Multiple tubes can be installed so that multiple transducers can be used simultaneously.

Disadvantages (Parker-Stetter et al., 2009):

- Severe adjustments have to be made to the structure of the vessel. - Mounting construction can present an obstacle on the vessel.

Figure 2.2, taken from Parker-Stetter, S. L. et al., 2009: Illustration of pole-mounted installation.

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The fourth installation method is the most common, which is hull mounted. This way, the transducer is mounted inside the hull of the vessel, with the lower limit of the transducer positioned equal to the lower limit of the hull (figure 2.3). The transducer is always positioned in the lowest part of the vessel, to avoid interference from turbulence created by the vessel movement. If a keel is present, the transducer can be installed inside this structure, which brings the transducer lower under the surface. As an optional structure, a lowering system for the transducer can be installed in the hull or keel (Parker-Stetter et al., 2009). This was done in the Netherlands on the RV Tridens, commissioned by Rijkwaterstaat who is responsible for the design, construction and management of the main infrastructure facilities in the Netherlands, by installing an extendable platform on the dropkeel. This allows the transducer to be lowered three meters below the dropkeel, reducing the interference of air bubbles on the lower surface of the keel (Damen Maaskant_Shipyards, n.d.).

Advantages (Parker-Stetter et al., 2009):

- The transducer can be positioned at the most stable location on the vessel, which reduces vessel movement induced interference in the echosounder performance.

- The transducer stays fixed to the vessel, so deployment and removal time is reduced. - Mounting construction presents no obstacle to other procedures on the vessel

Disadvantages (Parker-Stetter et al., 2009):

- Severe adjustments have to be made to the structure of the vessel - The only way to make adjustments to the transducer is by bringing the vessel into a dry-dock,

which is very time consuming and expensive.

Figure 2.3, taken from VLIZ - RV Simon Stevin: Illustration of the hull-mounted installation of a Kongsberg EM2040 MBES.

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B. Calibration

For scientific research it is important that the echosounder tool can measure target abundances and size accurate, during the whole lifetime of the echosounder tool. To ensure this, the system should be checked regularly for proper functioning. This way the erroneous settings can be fixed. This process is called calibration (EIFAC/CEN workshop experts, 2014). There are three different calibration processes which will be discussed now.

A full instrument and equipment calibration is conducted by the echosounder manufacturer once a lifetime, during the construction of the echosounder. All parts of the system are checked for standard performace. It can be necessary to perform an additional full instrument and equipment calibration when the transducer, transducer cable or echosounder experienced physical trauma during a survey or transport. This calibration is performed for every used transmitted pulse length, source level of the transmitter and receiver gain (EIFAC/CEN workshop experts, 2014).

A beam pattern calibration is conducted by the echosounder owner or echosounder provider at least once a year or when the transducer or transducer cable experienced physical trauma during a survey or transport. The aim of this calibration is to calibrate every beam and adjust the occurring error in the directivity capabilities of the echosounder. A standard target (see BOX 4), from which the acoustic properties are known, is positioned underneath the transducer at a certain fixed depth. This depth should outrange at least two times the theoretical near-field range. The standard target is detected and TS and the angle location of the detected target are provided by processing of the results. This observed angle value can be compared to the predicted angle value, derived from standard directivity measurements provided by the echosounder manufacturer. Subsequently, an overview of acceptable deviation values for the measured calibration parameters will be provided as well, to consider if the transducer is calibrated and functional (EIFAC/CEN workshop experts, 2014; Jech, Chu, Foote, Hammar, & Hufnagle, 2003). Exact water temperature and salinity values are needed, which are used to calculate the speed of sound and the absorption coefficient of the seawater. The temperature is measured in 1 m intervals throughout the whole depth range of the water column. From this interval, the mean water temperature can be calculated. The estimated duration of this calibration depends on the type of echosounder system. BioSonics Inc. recommends a performance of the beam pattern calibration for their BioSonics DT-X split-beam echosounder by the BioSonics technicians. This can take up to two or three days and includes a cost of about 1000.00 USD$. As MBES have multiple beams, this calibration can take up a longer time, depending on the extend of the beam fan of the MBES system. A standard target test is conducted by owner before every survey, at the site, to test if the system is working correctly and to correct for changing environmental conditions. Similar to the beam pattern calibration technique, a standard target is positioned underneath the transducer at a certain predefined locations. The standard target is consecutive detected on every predefined location in the beam and the TS is calculated. This TS can be compared to a reference value, which is provided by the echosounder manufacturer (table 2.1). When the deviation of the detected target strength to the reference value is larger than allowed, a beam pattern calibration and or full instrument and equipment calibration is required (EIFAC/CEN workshop experts, 2014; Jech et al., 2003).

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BOX 4: Standard target

During the standard target test, a target is positioned in the beam of the echosounder. To avoid unwanted reflections, the target is supported by the least possible amount of material, most often nylon (Simmonds & MacLennan, 2006). By moving the target through the beam, the acoustic axis can be found by selecting the highest echo. This allows on-axis calibration and positioning of the target on a certain angle of the main axis (Jech et al., 2003) The standard target is a solid sphere, most often composed out of a ceramic, steel, copper or brass. Tungsten carbide (ceramic) and copper spheres appeared to give the best results (Foote & MacLennan, 1984). Both materials describe a very high density which creates a strong and pure reflection. As the spheres are homogenous, the orientation of the sphere is irrelevant.

Different installation positions of the transducer require different positioning of the standard target. The calibration descriptions above, are all applicable for a hull mounted echosounder where the standard target is positioned underneath the transducer underneath the vessel. For a transducer fixed on a towed body, the standard target is deployed underneath the towed body (figure 2.4 a). With a pole mount installation, the attachment lines are fixed to the pole (figure 2.4 b) (BioSonics Inc., 2004). A possible difficulty, which can occur during the calibration of a transducer fixed on a towed body, is to keep the towed body stationary during the calibration process (Parker-Stetter et al., 2009).

Table 2.1, adapted from Simmonds and MacLennan, 2006: Table with target strength (TS) values of a tungsten carbide spheres, for different operating frequencies and for a fixed speed of sound of 1490 m*s-1. Also the diameter is given of the standard target for each operating frequency.

Figure 2.4, taken from BioSonics Inc., 2004: Deployment methods for a standard target on a (a) transducer fixed on a towed body or (b) a pole mounted transducer.

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C. Survey conditions

Wind speed, wave height and water flow are important factors in acoustic surveys. Rough weather is most often linked to strong wind and large waves. These conditions lead to the appearance of entrained air bubbles in the surface layers of the water column, which can cause attenuation and signal blocking (EIFAC/CEN workshop experts, 2014). Besides this, air bubbles provide a large contrast to the surrounding watervolume and will create a strong detectable backscatter. This can provide error in the target detection and because of the high variability in error, this is difficult to compensate for (Simmonds & MacLennan, 2006). Other sources of extra attenuation of acoustic signals are abiotic particles (sediment) and biotic particles (e.g. detritus, marine snow, plankton) in the water column at high flow sites (Melvin & Cochrane, 2015). These particles form a physical barrier for the acoustic signals to pass through. Because of ship movement (i.e. roll and pitch), an echo will arrive at a different angle than from the incident sound wave. Most echosounders have roll, pitch and jaw stabilization systems which compensate for this difference. However, the more movement, the more possible error that can occur (Simmonds, Williamson, Gerlotto, & Aglen, 1992). The vessel speed during a survey is dependent on these weather conditions. As wave-induced air bubbles in the surface layers can cause more error in the recordings, the vessel speed should be reduced in case of bad weather. In some cases, the weather conditions become this bad that data quality cannot be maintained anymore (Parker-Stetter et al., 2009).

In general, acoustic surveys are most often performed at a vessel speed of around 5 kn (Parker-Stetter et al., 2009; Parsons, Parnum, & Mccauley, 2013). In combination with a trawl survey, the speed is reduced to 3 to 4 kn (Hannachi, Ben Abdallah, & Marrakchi, 2005). Echosounder manufacturer BioSonics recommends an average vessel speed of 5 to 7 kn to use in combination with their echosounder tools. They also claim to have received feedback from clients, being able to collect qualitative data at vessel speeds approaching 10 kn (pers. comm. with Eric Munday, contact person of SUBSEA 20/20 Inc., representing BioSonics Inc.). Echosounder manufacturer Kongsberg Maritime recommends an average vessel speed of 4 to 5 kn, during acoustic surveys with Kongsberg Maritime and Simrad echosounder tools (pers. comm. with Kevin Weerman, Field Engineer of Subsea and Hydrographic at Kongsberg Maritime Holland BV). Echosounders can be used both in a stationary position as in a mobile survey, mounted on or dragged by a moving vessel. A study from Parker Stetter et al, 2006 has shown that there is no clear difference in obtained target strenght from the detected targets measured by a moving (vessel speed of 5.8 kn) or a stationary transducer (Parker Stetter, Rudstam, Stritzel Thomson, & Parrish, 2006).

Changing environmental conditions of the seawater can also have important consequences for certain parameters for echo-integration of acoustic signals (see BOX 5).

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BOX 5: Changing parameters, under changing environmental conditions in the sea.

It is important to notice that depth calculations are done by using the value of the speed of sound. The speed of sound and the absorption coefficient are important parameters for echo integration. These parameters can differ depending on the local conditions, such as water temperature, water pressure and salinity.

The salinity of the water column can differ, depending on the measuring depth and location. Many seas and oceans have a thermocline, which can give in some cases a very distinct difference in sea water temperature. These change should be taken into account during the echo integration (Simmonds & MacLennan, 2006)

The speed of sounds is dependent on the frequency and the wavelength of the acoustic signal.

Speed of sound (m*s-1) = frequency (Hz) * wavelength (m)

The frequency emitted by the echosounder always stays the same unless the settings of the echosounder are changed. When the vessel is entering a water volume with different environmental conditions, such as changed water temperature, different water pressure and or changed salinity, the local speed of sound can differ. Because of this, the wavelength can differ (L3_Communications, 2000a).

These are important factors to take into account during acoustic surveys in changing environmental conditions.

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2. Echosounder tools

A. BioSonics DT-X split-beam echosounder

a. General information

The BioSonics DT-X is a portable scientific split-beam echosounder. It can operate up to 10 transducers with its multi-channel capabilities. The transducer is designed to accommodate a wide range of frequencies, being 38, 70, 120, 200, 420 and 1000 kHz. Ping rates can be selected from a broad range, being from 0.01 up to 30 pps (pings per second). The pulse duration comes in a range from 0.1 to 1.0 ms. The detection range is limited from 0.5 m below the surface down to 2000 meters (BioSonics Inc., 2013a, 2015). The housing of the transducer is made out of anodized aluminium, urethane and stainless steel and the transducer signal cable has a maximum length of 275m. The transducer is normally mounted to a pole or a transducer cage, which can be winched down and lowered into survey position (BioSonics Inc., 2015). The output of this split-beam echosounder is an accurate target strength (TS) measurement, Sv split-beam pings and the angular positions of the objects in the water column.

The echosounder got a full instrument and equipment calibration during the construction process in the BioSonics factory. BioSonics recommends performing a standard target calibration check, prior to each survey project. This is done by the use of a calibration sphere which is purchased from BioSonics Inc. They also recommend annual beam pattern calibration at the factory, but this is not a requirement. After the calibration, the configuration settings of the echosounder can be checked. These settings include the ping rage, the pulse duration, the detection range and the environmental parameters such as pH, temperature and salinity of the sea water (Vandermeulen, 2011). The working method used when employing this echosounder is done as followed.

Both BioSonics computer and echosounder unit are switched on and connected to each other, via an Ethernet connection hub. Next, visualization software, in this case BioSonics Visual Acquisition DT-X software, is opened. The echosounder is activated, starts to ping and checked for correct data streaming. When also the echosounder settings are checked, a recording can be started of the water column detections which is visualized live (BioSonics Inc., n.d.). Following Vandermeulen, H., 2009, one day of performing acoustic surveys requires to two days of data processing.

The output of the BioSonics DT-X split-beam echosounder is recorded in a DT4 file format, which is stored together with the metadata. It is important to mention that two of these metadata variables should not be used for analysis. These are the absorption coefficient and the sound velocity values. These values are in this variable list because of historical uses and are now decided to be unreliable (BioSonics Inc., 2013a). Especially because this echosounder can include transducers with different frequencies, one single value for these variables should not be noted. Instead, these values can be manually calculated (BioSonics Inc., 2013a). The obtained variable output of the binary DT4 recording files are TS, Sv and the angular positions. Two post-processing software packages to analyse the .dt4 file format are BioSonics Visual Acquisition DT-X software and Echoview software.

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Figure 2.5, print screen from BioSonics Visual Acquisition DT-X software: playback mode of 20151008_083843.dt4 data file, containing a recording from the water column at a sampling location in the BPNS. (coordinates: 51° 17.75289’N; 3° 2.98494’E): Adjusting the range scale limits for better visualization.

b. Demonstration of the BioSonics DT-X split-beam echosounder

On October 8th 2015, a demonstration of the DT-X was given by BioSonics Inc. on the RV Simon Stevin. The split-beam echosounder was lowered in the water by the use of a telescopic arm mounted on the starboard side of the working deck of the vessel. From 08:00h (CEST) until 13:30h (CEST), 14 acoustic water column recordings were performed. These were all stored in the assigned .dt4 format on an external hard drive disk for later analysis, during the processing. After post-processing of the water column recordings with BioSonics Visual Acquisition DT-X software, the total amount of detected fish targets per recording could be obtained. Before this, an exploration of the detection capabilities in the software package was performed. Following figures give a highlight of the main findings for optimal visualization in the echogram.

A first setting which can be adjusted is the range scale limit. This way, everything below the detected seabed line can be excluded from the visualization, dedicating the whole screen to the water column zone only. For the example shown in figure 2.5, the range scale limits were adjusted. The minimum range limit was kept at the default value of 0.98 m below the surface. The maximum range limit was adjusted from the default value of 19.98 m to 10.00 m. This adjustment provides a more clear visualization of the water column zone.

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Next, the amplitude range scale can be adjusted to exclude noise from the visual. The default amplitude range in the BioSonics Visual Acquisition DT-X software is set on a minimum of -130 dB. This value is adjusted to -75 dB and -40 dB.

Increasing the lower limit of the amplitude range scale decreases the amount of noise visualized on the echogram (figure 2.6 a, b, c). The preferred amplitude range scale is however dependent on the study aim and studied target species. By adjusting the amplitude range scale to the amplitude range of the target species, a more detailed visualization can be given of the target species in the water column.

Figure 2.6, print screen from BioSonics Visual Acquisition DT-X software: playback mode of 20151008_083843.dt4 data file, containing a recording from the water column at a sampling location in the BPNS. (coordinates: 51° 17.75289’N; 3° 2.98494’E): Adjusting the amplitude scale limits for better visualization. (a) Minimum amplitude limit is -130 dB. (b) Minimum amplitude limit is -75 dB. (c) Minimum amplitude limit is -40 dB.

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As a third finding, surface turbulence zones are examined regarding their effects on target detection capabilities. Figure 2.7a shows a turbulence zone close to the surface. The cause of this turbulence is unknown and can be both originate from vessel or engine induced air bubbles or from biotic targets such as micronekton (Huntley & Zhou, 2004). This is possible as the frequency of the transducer used for this demonstration is 200 kHz, which is in the range of echosounder frequencies that can enable plankton detection (see chapter 1.2.C).

After adjusting the amplitude range scale to a minimum amplitude limit of -40 dB, it becomes more clear what the effects of this turbulence is on the target detection capabilities. Attenuation and signal blocking seem to reduce strongly the detection capabilities of the echosounder, right below these turbulence zones (figure 2.7 b). This is also confirmed by a study of Mitson. et al, 2003 (Mitson & Knudsen, 2003).

The target counts, obtained from the recordings made during this demonstration will be further discussed in chapter 3.

Figure 2.7, print screen from BioSonics Visual Acquisition DT-X software: playback mode of 20151008_083843.dt4 data file, containing a recording from the water column at a sampling location in the BPNS. (coordinates: 51° 17.75289’N; 3° 2.98494’E): The effect of surface turbulence on the detection capabilities lower in the water column. (a) Echogram with a minimum amplitude limit of -130 dB. (b) Echogram with a minimum amplitude limit of -40 dB.

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B. IXBlue SeaPix 3D sonar

a. General information

The SeaPix multibeam echosounder is unique because it includes the third dimension in its detection capabilities. This MBES can produce one or more swathes simultaneously along or across the vessel axis (IXBlue, 2013), while classical MBES system produce one swatch and create the third dimension in the water column recording by sailing a transect. As for most MBES systems, the transmitter and receiver are positioned in a Mills Cross position (as explained in chapter 1.3.B.c).

This MBES has a single operation frequency of 150 kHz and a narrow beam width of 1.6°. It transmits monochromatic or linearly frequency modulated pulses (chirp)(see BOX 2) with a pulse length from 100 µs up to 20 ms (Mosca et al., 2015). The Inertial Motion Unit (IMU) increases the motion stability of the transmitted and received beams. All of these elements lead to more realistic fish resolution. The minimum individual target size discrimination level (resolution) is set on 7.5 cm and the minimum inter-individual target size discrimination level is 15 cm (IXBlue, 2013, 2016).

This MBES receives a full instrument and equipment calibration and beam calibration during the production process in the factory. The client is recommended to perform an installation offset calibration procedure (patch test) before every survey project, to remove all the offsets. This is a new developed calibration process, in which a TS calibration map is created based on the physical characteristics of the MBES transmitter. This new in-situ calibration process does not require the vessel to stagnate, which influences survey time positively (Mosca et al., 2015) The extra feature of the SeaPix is that this Mills Cross composition is steerable. This creates a volume coverage of 120° x 120°. Both transducer elements, each consisting of 64 elements, can operate as both transmitter or receiver. These 64 beams are equally divided along the -60° to +60° range (IXBlue, 2013). Four operation modes are possible (IXBlue, 2013):

1) STV (Sonar Transversal Vertical): classical MBES operation mode. The STV tilt angle is 90° fixed (vertical sounding).

- Transmitter: along-track - Receiver: across-track

2) STT (Sonar Transversal Tiltable): transverse swath can be tilted forward and stern. The STT tile

angle can be selected from the range of 90° (vertical) to +30° under the surface. - Transmitter: along-track - Receiver: across-track

3) SAT (Sonar Axial Tiltable): for visualization of an along-track section of the water column. The

SAT tilt angle can be selected within the range +50° (starboard under the surface) to -50° (port under the surface), including 90° (vertical).

- Transmitter: across-track - Receiver: along-track

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4) SAS (Sounder Axial Scanned): volume scan under the vessel (also referred to as SAV). The SAS tilt angle with range +50° (starboard under the surface) to -50° (port under the surface), including 90° (vertical) is automatically scanned.

- Transmitter: across-track - Receiver: along-track

All of these four operation modes (STV, STT, SAT, SAS) can run and be visualized at the same time. Additionally, all operation modes can be combined into one 3D omnidirectional viewing mode (see figure 2.8).

Besides the vertical looking mounting positions, this MBES can also be mounted as a side looking and forward looking echosounder. Because of the 3D capabilities different viewing points can be selected for the echogram visualization. In case the MBES is side looking mounted, the echogram can be selected on horizontal side looking or vertical side looking. For the forward looking mount, both horizontal looking forward and vertical looking forward echograms can be selected (IXBlue, 2013).

The innovative feature of the fish school detection capabilities of the SeaPix, is the improved near surface biomass assessment. Because of the forward looking surface echograms, near surface shoals can be better detected and more precise processed. The study of Mosca et al. 2015 has showed that the SeaPix has comparable detection capabilities for abundance assessment, than the commonly used SIMRAD EK60 scientific split-beam echosounder (Mosca et al., 2015). In that study, the SeaPix was operating at 150 kHz with pulses of 0.1 ms length. The SIMRAD EK60 was operating at 70 kHz, with 1 ms pulse length.

Figure 2.8, taken from IXBlue, 2016: Vertical looking mounting positions, including STV, STT, SAT and SAS operation modes.

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The in-house built software of IXBlue for the SeaPix 3D sonar is called SEAPIX Manager Software SPX. This software includes the viewing modes STV, STT, SAT, SAS, ECHO, SONAR, 2D and 3D. Within the biomass analyser processing mode, target classes can be created, in which threshold filters can be installed and linked to a target class name. When a fish school occurs, composed out of target species with each a distinct acoustic mark, these classes can be separated and analysed. This is part of the Geographical Biomass Analyzer (GBA) Fish Class processing. Subsequently an overview can be created of the fish class ratio of the analysed water volume (IXBlue, 2016).

The obtained variable output from the SeaPix IXBlue 3D sonar is Sv, TS and BS. This third variable, BS, represents the backscatter from the seabed. This MBES provides, thus, both calibrated water column and seabed data. Echoview software and Movies 3D (developed by IFremer) provide the opportunity to perform post-processing on the converted HAC output data format of the SeaPix MBES (Mosca et al., 2015).

b. Demonstration of the SeaPix IXBlue 3D sonar

A demonstration of the IXBlue SeaPix 3D sonar by IXBlue was scheduled on April 27th and April 28th

2016, to be performed on the RV Simon Stevin. Due to a damaged transducer during a previous demonstration in Peru, the demonstration was cancelled on April 25th. The rescheduling of the demonstration has yet to be agreed. Therefore, no recordings were collected and thus, no exploration of the detection capabilities of the SeaPix 3D sonar in the North Sea could be done.

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C. Kongsberg EM2040 MBES

a. General information:

The Kongsberg EM2040 MBES, is the echosounder tool fixed on the RV Simon Stevin (see chapter 1.3.D). This MBES is developed for bathymetric research. Examples of the applications are seabed and habitat mapping and inspection of underwater infrastructure. However, mapping of biomass in the water column also belongs to the features of this MBES. It is possible to simultaneously record water column data and bathymetric data. The operating frequencies range from 200 to 400 kHz. For normal operations, 300 kHz is recommended as operating frequency, as this provides a balance between high resolution and depth capabilities. The maximum angular coverage of the beam fan is 200° (Kongsberg_Maritime, 2015b).

The Kongsberg EM2040 MBES comes fully calibrated from the factory at purchase. Because this MBES is, however, developed for bathymetric purposes (QPS, n.d.), a calibration for water column detection capabilities does not exist. Because of this no quantitative assessment can be done.

The output data files are composed out of two data types, being .all and .wcd. The .all file contains the metadata of the water column recordings, being position GPS fixes and heading data. Position GPS fixes data file contains the coordinates (latitude and longitude) at every ping recorded. The heading data gives an overview of the followed direction the vessel took during the recording. This is an orientation described in degrees. The second data type has a .wcd file extension, which stand for Water Column Data file. This file contains the water column recording of the MBES system. From these output data, two variables can be deducted, being Sv pings and unspecified dB pings. The variable Sv pings contains Sv data (see chapter 1.3.B) which are derived from the unspecified dB ping variable. These unspecified dB pings contain sample amplitudes calculated as followed: Amplitude = Stored Value * 0.5 (dB), in which the stored value is an integer in the range [-128, 127], as read per ping from the water column datagram (Echoview_support, n.d.-c). Target strength (TS) values are not part of the output of this MBES, as this requires calibration (Trenkel et al., 2008).

b. Demonstration of the Kongsberg EM2040 MBES

On August 21st 2015, a demonstration of a water column recording with the Kongsberg EM2040 MBES was given by Wim Versteeg, senior marine technician at the Flanders Marine Institute (VLIZ), on the RV Simon Stevin. From 08:50h (CEST) until 13:00h (CEST), 4 acoustic water column recordings were performed. Water column recordings can be both stored as a .all file format or as a separate water column file, being the .wcd file format. It is, however, not possible to store water column recordings as both file formats simultaneously (Kongsberg_Maritime, 2013). In this case, the water column recordings were all stored in a .wcd format. All metadata was stored in the standard .all file format. Both data files were stored on an external hard drive disk for later analysis.

The Kongsberg EM2040 MBES is hull-mounted in the RV Simon Stevin, thus initial installation of the transducer was not required.

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As a first step, the hardware is set up. To avoid acoustic interference from the Teledyne odom echotrac CV-300 single beam echosounder, it is recommended to switch the single beam echosounder off. Next, the processing unit and work station PC are turned on. When the setup of the hardware is completed, the software can be opened. The operational software for this MBES is SIS (Seafloor Information System). To obtain the water column window view, this option can be selected from ‘Frame selection’ button (figure 2.9). On the x-axis, the across track distance (m) is shown, while on the y-axis, the depth range (m) is shown (Kongsberg_Maritime, 2013).

During the demonstration of the Kongsberg EM2040, the Teledyne odom echotrac CV-300 single beam echosounder was switched on for a moment, to compare the visual of the simultaneous recording of the MBES and the single-beam echosounder.

Figure 2.9, taken from Kongsberg Maritime, 2013, SIS (Seafloor Information System): Illustration of water column visual with associated seabed bathymetry visual.

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Chapter 3 - Echosounder data analysis

1. Material and methods

A. Acoustic sampling

Since 2012 acoustic recordings have been collected during several research trips with the RV Simon Stevin. These recordings have been performed with the hull-mounted Kongsberg EM2040 MBES at an operating frequency of 200 kHz. All water column recordings have been stored on the data server of the Flemish Marine Institute (VLIZ) for post-processing. This whole data set comprises 598 files, in 15 separate sampling files (see table 3.1), covering 662 GB of water-column recording data files, in .all and .wcd file format.

Echosounder: Kongsberg EM2040 MBES

Sampling ID Number of water

column recordings (files)

Coordinates

Longitude (degrees) Latitude (degrees) 13FEB_MRU 10 2° 33' 38.26944417852'' E 51° 20' 34.30092743412'' N 13FEB_OCTANS 7 2° 33' 36.799202280312'' E 51° 20' 36.57839764092'' N 13FEB_SIDENOISE 4 2° 37' 4.101611965608'' E 51° 19' 49.22400517644'' N 120917 22 3° 11' 21.490425574368'' E 51° 24' 55.96180945812'' N 130226_Lifewatch 3 2° 22' 19.614008210124'' E 51° 25' 11.19358679808'' N 130304_ST13121 74 3° 6' 46.77479984916'' E 51° 21' 21.77999963136'' N 130306_Circle 4 2° 55' 38.11079854668'' E 51° 21' 31.89239991216'' N 131113_WaTuR 15 3° 7' 17.410800008172'' E 51° 22' 17.84639990676'' N 150714_CW 4 2° 47' 10.042800193716'' E 51° 14' 58.678800261'' N 151010_Flinterstar 17 3° 3' 17.299123654572'' E 51° 24' 34.68930155028'' N Baeye001 88 2° 53' 24.536400058428'' E 51° 13' 54.5268002628'' N data_Matthias_Baeye 18 3° 2' 59.211600801288'' E 51° 25' 43.0464018324'' N Demonstration 7 2° 45' 57.452400026388'' E 51° 38' 49.9596030438'' N MB_CTM_juni2013 21 3° 2' 11.763597462072'' E 51° 27' 3.43800175104'' N Wrakken_20150821 5 2° 59' 43.576800596196'' E 51° 34' 47.07120076788'' N

Total amount of water column

recordings 299 files

During the demonstration of the BioSonics DT-X scientific split-beam echosounder on October 8th 2015 (see chapter 2.2.A), 14 water column recordings were performed (see table 3.2). These were all stored on the data server of the Flemish Marine Institute (VLIZ) for post-processing. These data files are all in DT4 (.dt4) file format.

Table 3.1: Overview of the water column recordings collected since 2012 by use of the hull-mounted Kongsberg EM2040 MBES on the RV Simon Stevin. For each sampling file, the sampling identification code and the amount of recorded water column files are given. Also the coordinates in degrees of the sampling location are represented.

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Echosounder: BioSonics DT-X scientific split-beam echosounder

Sampling ID Number of water

column recordings

Coordinates

Longitude (degrees) Latitude (degrees) VLIZ_BIOSONIC_08102015 14 2° 29' 57.6" E 51° 23' 45.0'' N

Total amount of water column recordings 14 files

All surveys have been performed on different locations in the BPNS. For each survey, the coordinates of every water column recording received a location tag in the geographical information program Google Earth. These location tags give an overview of the location in the BPNS for each acoustic survey (figure 3.1).

Table 3.2: Overview of the water column recordings collected on October 8th 2015 by use of the BioSonics DT-X scientific split-beam echosounder on the RV Simon Stevin. For each sampling file, the sampling identification code and the amount of recorded water column files are given. Also the coordinates in degrees of the sampling location are represented.

Figure 3.1, taken from Google Earth: Overview of the sampling location of each survey (sampling ID). (see Addendum 3.1, for version in full size).

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B. Data visualization

The received echo signal can be visualized live on the display of the work station, during the acoustic sampling. Different targets are visualized as different contrasts. Originally this was in a grey-scale display, where a strong target detection was reflected as a dark visualization. These days, colour displays became standard. Different colours represent the different gradients in the range of detection strength. Besides differences in backscattering strength, relative position in the water column can also be seen as the system can calculate its depth. The upper limit at which the transducer can perform measurements, is delineated as the transmission limit line (see figure 3.2). This is the position of the transducer in the water column and can be close or distant from the surface, depending on the mounting position of the transducer. For a hull-mounted echosounder, the transmission limit line will be very close to the surface (see figure 3.2 (b)), while for a transducer fixed on a towed-body this line can be very distant from the surface. Thus, the target will be positioned on the echogram on a certain distance from the transmission line, which is proportional to the distance between the target and the transducer in the water column. The depth of this object is calculated by using the formula of speed of sound (Simmonds & MacLennan, 2006).

Figure 3.2, adapted from Simmonds and MacLennan, 2006, Fisheries Acoustics: Theory and Practise, 2nd edn.: (a) structure of an echosounder. On the display, several echo detections are shown, such as the seabed, targets and the transmission line. (b) Example of an echogram, in which the transmission line is highlighted. In this case the line is very close to the surface.

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C. Data post-processing

a. Exploration of software packages

Data post-processing in hydroacoustic research depends highly on software bundles that can perform high-speed analysis of echo-integration data. The outcome of this software generates quantitative variables, such as Sv (backscattering volume) and TS (target strength). In highly developed software bundles, immediate density estimates of fish schools can be performed. This is the case for Movies+ software, developed by IFremer, which includes an automatic shoal detection algorithm (Berger, Durand, & Marchalot, 2002).

Post-processing software bundles are designed to interpret the data gathered by calibrated scientific echo sounders. For recreational fish finders, however, this kind of software is lacking. This impedes the usage of recreational fish finder for scientific purposes. McInnes A. M. et al., 2015 tackled this issue and designed the FISH (Fish-finder Image Segmentation Helper) program. This program is developed in Java and enables visualisation and basic echo-integration of fish schools. The additional FISH-rev reviewing package can extract school parameters and write these in a common comma-separated value (.csv) output file, which can be interpreted by any spreadsheet program such as Microsoft Excel (Mcinnes et al., 2015).

Several echosounder companies and private software providers developed software bundles to post-process acoustic recordings from echosounder tools. Three important software providers that are discussed in this report are BioSonics, Inc., Quality Positioning Services BV (QPS) and Echoview Software Pty Ltd (formerly Myriax Software Pty Ltd).

BioSonics Visual Acquisition DT-X

BioSonics, Inc. provides the free software package Visual Acquisition DT-X (version 6). This software is in-house built for the BioSonics DT-X and MX Echosounder Systems. The main functions that are included in this software package are real-time data acquisition, storage and playback (BioSonics Inc., n.d.).

A demonstration version of this software package can be downloaded free of charge from the download page of BioSonics. After completing the download registration, access is granted to the BioSonics download webpage, on which three demonstration software packages can be downloaded, including Visual Acquisition DT-X.

The window of the Visual Acquisition DT-X software is mainly designed for logging and live processing of water column data. Post-processing is done by the use of the ‘playback’ button. A DT4 file can be selected and uploaded in the workflow. Next, several parameters can be adjusted to optimize the visualization (see chapter 2.2.A.b). Targets can be manually selected from the echogram. By clicking on the selected target, the frequency distribution for that certain ping is shown in the attached graph. The amplitude of the target, which is the target strength (TS) can be read from this graph.

The BioSonics Visual Acquisition AutoTrack is an optional module for this software packages which is not included in the free demonstration version. This module computes fish tracks from the detected targets in the water column recordings.

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QPS Fledermaus

The QPS software bundle contains four packages, being QINSy, Qastor, Qimera and Fledermaus. The purpose of QINSy is hydrographic data acquisition, while Qastor is designed for advanced piloting and navigation. Qimera and Fledermaus are both specified towards processing and analysis, where Qimera is the main hydrographic processing tool. However, this tool is primarily developed for bathymetric studies. Fledermaus is a 4D geo-spatial processing and analysis tool, mostly used for processing geographical data for ocean mapping.

The Flemish Marine Institute is licensed with a dongle for the Fledermaus package. This contains multiple modules, such as Fledermaus (64 bit), FMMidwater, FMGT, FMCommand, DMagic and Crosscheck. For water column data, FMMidwater and Fledermaus were used. FMMidwater and Fledermaus are mainly used for dealing with water column recordings. FMMidwater is designed to import sonar files and convert them to a GWC (Generic Water Column) format. This format can be visualised and be filtered with several threshold parameters.

A first step in the processing is adding the sensor and navigation files in FMMidwater. The sensor files are in the water column data format (.wcd) and the navigation files are included in the metadata in the .all format files (figure 3.3)

Next, the sensor and navigation file are combined into the GWC (.gwc) file format. This is done by the use of the sonar data converter tool, selected in the tools menu. This tool will open a GWC conversion wizard (figure 3.4).

Figure 3.3, taken from FMMidwater: Illustration of source file selection in FMMidwater. Sensor files are included in the .wcd data files and the navigation information is stored in the .all data files.

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Additional in this GWC conversion wizard, a downsample factor can be selected. Some echosounders tools have such a high resolution and ping speed, that the water column data can become highly oversampled and file sizes extremely large. For visualization purposes, the full resolution is often not needed (QPS & SAAB, 2015). This downsample factor can range from 0 to 32.

After finishing the conversion, the GWC file can be visualized and filtered by changing several threshold parameters. The standard visualization made is a fan viewing mode. This can be changed to a stacked viewing mode, to obtain a clear overview of the whole dataset (figure 3.5 (a)). By adjusting threshold parameters, noise can be reduced and targets will be visualized more clear. The parameters that can be adjusted are the beam range, the visualized depth range and the amplitude range. In this case, the visualized depth and amplitude range were adjusted, which resulted in a clear overview of the detected targets in the water column (figure 3.5 (a) and (b)).

Figure 3.4, taken from FMMidwater: Illustration of GWC conversion wizard. The sensor (.wcd) file is selected as water column source and the navigation (.all) file is selected as navigation source.

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Figure 3.5, taken from FMMidwater: Overview of the FMMidwater visual. (a) Default fan viewing mode for multibeam water column recordings. (b) Conversion to a stacked viewing mode, which is in 2D. (c) By adjusting threshold parameters, a better visual can be obtained. In this case, the maximum visualization depth is reduced and the amplitude

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Because the Kongsberg EM2040 MBES does not provide calibrated water column recordings, the echogram can only be visualized by the use of raw signal input. The Sv and TS signal options were not activated and thus could not be selected for visualization.

Subsequently, the GWC file can be exported as a SD (scene) file format, which can be uploaded in Fledermaus for final 3D visualization (figure 3.6). The echogram can be rotated and adjusted in scale. By use of the time bar, the scene can be played and the echogram will follow the sampling path in the 3D window.

Fledermaus software initially seems to be the logical choice in post-processing software as the majority of supported data formats are related to Kongsberg echosounder tools. Indeed, the Kongsberg EM2040 MBES, mounted on the RV Simon Stevin, is part of the list of supported multibeam systems (see BOX 6). However, the post-processing opportunities are rather limited and restricted to visualization only. Additionally, the Sv and TS viewing modes are inactive, because the input water column data are not calibrated.

Figure 3.6, taken from Fledermaus: Overview of the Fledermaus visual: MBES echogram along the survey transect in 3D.

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BOX 6, taken from QPS, SAAB, 2015: FMMidwater Supported Data Formats

FMMidwater supports a range of file formats that contain water column time-series data from either single beam or multibeam systems. Ancillary file types can also be loaded to aid in processing. Currently supported sonar file types are is listed below. Kongsberg (.all) Files – Support for .all files containing datagram 0x6B. Example sonars logging this file type include the EM

122, EM 302, EM 710, EM 2040, EM 3002 and ME 70. Kongsberg (.wcd) Files – Support for .wcd files containing datagram 0x6B. Depending on the settings of the topside, water

column data can be logged to a separate file type while all other packets are logged to a .all file. If the .wcd file lacks navigation and system configuration information, the user needs to additionally load the matching .all file which contains required system configuration and navigation data. This type of processing is explained in more detail in section 1.7.3.1. Example sonar types are the same as the .all format.

Kongsberg / Simrad (.raw) Files – Support for .raw files containing datagram 'RAW0' datagram. Example sonars logging this file type include the ME 70, EK 60, and ER 60.

Kongsberg / Simrad (.ek5) Files – Support for .ek5 files containing datagram 0x3356 (VolumeBS_1), 0x3256 (VolumeBS_2) and 0x3356 (VolumeBS_3). Example sonars logging this type include the EK 500.

Imagenex Delta-T (.83b) Files – Support for .83b files containing datagram '83b' (Beam Output). Reson (.s7k) Files – Support for .s7k files containing datagram 7008 or 7018. Example sonars include 7125 and 7101. SEGY (.seg, .sgy, .segy) Files – Support for SEGY files containing trace datagram. Example sonars logging this type include

EdgeTech Chirp systems. Typically, sub-seabed time-series data contains part of the water column prior to seabed penetration. FMMidwater simply treats the sub-seabed channel as a single beam echo sounder.

DBM (.dbm) Files – DeBeers mining format. Triton Imaging (.xtf) Files – Support for .xtf files containing Sonar (type 0) datagram with sub-seabed channel. POSPac (sbet.out) Files* – POSPac data can be loaded as the navigation source during the GWC file creation.

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Echoview

Echoview is a software package for hydroacoustic data processing, focused on water column and seabed echosounder data. This processing software is used by researchers in several countries across the North Sea, such as the United Kingdom, Norway and Germany. Echoview software differs from the other software bundles as the focus here is put on marine and freshwater ecosystem studies. Some fields Echoview is specialized in stock assessment, behaviour ecology and habitat classification. Furthermore, the software bundle contains several modules (figure 3.7), which can be selected and compiled on demand.

A demonstration version can be downloaded free of charge from the Echoview website. It allows to generate visuals from the uploaded data file. To reach this point, a new Echoview (EV) file should be created which opens an empty work flow. Next, both the .all and .wcd file from one sample recording can be uploaded and added to the work flow. From this point all available variables can be explored. New variables or lines can also be assigned to perform a further analysis of the data.

First an overview is given to show the different object icons and what they represent (figure 3.8).

Figure 3.7, taken from Echoview , 2015, Echoview Post-Processing software: brochure.: Overview of the Echoview modules

Figure 3.8, Overview of the different variable object icons in Echoview.

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Demonstration mode limits all variables to 5000 measurements and inhibits to save the created EV file. Therefore, a request for a time dongle license was sent to Echoview. Soon this request was granted and a time dongle was sent from the Echoview office in Hobart, Tasmania towards the Marine Biology department of the University of Gent, Belgium. This came cost-free and included a full support from Echoview acoustic experts.

The time dongle created the possibility to explore all the assets of Echoview software bundle the fullest and included all working modules. Besides this, all created EV files can be saved. This time dongle allowed an extensive analysis on the usability of Echoview software for North Sea acoustic purposes.

Similar to the free demonstration version, a new EV-file is opened and both .wcd and .all file are uploaded. The initial dataflow contains two data variables, Sv pings and unspecified dB pings (see Chapter 2.2.C.a) which originate from the echosounder transducer. Additionally, metadata is obtained from the .all file. This metadata includes the position GPS fixes and the heading data (see chapter 2.2.C.a) (figure 3.9).

Figure 3.9: Echoview dataflow after uploading the water column output files (.wcd and .all file format) from the Kongsberg EM2040 MBES.

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Next, the variables can be opened for visualization (figure 3.10).

For each variable, the variable properties can be adjusted. This includes the adjustment of the amplitude threshold range and the color scheme and its range limits. To perform further processing, new variables can be created (figure 3.11).

For multibeam echosounders, the required operand for processing is a variable with Sv or TS data types. As for the Kongsberg EM2040 MBES, no TS data type is available because this MBES is not calibrated for water column recordings.

Calibrated single and split-beam echosounder can operate this variable by selecting a Sv or TS data type as operand.

Figure 3.10: Echoview window: visualization of two variables, provided in the water column data recorded by the Kongsberg EM2040 multibeam sonar. The left echogram provides a visual of unspecified dB pings. On the right is a visual of Sv pings. Both contain the same time fragment.

Figure 3.11: Creating a new variable in Echoview. In this illustration, the Background noise removal variable is selected, which estimates the background-noise level and subtracts this from the value of each sample (Echoview support, n.d.-b).

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From this point, a combination of processing variables can be assigned to accurately implement the study aim. In fisheries research, the most common processing output is single target detection and school detection. School detection can be performed from the Sv ping variable, while single target detection is performed with a TS variable as operand. When TS data are not available as output from the water column recordings, conversion variables can be added to the workflow and make single target detection possible.

The wide range of applicable variables for post-processing of water-column data, makes the Echoview software package applicable for a large range of echosounder tools (see BOX 7).

BOX 7, taken from Echoview Support, 2016: Echoview supported echosounder tools: Single, split, dual beam and wideband echosounders

• BioSonics Model 102, DE4000, DE5000, DE6000, DT4000, DT5000, DT6000 and DTX series of echosounder • Furuno FQ80, ETR-30N and FCV-30 echosounders • HTI Models 241/243/244 split beam digital echosounder system • Kaijo KFC-500, KFC-1000, KFC-2000, KFC-3000, and KFS Precision Acoustic Systems PAS-103 Single-beam and

PAS-103 Split-beam echosounder • Simrad EK80, EK60, Ex70, EK15, EQ60, ES60, EY60, EK500, EA500, EY500, EA600, and EA400 echosounder • SonarData EchoListener SciFish 2100

Wideband and Broadband echosounders • Simrad EK80 Scientific wideband echosounder

Multibeam sonars • Kongsberg EM 3002, EM 3002D and EM 710 multibeam echosounders • Kongsberg Mesotech SM20 multibeam echosounder • Kongsberg Mesotech M3 multimode multibeam sonar (See also Imaging sonars) • RESON SeaBat 6012, 7000, 7125, 7128, T20-P, 8101 and 8125 multibeam echosounders (equipped with the

optional hardware extension for digitized sonar images) • Simrad Mesotech SM2000 FR multibeam echosounder with recording kit • Simrad ME70 multibeam echosounder • Simrad SH90 high resolution, high frequency fishery sonar • Simrad SX90 long range, low frequency omnidirectional fish finding sonar • WASSP WMB-3250 multibeam sonar

Imaging sonars • Sound Metrics DIDSON Dual-frequency IDentification SONars • Sound Metrics ARIS Dual-frequency sonars • BlueView 2D imaging sonar • Kongsberg Mesotech M3 multibeam imaging sonar (See also Multibeam sonars)

Scanning sonars • Kongsberg Mesotech MS 1000 scanning sonar • Simrad SH80 scanning sonar • Simrad SP70 scanning sonar • ADCP sounders • RD Instruments Workhorse series of ADCP (Acoustic Doppler Current Profilers)

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b. Post-processing methods

Echoview is a post-processing software package developed for a wide range of echosounder tools (see BOX 7). All water column data files, recorded by the Kongsberg EM2040 MBES and BioSonics DT-X split-beam echosounder, which are available on the server of VLIZ, can be processed by the use of Echoview. In contrast, the BioSonics Visual Acquisition DT-X software package is specifically designed for processing of the output of the BioSonics DT-X split-beam echosounder. Kongsberg recordings can thus not be interpreted by this software package. QPS Fledermaus and FMMidwater seem to be limited in post-processing potential, as they are mainly aimed on advanced visualization performances.

Because of these arguments, the conclusion was made to use Echoview software for the post-processing of the water column data.

Post-processing BioSonics data with Echoview

The first step to perform an accurate processing, is to create a dataflow with all the necessary variables to obtain a single target detection. The BioSonics DT-X split-beam echosounder data is used to create the first Echoview workflow (figure 3.12). To add the first variables, the water column data files recorded with the Biosonics DT-X split-beam echosounder are uploaded in the software dataflow. Three output variables are obtained from the transducer, being the TS split beam pings, angular position split beam pings and Sv split beam pings variable. As this echosounder is calibrated for water column recordings, a TS output type is obtained which can be directly used as operand for a single target detection variable. This variable is imported by creating a new variable in the workflow and selecting the ‘Single target detection – split beam’ variable. Both the TS split beam pings and angular position split beam pings variable will be automatically selected as operands. If not, this can be selected in the variable properties. To obtain an accurate target detection, it is important to exclude possible source of error, such as the surface turbulence and the seabed dead zone (see chapter 1.3.C).

A surface line is created as an editable line with a fixed depth that refers to the turbulence depth. A cause of surface turbulence could be entrained gas bubbles due to wave action, vessel movement or engine propulsion or turbulence due to micronekton (Huntley & Zhou, 2004). To exclude seabed echoes, a second editable line should be created. The profile of this seabed line can be calculated by an automated ‘best bottom candidate’ algorithm. If turbulence occurs above the seabed, the seabed profile line can be extended by importing an offset line, which will increase the depth of the seabed profile line with a certain offset value. If the turbulence describes an irregular pattern during the course of the recording, a new line can be manually drawn on the echogram. The final exclusion lines are then selected as the exclusion limits in the variable properties of the single target detection variable (figure 3.12). Besides this, some detection parameters have to be entered such as the TS threshold (dB) and the pulse length determination level (PLDL). The TS threshold value is the lowest TS value for which targets should be included in the results. The default PLDL value is 6 dB and should rarely be changed. This value refers to the far-field characteristics of a sound wave (see chapter 1.3.C.a).

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Figure 3.12: Echoview dataflow for post-processing of water column recordings from a Biosonics DT-X split-beam echosounder. The TS split beam pings, angular position split beam pings and Sv split beam pings are default output variables from the echosounder recording. A single target detection variable is selected, with the TS split beam pings and angular position split beam pings variable as operand. As detection limits, the surface and seabed profile line are installed. The surface line is a line at a fixed depth. The seabed profile line is an editable line created by an automated ‘best bottom candidate’ algorithm.

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Post-processing Kongsberg data with Echoview

The Kongsberg EM2040 MBES water column recordings can be used to create a workflow for multibeam target processing. This Echoview (.EV format) dataflow template was created by the Echoview team. It contains all steps to analyse multibeam fish targets. It starts from the Sv pings variable which contains the volume backscattering data from the water column recording. From that point two pathways can be followed, both leading to a variable with single target identification (figure 3.13).

Figure 3.13: Echoview dataflow for post-processing of water column recordings from a Kongsberg EM2040 MBES. Sv pings and unspecified dB pings are the default output variables from the echosounder recording. Two extensive pathways are added to perform single target detections.

Pathway 1

Pathway 2

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The left pathway is designed to obtain single target counts and perform calculations on swimming speed and direction. The second pathway is less complex and thus faster to run due to the fact that it is limited to obtaining single target counts only.

However it is important to mention that this template was initially designed by the Echoview team to analyse data collected with DIDSON/ARIS echosounder tools. Because of this, it could not be assured that all variables would perform similarly in the analysis of data collected by a Kongsberg echosounder tool. The Echoview experts stated that the Kongsberg EM2040 MBES provides data of a lower resolution, than DIDSON/ARIS echosounders. Keeping this limitation and our study aim to analyse the ability to identify targets in the water column and quantify them, in mind, the choice was made to use the second pathway. This will provide a target count as final result, run faster and thus increase the number of data files that can be analysed during the study.

First both pathways will be briefly discussed to understand the different steps in the process.

Pathway 1 (figure 3.13, 3.15):

As a first step, a copy is made from the Sv pings to avoid adjusting the original data, as this could interfere with the processing in the second pathway. This copy is number 1 in the pathway. From here on, the numbering shows the followed path. The 2nd step in the pathway is the creation of a maximum intensity variable, which produces an echogram from the multibeam data in a stacked view. For every ping, a stacked view is created in which the maximum value of all the corresponding beams for each range is selected. This creates the highest contrast in the visual and thus the best starting point for accurate seabed profile selection. The seabed dead zone has been discussed already and now comes into practise. The seabed and a certain area above the seabed create a backscatter which should not be assigned to fish targets. To avoid this, the seabed profile line is created, based on the maximum intensity variable. This 3rd step contains a stacked visual of the seabed depth for each ping in the recording. This seabed profile can then be selected as the lower exclusion limit for target detection.

A multibeam target detection variable is assigned to the Sv pings copy, created in step 1, in which multibeam targets are created from groups of adjoining data points. This is the 4th step in the first processing pathway. For each target the range and major axis angle is given, based on the geometric centre of the data points group. The major-axis angle is the angle from the axis of the beam along the major axis (figure 3.14). As seen from the transducer, the angle value increases towards starboard.

Figure 3.14, taken from Echoview support: overview of the

major, minor and beam axis of an echosounder beam.

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A specific maximum detection range is entered to exclude detection beyond this point, as the seabed profile line cannot be assigned to a 3D multibeam target detection variable (step 4). The seabed profile line is calculated based on a 2D stacked view and thus can be only included in a further step in this pathway, when a conversion will be made to a 2D single beam acoustic variable. When there is no specific maximum range assigned the detection will be performed on the full range shown in the visual, while a substantial part of this visual could be assigned to the seabed and thus will not be included in the target detection. This can decrease the processing time substantially. For example, the analysis of a recording in which the maximum depth of the water column does not exceed 10 m, the maximum range must be set at 10 m. The multibeam target detection variable is visualized as a 3D multibeam echogram, in which the targets are highlighted. Following on this, step 5 creates a target conversion variable. In this operator, single target data is generated from the multibeam target variable. A certain range (m) is assigned, which will be the threshold for assigning a detection to the same target or to a new one. When two echo detections are within this assigned range, they will be joined together and form one single target.

As a last step, thresholding is done and exclusion lines are assigned. This is the final variable in the first pathway. As a lower exclusion limit, the seabed profile line is assigned. This implies that no detections below this line will be included in the results. To deal with the seabed dead zone, a seabed offset can be created. This is a virtual line to which a linear offset range is assigned. This range is sample specific and should be manually calculated by analysing the multibeam echogram or entered based on knowledge of previous recordings in the same area. An upper exclusion limit can be assigned as well. This is done by creating a second virtual line and selecting the preferred range.

Figure 3.15: overview of the obtained variables of the first pathway in the multibeam target detection workflow in Echoview. Below, in the middle, the Sv pings copy can be seen. Above this copy, is the visual of the maximum intensity stacked view variable. On the right the calculated seabed profile and the multibeam target detection variable are visualized. On the down left corner, the target conversion variable can be seen, which converts the target detection variable from a 3D fan view to a 2D stacked view. In the upper left corner, the target variable can be seen, which implements the upper and lower exclusion limits.

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Pathway 2 (figure 3.13, 3.16):

This pathway contains fewer steps and thus needs a shorter processing time.

As a first step (A), a maximum intensity variable is created, similar to the first pathway. This operator uses the Sv pings variable as operand. If more pathways would be added to the template, it is advised to first make again a copy of the Sv ping variable. This way, the original Sv ping data is saved for later use. Step B converts the Sv data format to another data format. The output types are TS, Sv and unspecified dB. In this case, the output type is selected on TS. As an operand, this variable uses the maximum intensity variable from step A. The advantage of this conversion variable is that the input variable is not changed. The third step (C) contains a single target detection, operating a single beam data format. Because of the Sv to TS conversion (step B), this conversion variable can be selected as input operand and a detection of single targets can be performed. Similar to the BioSonics processing workflow, detection parameters have to be assigned in the variable properties of the single target detection variable. The main parameters is the TS threshold (dB) to determine which targets should be included in the results.

As in pathway 1, two exclusion zones can be assigned in the single target detection variable, the surface exclusion limit and the seabed exclusion limit. Again a seabed offset virtual line can be assigned to avoid detection in the seabed dead zone. The range of the seabed offset zone can differ, due to differences in the calculations of the target detection variables between both pathways. This implies that for both pathways a separate seabed offset line should be created. From this single target detection variable a final threshold variable can be created, to filter the targets by adjusting specific parameters. These target property threshold parameters remove single targets for which the properties do not fall within the specified range. The threshold can be defined by target area, target length, target orientation, target range extent, etc... Both a maximum and minimum threshold can be assigned.

Figure 3.16: overview of the obtained variables of the second pathway in the multibeam target detection workflow in Echoview. On the left, the Sv pings variable is visualized. In the upper middle, the maximum intensity variable is shown. The target detection variable is located in the right upper corner. In the middle, the target detection threshold variable is visualized. The seabed profile line is located below. (see Addendum 3.2, for version in full size).

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After completing the preferred pathway, an analysis can be made of the detected targets. In this case, the second pathway was used. The two final target variables, being the single target detection variable and the target property threshold variable, give a stacked view of all detected single targets. By adjusting the parameters, the detection limit can be made more or less strict and false detections due to turbulence will be filtered out. Fish targets have been studied extensively regarding their target strength (TS) in acoustic echo-integration. Small fish species have been proven to describe, on average, a target strength around -50 dB (Hannachi et al., 2005). To limit the amount of detected targets and interfering noise, this limit was increased to -40 dB, during this study.

For fish analysis, the most common analysis parameter is fish tracks. Due to the mobility of a fish, it shows a certain track. This means it occurs in the recording on the same position in the water column during a number of following pings. The minimum number of pings in one fish track, the minimum number of single targets in one fish track and the maximum gap in pings between single targets in one fish track can be manually assigned. These values should be specified according to the aim of the study. Knowledge on the acoustic properties of the target species is thus an important asset for assigning these parameters. As for this explorative study, there are no predefined targets or knowledge on target properties. Therefore, these parameters were set on the Echoview default values, being a minimum of 3 single targets in a track and 3 pings in a track. The maximum gap between single targets to belong to the same fish track is assigned to be 3 pings.

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Spreadsheet calculations

Besides the fish track counts, other variables such as the sampling duration (s), the average vessel speed (kn), the covered distance (m), beam fan angle (°) and water column depth (m) can be obtained by converting some of the output results from the Echoview post-processing, in Microsoft Excel. The sampling duration is obtained by calculating the time difference (HH:MM:SS) between the start and stop time of the recording and convert this difference to seconds (s). The average vessel speed (kn) is manually determined by running through the recording and observing the course of the vessel speed during the recording. The covered distance x is obtained by combining the output from the two previous calculations, being the sample duration (s) and the average vessel speed (kn). By converting the average vessel speed from knots to m*s-1, the formula of speed (speed equals distance divided by the time) can be used to calculate the covered distance x during the water column recording. Echoview provides the angle between the centre and the outermost beam of the fan. This angle is in this analysis represented by α(°). The total fan angle of the fan is then equal to two times the angle α(°), being angle β(°) (figure 3.17 a). The water column depth R is calculated in Echoview, by the use of the automated ‘best bottom candidate’ algorithm. This value can be obtained from the information window of the echogram (figure 3.17 a).

Additional to all these variables, the total ensonified water volume is calculated. This allows to calculate for each recording, the amount of detected fish tracks per ensonified volume unit. This is done by calculating the surface A (m²) of the ensonified water column in each ping. Because of spherical composition of the beams in the fan, a circular segment is described. The formula to calculate the surface of a circular segment is:

A = 0.5 * R² * (β – sin(β)) (m²).

Subsequently, the ensonified volume (m³) is calculated by multiplying the surface of the ensonified water column (m²) with the covered distance (m) (figure 3.17 b).

This is applicable for the Kongsberg EM2040 MBES water column recordings, as a multibeam echosounder has a beam fan in a spherical composition. The BioSonics DT-X split beam echosounder uses only one beam, of a beam width of 6.7°. This beam width can be used as the total angle β of the circular segment. By dividing the total amount of detected fish tracks (#) with the total ensonified volume (m³) and multiply this results by 1000, the total amount of detected fish tracks per 1000 m³ volume unit is calculated for each water column recording.

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Figure 3.17: Illustration of a multibeam echogram. (a) a cross-section of the water column recording, provides an echogram for each pings. The fan is composed out of an array of beams, describing a certain angle. The standard angle output obtained from the water column data (.wcd) file format is the angle between the centre and the outermost beam. This angle is represented by α. The total fan angle is equal to two times the angle α, being angle β. The depth of the water column (R) is also visualized, being the default seabed depth calculation in Echoview. (b) Illustration of the total ensonified water volume during a recording. A certain distance x (m) is covered by the ensonified beam fan. The surface A (m²) of the ensonified water column is represented by a circular segment.

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c. Statistics

Statistical analysis is done by the use of SAS (Statistical Analysis Software) (see Addendum 2). The aim is to find possible correlations between the dependent variable and the independent variables. The dependent variable is the obtained amount of detected fish track. The independent variables are the sampling duration (s), the average vessel speed (kn), the covered distance (m), the water column depth (m), the survey ID and the echosounder tool. The survey ID and echosounder tool are discrete and thus are implemented as class variables in SAS. The other independent variables are numerical and don’t need additional labelling. Normal distribution of the data is examined by the use of a Shapiro Wilk test. The correlation are performed by the use of a general linear models (GLM) or generalized linear mixed models (GLMM), depending on the outcome of the normality test. After assigning all the class variables, the model can be entered. This model includes both the dependent variable and the independent variable, which is selected to be analysed. SAS processes the model and provides an output which includes the probability (p-value) for the null hypothesis (H0) to be accepted. Besides the p-value, the F-ratio from the F-test and the amount of freedom degrees (DF) is given. Additional to these values, a graph is provided which plots the results of the model. For discrete independent variables, a box plot will be given for each category. The mean value for each category can be provided, by the use of the LSMeans protocol. These mean values are also plotted on a LSMeans graph. For numerical independent variables, the estimate of the intercept and slope value of the best-fit trend line can be obtained. A scatter plot of the detected fish tracks in relation to the independent variable, is provided. On this plot, the best-fit trend line is visualized, including the 95%- confidence intervals (CI).

An example of a SAS-code to analyse the correlation between the dependent variable and a discrete independent variable:

- proc glm data=DATA; - class INDEPENDENT_VARIABLE; - model DEPENDENT_VARIABLE = INDEPENDENT_VARIABLE ; - lsmeans INDEPENDENT_VARIABLE; - run;

A second example is the SAS-code to analyse the correlation between the dependent variable and a numerical variable:

- proc glm data=DATA; - model DEPENDENT_VARIABLE = INDEPENDENT_VARIABLE/solution; - run;

In case of a complex error structure, which is common in biological data, a generalized linear mixed model. In SAS this is called as follows:

- proc mixed data=DATA; - class INDEPENDENT_VARIABLE; - model DEPENDENT_VARIABLE = INDEPENDENT_VARIABLE /solution ddfm=satterth; - random INDEPENDENT_VARIABLE; - run;

To analyse multiple independent variables, all selected independent variables are subsequently entered on the same provided space as show above. All discrete independent variables should be assigned to a class variable.

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2. Results

A. Fish track counts

The output of the post-processing is the total amount of detected fish tracks in each water column recording. As a final result, the total amount of detected fish tracks per 1000 m³ volume unit is calculated for each water column recording. The calculated sampling duration (s), average vessel speed (kn), covered distance (m), beam fan angle (°) and water column depth (m) are also included in the results (see Addendum 1.1). There is a high variability within the amount of detected fish tracks per 1000 m³ volume for each sample.

Value Survey ID

Sample ID

Vessel speed (kn)

Time duration

(s)

Covered distance

(m)

Depth (m)

Volume (m³)

Target counts

(#)

Targets (# per

10³ m³)

Highest MB_CTM_juni2013

0012_20130626_SimonStevin

0.10 1800.00 92.60 8.00 1219.23 16527 13555.32

Lowest 13FEB_SIDENO

ISE

0001_20130213_SimonStevin

12.00 135.00 833.40 26.00 507230.36 165 0.33

The highest obtained value is 13555.32 detected fish tracks per 1000 m³ in sample 0012_20130626_SimonStevin of the MB_CTM_juni2013 survey, collected on June 26th 2013. The total amount of detected fish tracks is 16527 tracks. The water column, with a depth of 8m, was recorded for a total duration of 1800.00 s (30 min) at an average vessel speed of 0.10 kn. The total covered distance was 92.60 m, in which the water column was ensonified with a beam fan angle of 80°. The total ensonified volume was not higher than 1219.23 m³ (table 3.3). The lowest amount of detected fish tracks per 1000 m³ volume is in sample 0001_20130213_SimonStevin of the 13FEB_SIDENOISE survey, collected on February 13th 2013. The total amount of detected fish tracks is 165 tracks. With a total ensonified volume of 507230.36 m³, the amount of detected targets per 1000 m³ is 0.33 tracks per 1000 m³. The water column, with a depth of 26 m, was ensonified at a beam fan angle of 140°, for the total duration of 135 s. The vessel was sailing at a speed of 12 kn, which makes the total covered distance 833.40 m (table 3.3).

All the independent variables show a high variability as well. For example, the water column recording with the largest covered distance was sample 0006_20130626_SimonStevin of the MB_CTM_juni2013 survey, collected on June 26th 2013, with a total covered distance of 11112.00 m (11.11 km). This is in contrast with the shortest covered distance of 8.75 m in sample 0052_20121127_SimonStevin of the data_Matthias_Baeye survey (samples with a time duration of less than 1 min excluded).

Table 3.3: Overview of the obtained variables from the sample in which the highest amount of fish tracks per 1000 m³ were detected and the sample in which the lowest amount was detected.

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The most shallow ensonified water column was recorded in sample 0006_20130304_SimonStevin of the 130304_ST12121 survey, collected at March 4th 2013, with a water column depth of 4 m (samples in harbours excluded). The deepest ensonified water column was sample 20151008_131035 of the VLIZ_BIOSONICS_08102015 survey, collected at October 8th 2015, with a water column depth of 31.5 m (see Addendum: Table 1, for the results from the post-processing in Echoview).

Every survey location is sampled during one survey. These surveys have been performed at different moments and different seasons, over the past four year. All survey locations are not represented by one similar season.

B. Statistical analysis

To explore the data, some statistical models are used to illustrate relations in the data.

First, the differences in amount of detected fish tracks per 1000 m³ volume unit between the different survey locations in the BPNS)(see chapter 3.1.A) are shown (figure 3.18).

There seem to be differences between the different sampling locations, regarding the amount of detected fish tracks. Survey 130304_ST13121, data_Matthias_Baeye, MB_CTM_Juni2013, Wrakken_20150821 and BIOSONICS_08102015 appear to obtain the highest detection amounts in their samples. These five survey have all been performed during different months, being respectively March, November, June, August and October.

Figure 3.18, taken from SAS: Illustration of the differences in total amount of detected fish tracks per 1000 m³ (y-axis) between all the different survey locations (x-axis), represented by box-plots.

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In chapter 2, three echosounder tools are compared, from which two of them are represented in this dataset, being the Kongsberg EM2040 MBES and the BioSonics DT-X split-beam echosounder. By the performance of a general linear model, a possible difference in detection capabilities between the two echosounder tools is shown by their differences in amount of detected fish tracks per 1000 m³. The Kongsberg EM2040 MBES shows a mean value of 1052.56 detected fish tracks per 1000 m³, which is significantly lower than the mean value of 2464.604 detected fish tracks per 1000 m³, obtained from water column recordings performed by the BioSonics DT-X split beam echosounder (p-value = 0.0249, F-value = 5.17, DF = 1) (figure 3.19).

However, results from the Shapiro-Wilks show that the data are not normal distributed (p-value < 0.0001). This implies that a generalized linear mixed model should be used, which incorporates additional error structures in the data.

The Kongsberg EM2040 MBES is used in multiple surveys. The variation which is explained by these differences in survey location should be incorporated as the random factor. Now, the difference in echosounder tool seems to not significantly explain the variation in amount of detected fish tracks per 1000 m³ volume unit (p-value = 0.2367, F-value = 1.68, DF = 1). The obtained parameter estimates of the mixed model show a much larger residual variation (3909095), than for the variation around the different survey locations (804228).

Similar to the GLM, the generalized linear mixed model also provides the mean values for both echosounder tools. The BioSonics DT-X split beam echosounder shows a mean value of 2288.56 detected fish tracks per 1000 m³, with a standard error (SE) of 1040.89 detected fish tracks.For Kongsberg EM2040 MBES, the obtained mean value is 865.75 detected fish tracks per 1000 m³ with a standard error of 349.45 detected fish tracks (see Addendum 1.4). Because of the large SE of both means, the difference between the mean value of the data from both echosounders is not signficant.

Figure 3.19, taken from SAS: correlation between the total amount of detected fish tracks per 1000 m³ (#)(y-axis) and the echosounder tool used for the water column recording (x-axis), represented by box-plots. The P-value of the H0-hypothesis and F-value are provided in the right upper corner.

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C. Influence of turbulence on the detected fish tracks

During the post-processing of the water column data in the Echoview software package, exclusion limits are assigned as range limits for the single target detection variable. This avoids the inclusion of target detections originating from the seabed, surface or turbulence zones (see chapter 3.1.C.b: Post-Processing BioSonics data). The BioSonics DT-X split beam water column recordings are processed by initially using the seabed and surface line as exclusion limits for single target detection. This seabed profile line is calculated by the automated ‘best bottom candidate’ algorithm, while the surface line is set on a fixed depth. Thereafter, the surface turbulence is manually delineated by a turbulence line and a seabed offset zone installed at a fixed range 0.6 m above the seabed profile line, to avoid interference with the seabed backscatter. For both cases, the total amount of fish tracks is calculated. These are absolute data and the sum of both categories represents the total amount of detected fish tracks in the water column recording (see Addendum 1.2) (plot 3.8). For all 14 water column recordings, the turbulence source is located at the surface. To correct for the differences in total amount of detected fish tracks, the relative values are represented in percentages (plot 3.1).

For sample 1, 6, 7, 9, 10, 11, 12, 13 and 14, more than 50 % of the total amount of detected fish track is assigned to the turbulence zones. On contrary, in sample 8, 95.24 % of the total amount of detected fish tracks belongs to the detected fish tracks outside the turbulence zones (plot 3.1).

As an analysis of the influence of turbulence zones on the detected fish track counts, the amount of fish tracks detected in and outside the turbulence zones are compared and visualized by boxplots, by the use of SAS. (figure 3.20).

Plot 3.1: BioSonics DT-X split beam water column data: the influence of turbulence on the detected fish track counts. 14 samples are represented (x-axis) by the relative percentage of detected fish tracks in the turbulence zones (%)(blue) and the relative percentage of detected fish tracks outside the turbulence zones (%)(orange)(y-axis).

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There is no significant difference between the amount of detected fish tracks in and outside the turbulence zones (p-value = 0.8835, F-value = 0.02, DF = 1). This implies that those zones, which are assigned to be turbulence and create noise, on average account for an equal amount of detections of fish tracks than the other turbulence-free zones, in the BioSonics water column recordings.

Four Kongsberg EM2040 MBES water column recordings are processed by initially using the surface line and seabed offset (0.6 m above the seabed) as exclusion limits for single target detection. Thereafter, the same process is followed as for the BioSonics DT-X split beam water column recordings. The surface and or seabed turbulence zones are delineated when turbulence occurs. Zonation can occur, in which a clear zonation in the detected fish tracks can be seen on the visual of the echogram. The four selected water column recordings, each have a different turbulence source, zonation pattern or combination of turbulence sources and zonation patterns.

Sample 1: bottom turbulence

Sample 2: surface turbulence

Sample 3: surface turbulence and a zonation pattern in the detected fish tracks outside of the turbulence zone.

Sample 4: No turbulence zones and a clear zonation pattern in the detected fish tracks.

The four samples are represented in a graph, in which for each sample the amount of detected fish tracks in and outside the turbulence zones is visualized (see Addendum 1.3) (plot 3.2).

Figure 3.20, taken from SAS: The difference in amount of detected fish tracks per 1000 m³ volume (y-axis) between turbulence and turbulence-free zones of the water column (x-axis). The P-value of the H0-hypothesis and F-value are provided in the right upper corner.

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In sample 1, the detected fish tracks are originating from both in and outside the turbulence zones, while sample 2 and 3 show a minimal amount of detected fish tracks inside the turbulence zones (blue bars). For sample 4, no turbulence zone was detected and thus all samples are included within the total ensonified water volume. In both sample 3 and 4, a zonation pattern is assigned, which is included in the outside-turbulence zones (orange bars) (plot 3.2). Next, the detected fish tracks are represented as relative values in percentages. For each sample, the amount of detected fish tracks in each category is given in percentages (plot 3.3).

Plot 3.2: Kongsberg EM2040 MBES water column data: the influence of turbulence on the detected fish track counts. 4 samples are represented (x-axis) by the amount of detected fish tracks in the turbulence zones (#)(blue) and the amount of detected fish tracks outside the turbulence zones (#)(orange)(y-axis).

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Sample 1, 2 and 3 contain detected fish tracks which are located in the turbulence zone. In sample 1, 50.32 % of the total amount of detected fish tracks is assigned to the turbulence zones, which is located at the bottom. In sample 2, 11.17 % of the total amount of detected fish tracks is assigned to the turbulence zone, which is located at the surface. Sample 3 contains both a turbulence zone and a zonation pattern. 13.43 % of the total amount of detected fish tracks is located in this turbulence zone, which is located at the surface. Within the detected fish tracks that are located outside of this turbulence zone, 76.64 % is assigned to the lower zone and 11.19 % to the upper zone. In sample 4, no turbulence zone is present. The zonation pattern divides the detected fish tracks in two zones. The upper zones contains 22.20 % of the total amount of detected fish tracks, while 75.55% of the total amount of detected fish tracks is located in the lower zone (plot 3.3).

Plot 3.3: Kongsberg EM2040 MBES water column data: the influence of turbulence on the detected fish track counts. 4 samples are represented (x-axis) by the relative percentage of detected fish tracks in the turbulence zones (%)(green), outside the turbulence zones (%)(blue), in the upper zone, outside of the turbulence zone (%)(yellow) or in the lower zone, outside of the turbulence zone (%)(orange)(y-axis).

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Discussion

Reflective properties of fish

Target strength is used to express the strength of the backscattered sound wave originating from a target in the water column. From this target strength, a target length can be calculated by the use of post-processing software packages. This is, however, based on the assumption that the obtained target strength represents the full acoustic reflection from the individual. Fish can swim freely through the water column and thus swim up or down. While doing this, the fish describes a certain positive or negative tilt angle (see chapter 1.2.B). This swimming behaviour can also be caused by interference with an approaching vessel. Vessels have been proven to cause an avoidance reaction in fish. This is most often translated in swimming downwards away from the vessel (Gerlotto et al., 1999; Onsrud, Kaartvedt, Røstad, & Klevjer, 2004). A change in tilt angle translates into a change in reflection strength, and thus a different target strength value for the detected target (Simmonds & MacLennan, 2006). In such a case, the obtained target length can be from a larger fish swimming at a certain angle and therefore reducing its reflection surface.

Fish track counts

Since all multibeam water column recordings have been collected during different survey projects, certain conditions such as the vessel speed, the sampling duration, the beam fan angle and the water column depth differ strongly between the different surveys (see Addendum: Table 1). This implies that the total water volume, ensonified during the different surveys, is different and the total target counts cannot be compared. Because of this, the ensonified water volume is calculated, by which the target counts can be divided. From this calculation, the number of targets per volume unit is obtained. Because the target counts from all the water column recordings are adjusted to the same volume unit, the total target counts can be compared between the different water column recordings.

In exception of two surveys, being VLIZ_BIOSONICS_08102015 and Wrakken_20150821, all water column recordings have been collected during survey projects which were not aimed on fisheries research. Therefore, the survey conditions were strongly different and often unfavourable for the collection of water column data. An example of this, is the changing vessel speed during many recordings. These recordings are most likely a combination of multiple bathymetric measurements, in which the vessel subsequently manoeuvres over certain seabed structures. This creates a lot of surface turbulence, which expands the surface blind zone and inhibits a correct detection of the fish targets. A second remark is that the average vessel speed of some samples does not exceed 1 kn. This brings the assumption that the vessel was stagnating and the sea current moved the floating vessel, creating a certain detectable vessel speed. During this stagnation, fish and other targets can move through the beam fan and be detected. The total ensonified water volume during the recording, however, will be low. Because of this, the total amount of detected fish tracks per 1000 m³ volume can reach remarkably high amounts. This is the case for the water column recording with the highest amount of detected fish tracks per 1000 m³, as mentioned in the results. Additional to this, a vessel speed of 0 kn does not imply that no water volume is passing through the beam fan while recording the water

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column. This complexity makes a simple linear regression between the average vessel speed and the amount of detected fish tracks little representative. To get insights on the influence of all the obtained variables on the amount of detected fish tracks, an exploration was done by the use of SAS, to observe remarkable patterns in the data. The data exploration showed that there are differences in amount of detected fish tracks between the different sampling locations. This can, however, not be proven statistically, as not all sampling locations have been sampled in the same season and on the same time of the day. In 2004, Onsrud, et al. demonstrated vertical migration behaviour, related to day and night patterns, in several pelagic fish species (Onsrud et al., 2004). Another study has shown that seasons also have a difference on the acoustic properties of certain fish species. The study of Gauthier, et al., 2004, has demonstrated seasonal differences in TS of a herring species, due to a change in gonad size in the spawning season (Gauthier & Horne, 2004). Additional to this, water flow rates are fluctuating strongly in the North Sea. This makes the conditions in acoustic surveys, performed in different seasons, even more unique and thus impossible to compare statistically. A statistical proof for the significant influence of different survey locations could, however, demonstrate possible hot spots in the BPNS, in which fish aggregate and reside in higher densities at certain structures such as shipwrecks and wind turbine farms (Mallefet et al., 2008; Reubens, Degraer, & Vincx, 2011). These areas provide not only a refugium for predatory species, but also provide more food sources and nursing grounds (Mallefet et al., 2008). Secondly, the difference in echosounder tool, used for the acoustic recording, regarding the detection capabilities was compared between the different samples. This did presuppose that there is a significant difference in amount of detected fish tracks between the samples obtained by the Kongsberg EM2040 MBES or BioSonics DT-X split-beam echosounder. By performing this comparison with a generalized linear mixed model, in which the nested effect of the different survey locations is incorporated, gave more insigts in this matter. This test showed that there is no signficant difference in detection capabilities between the different echosounder tools.

Post-processing in the Echoview software package

The post-processing template in Echoview contains the single target detection variable, which provides an output in fish track counts. This implies that all the detected fish tracks relate to the presence of an individual fish. It is, however, doubtable that all the obtained fish tracks are actual fish. The use of fish tracks for target interpretation originates from the use of stationary echosounder tools, to detect targets swimming through the beam. All acoutic surveys, obtained with the RV Simon Stevin, have been performed on speed, with a different vessel speed for every survey. Ensonifying fish with on a higher survey speed will create shorter fish tracks than at a low vessel speed, if a same direction and swimming speed of the fish is assumed. This makes the thresholding of these fish tracks a complex matter. Acoustic surveys are often combined with trawl surveys, in which the caught individuals are determined and categorized. This give the opportunity to validate the acoustic findings. This is called ground truthing (Doray, Mahevas, et al., 2010; Mackinson et al., 2005). Because of the lack of this ground truthing in this study, no determination can be made on the detected targets.

Shallow, high-flow sites, such as the Southern North Sea, have been proven to create difficult circumstances for acoustic surveys, because of the resuspension of seabed material by the water current(Eisma & Kalf, 1979). High flow rates of suspended and particular matter create a large amount of backscatter (Melvin & Cochrane, 2015). This backscatter can be, mistakenly, assigned to fish targets

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by an automated target detection program. This backscatter should then be manually detected and assigned to turbulence. This makes the detection of fish more complicated. Additionally to this, entrained air bubbles in this turbulence can attenuate or block the acoustic signal. This blockage, will inhibit the ensonification of the part of the water column below this turbulence area (Melvin & Cochrane, 2015). Besides, turbulence caused by air bubbles, organisms can also create an unwanted backscatter of the acoustic signal. Zooplankton has been proven to be detectable at an operating frequency down to 38 kHz (Stanton et al., 1996). The water column recordings, obtained during the demonstration of the BioSonics DT-X split-beam echosounder and acoustic surveys with the Kongsberg EM2040 MBES are performed at an operating frequency of 200 kHz, which is largely within the range of frequencies applicable for zooplankton detection. The knowledge, however, on the acoustic backscatter properties of the different zooplankton groups is limited. This makes it difficult to determine whether certain backscatter is originating from zooplankton (Stanton et al., 1996). To counter this limitation, plankton could be sampled during an acoustic survey to perform a ground truthing, to confirm if zooplankton is responsible for the echo on the echogram (Onsrud et al., 2004).

To show the extent of this issue, the detected fish tracks were compared between the different delineated zones on the echogram of several water column recordings (see Chapter 3: Echosounder data analysis – Results: Influence of turbulence on the detected fish tracks). In some of those water column recordings, more than half of the total amount of detected fish tracks appeared to be originating from a zone that was defined as turbulence. This imposes a large short come on the detection capabilities of the single target detection variable in the Echoview software package. As mentioned before (see Chapter 3: Echosounder data analysis: Acoustic measurements - Data post-processing – post-processing methods), Echoview experts created this Echoview template to process DIDSON/ARIS data, which they claimed to be of a higher resolution than the Kongsberg EM2040 MBES water column recordings.

A possible solution could be to delineate these turbulence zones and exclude them from the target detection range. Until now, the case in which targets are mistakenly assigned to be fish targets, has been discussed. It is, however, also possible that determined turbulence zones contain targets which are actually real fish targets.This is illustrated by an example from the processing of a water column recordings from the Kongsberg EM2040 MBES (figure 3.21).

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On the multibeam echogram, a target can be seen in the right half of the echogram and a turbulence zone in the left half of the echogram. Because of the wide beam fan, different detections are done in different parts of the ensonified water volume. The depth range of the turbulence zone exceeds the depth range of the visualized target. During the post-processing, the multibeam echogram is converted to a stacked view single beam echogram. To obtain this, all beam are combined for each ping. The visualized target, now disappeared in the turbulence zone. If the choice will be made to exclude the turbulence zone from the target detection area, this target will not be included in the target counts (figure 3.22)

Figure 3.21, taken from Echoview.: Illustration of a water column recording from the Kongsberg EM2040 MBES. In the upper half, the maximum intensity variable is visualized which is an excellent tool for determining and delineating the turbulence profile lines. The multibeam Sv pings echogram is shown in lower half. On the multibeam echogram, both a target and a turbulence zone can be seen.

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Because of the survey conditions and post-processing difficulties, no absolute fish track counts were interpreted as results. This implies that no conclusions could be made regarding density. The obtained fish track counts could only be used relatively, to compare between the different water column recordings. This way, correlations could be found with independent variables.

To analyse the effect of turbulence on the detected fish track counts, turbulence zones have to be determined and delineated. Firstly, a distinction is made between a turbulence zone and a zonation pattern. Turbulence, caused by entrained air bubbles in the surface layers of the water column, create a strong backscatter which can be seen clearly on an echogram (figure 3.23).

Figure 3.23, taken from Echoview.: Illustration of the distinction between a turbulence zone and a zonation pattern. In the left upper corner, the maximum intensity variable is visualized which is an excellent tool for determining and delineating the turbulence profile lines. The multibeam Sv pings variable is shown in the left below corner. On the right is the single target detection variable in which all detected fish tracks are visualized, including the profile lines of the different delineated zones.

Figure 3.22, taken from Echoview.: Illustration of a water column recording from the Kongsberg EM2040 MBES. In the upper left corner, the maximum intensity variable is visualized. The multibeam Sv pings echogram is shown in the lower left corner. On the right, the single target detection variable is visualized. On this visual a target is encircled, which was determined from the multibeam echogram and here included in the turbulence region.

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On the multibeam echogram, this surface turbulence is seen in the left outermost beams. Below this surface turbulence zone, no other turbulence zone is observed. After calculating all the fish tracks in the water column recording, a clear zonation pattern is seen. The lower part of the water column contains a much higher density of fish tracks than the upper part. This difference is defined by the creation of a zonation line, which divides the detected fish tracks outside of the surface turbulence zone, in two separate zones.

During the analysis of the turbulence zones and zonation patterns, a discrepancy is noticed between the sum of the relative percentages of the detected fish tracks in the different assigned zones in the water column and the total amount of detected fish tracks for the whole water column. The detected fish tracks in the turbulence zones are obtained by creating manually the turbulence lines. This is done by creating the new line variable and activate it on the echogram. Then, the profile line can be manually selecting and updated. To determine the amount of fish tracks within a certain zone, the upper and lower exclusion limit are assigned in the variable properties of the target detection variable. After this, a selection on the graph is manually assigned, in which fish tracks will be created and counted. Within a water column recording, each zone has to be analysed for amount of detected fish tracks. An error can occur when not for every process the exact same detection range is selected. This causes the total amount of detected fish tracks, calculated with the outermost exclusion lines, to variate from the sum of the detected fish tracks of the different delineated zones within these limits, while in theory this should be exactly the same.

The standard procedure in post-processing of multibeam water column recordings include the use of a seabed offset zone. This offset zone is located at a certain distance above the obtained seabed profile line. The standard offset distance in this multibeam processing template is 0.6 m. This seabed offset zone is created to avoid interference from seabed echoes with the target detection. Demersal fish are an important fish group in the BPNS. They are extensively studied and important for commercial fisheries (Mackinson et al., 2005). They live on or close to the seabed. Because of this proximity to the seabed, they can be located inside the seabed offset zone and thus be excluded from the target detection. Besides this, most demersal fish species have no swimbladder (Chapman & Sand, 1974). Fish without a swimbladder are known to have a weaker backscatter than similar sized fish with a swimbladder (Foote, 1980) and thus are more difficult to detect as fish targets. Because of the difficult detection and possible inclusion in the seabed offset zone, this post-processing method for water column recordings is poorly applicable for the detection of demersal fish species.

The fish track detection algorithm in the Echoview software package is based on certain parameters in the single target detection variable. These parameters are the minimum number of pings in one fish track, the minimum number of single targets in one fish track and the maximum gap in pings between single targets in one fish track (see Chapter 3: Echosounder data analysis- Acoustic measurements – Data post-processing – Post-processing methods – software). These parameters are entered with the default value of 3 (Situation 1). By adjusting the parameters, different conditions are set for the creation of a fish track. Changing these values gives a clear change in number of detections. The explored target properties below provide an illustration of this.

Situation 1: All parameters are set to the default value. - Minimum number of single target per track: 3 single targets - Minimum number of pings per track: 3 pings - Maximum gap between single targets per track (pings): 3 pings

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The result of the target detection in the first situation is 170 detected fish tracks (figure 3.24).

Situation 2: Both the minimum number of single targets per track and minimum number of pings per track are increased. The maximum gap between single targets per track is decreased.

- Minimum number of single target per track: 5 single targets - Minimum number of pings per track: 5 pings - Maximum gap between single targets per track (pings): 1 ping

The result of the target detection in the first situation is 110 detected fish tracks (figure 3.25).

Situation 3: The minimum number of single targets per track and the minimum number of pings per track are increased (more severely than in situation 2). The maximum gap between single targets per track is kept on the default value.

- Minimum number of single target per track: 10 single targets

Figure 3.24, taken from Echoview.: Detected fish tracks (#) in the single target detection variable.

Figure 3.25, taken from Echoview.: Detected fish tracks (#) in the single target detection variable.

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- Minimum number of pings per track: 8 pings - Maximum gap between single targets per track (pings): 3 pings

The result of the target detection in the first situation is 40 detected fish tracks (figure 3.26).

Situation 4: The minimum number of single targets per track is increased (equal to situation 3). The minimum number of pings per track is kept at the default value and the maximum gap between single targets per track is decreased (equal to situation 2).

- Minimum number of single target per track: 10 single targets - Minimum number of pings per track: 3 pings - Maximum gap between single targets per track (pings): 1 ping

The result of the target detection in the first situation is 15 detected fish tracks (figure 3.27).

Figure 3.26, taken from Echoview.: Detected fish tracks (#) in the single target detection variable.

Figure 3.27, taken from Echoview.: Detected fish tracks (#) in the single target detection variable.

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All these detections have been performed on the same ping selection of the dataset 0022_20130304_150506_SimonStevin of the 130304_ST13121 survey, collected on March 4th 2013. Increasing the number of single targets necessary to be considered as a fish track, decreased strongly the number of detected fish tracks. As for situation 1 and 2 with a single target detection property of 3 and 5 single targets, the detected number of fish tracks was respectively 170 and 110 fish tracks. When this was increased to 10, the detected number of fish tracks was respectively 40 and 15, as can be seen in situation 3 and 4. Changing the number of pings needed to establish a fish track did not show a clear correlation with the detection properties. As for situation 1 and 4, the minimal number of pings is set on 3 (the standard value), the number of detected fish tracks are respectively 170 and 15, being the two most extreme values of this comparison. When the maximum gap in pings between single targets within a fish track is changed, the detection properties were slightly changed as well. The setting in situation 1 differed only in their maximum gap in pings from situation 2. For a maximum gap of respectively 3 and 1 ping, the outcome is 170 and 110 detected fish tracks. However, it should be mentioned that this is just a brief representation of the importance of selecting the correct variable properties. For this study, no previous knowledge and data is available. For this reason, the default values were used during the post-processing of the water column recordings, collected by the Kongsberg EM2040 MBES and the BioSonics DT-X split-beam echosounder. Further exploration in these variable properties can increase the accuracy of the results from the single target detection variable. Because of these difficulties regarding the post-processing of the water column recordings, the results shouldn’t be interpreted as absolute data for density measures. Therefore, the emphasis in this thesis is put on covariance analysis to discover significant relations between the amount of detected fish tracks per 1000 m³ and the independent variables.

All the results from the post-processing depend, of course, on the assumption that the detected fish tracks are actually created by fish. This is however not easy to proof, with the current used post-processing methods. As mentioned before, a high amount of noise can be assigned to suspended seabed material or plankton for example. Fish with a swimbladder are supposed to create the strongest backscatter, because of the entrained air in the bladder which creates a strong contract to the surrounding water volume (Jørgensen, 2003). Certain plankton species, which contain lipid globules and or air bubbles captured in their external structures, will create a backscatter as well, but of a weaker strength than fish, because of their smaller size and lower entrained volume of air bubbles or lipid globules (Stanton et al., 1996). This makes that the TS of these targets should be lower than for fish. The TS threshold in the single target detection variable in Echoview was set on - 40 dB, which is already a strict threshold even for fish. It was, thus, not recommended to increase the threshold even more. Because of this, no other parameter adjustments could be done during the single target detection, to improve the target detection of the water column data. Additionally, to make a distinction between different target classes, multiple echosounder frequencies should be used simultaneously during the recording. This way, the results obtained from the different frequencies can be compared and different target classes can be assigned based on their differences in TS (John K Horne, 2000).

Echosounder tools and their demonstrations

The BioSonics DT-X split-beam water column recordings were initially examined by the use of the BioSonics Visual Acquisition DT-X post-processing software package. From this analysis, the conclusion

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is made that the free demonstration version doesn’t provide sufficient post-processing methods to obtain target counts. These can only be obtained from the visual analysis of the water column recordings. After performing this visual analysis, only 1 targets was observed which could possibly be assigned to a fish target. Due to the low target count, the BioSonics DT-X split-beam water column recordings were further processed by the use of the Echoview software package. It should be, however, mentioned that BioSonics has an optional module in the BioSonics Visual Acquisition DT-X software package, being Auto Track (BioSonics Inc., 2013b). This module is only operational after the purchase of a license. A free try-out version could have been requested but because Echoview was able to process the DT4 file format, the choice was made to perform all analysis in the same post-processing software package to maintain uniformity.

Some of the water column recordings from the Kongsberg EM2040 MBES, are stored in very large data files. For example, the water column data files recorded during the WaTuR campaign (survey ID = 131113_WaTuR) on November 13th 2013, all describe 3.8 GB per file. Data files of this size are difficult to process in post-processing software. During the execution of the processing pathway, multiple variables perform simultaneously calculations on the water column recording. Additional to this, the echogram has to be zoomed out maximally to select the whole ensonified water column, to obtain the total amount of detected fish tracks. This requires the instant processing of the single target detection variable on the whole data file. This lead in some cases to waiting times exceeding 30 minutes or a crash of the software package. The processing time of the water column recordings increases strongly, when the multibeam water column data files exceed a file size of 1.5 GB. Several water column recordings, belonging to different survey ID’s could not be post-processed by the use of the Echoview software package because of this reason.

A comparison is made between the echosounder tools, regarding the total amount of detected fish tracks in the water column recordings. The echosounder tools included in this covariance analysis are the BioSonics DT-X split-beam echosounder and the Kongsberg EM2040 MBES. From this comparison, the BioSonics DT-X split-beam echosounder appeared to detect larger amounts of detected fish tracks per 1000 m³. It shoult be, however, mentioned that the amount of data files (14 files) obtained from one survey, during the BioSonics DT-X split-beam echosounder demonstration is rather limited, compared to the 105 analysed data files obtained from the Kongsberg EM2040 MBES. This implies that the results from the covariance study should be interpreted with caution.

The BioSonics DT-X split-beam data were obtained during the demonstration of this echosounder tool. Because the demonstration of the IXBlue SeaPix 3D MBES was cancelled no data was available to include in this analysis. It would have been interesting, however, to compare the multibeam water column recordings from the Kongsberg EM2040 MBES with the water column recordings from the IXBlue SeaPix 3D MBES. This because they are both multibeam tools, which both ensonify the water column with a large array of beams. The comparison between the BioSonics DT-X split-beam water column recordings and those from the Kongsberg EM2040 MBES provide insights on the detection capabilities of both echosounder tools but are a little representative. A split-beam echosounder ensonifies a small section of the water column. In the North Sea, densities of pelagic fish are rather low, which create a larger chance for a split-beam echosounder to ensonify an accidentaly fish-free water volume, than for a multibeam echosounder with a large beam fan ensonifying a same transect. Beside this, the only way to determine the detection capabilities of the IXBlue SeaPix 3D sonar is a demonstration in the North Sea in which the echosounder tool is used under standard North Sea weather conditions and sea state.

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Conclusions

Pelagic surveys are mainly carried out in the northern and central part of the North Sea. The southern part of the North Sea, including the Belgian part (BPNS) remains rather unexplored. This creates the opportunity for the Flemish Marine Institute (VLIZ), to take up this role and gain expertise in the use of echosounder tools for fish detection in the turbulent Southern North Sea. The use of echosounder tools for fish detection in the BPNS has proven its potential, to fill the gap of pelagic knowledge in the BPNS and to contribute to the general knowledge regarding the existing fish stocks in the North Sea

One of the first problems using hydroacoustics in fisheries research is the presence of turbulence. Especially in coastal waters, turbulence is an important source of noise and can increase the surface blind zone or seabed dead zone. Real fish targets can be masked by the turbulence, within these zones. Unfortunately, this is difficult to avoid and makes hydroacoustic processing of water column data challenging. The results from the post-processing of the water column recordings showed a high variability in amount of detected fish tracks per volume unit, ranging from 1 to 13555 per 1000m³ water volume . Furthermore, it has not been proven that those detected fish tracks are in fact real fish, since no ground truthing for fish and plankton was performed. The high variability in detection capabilities by adjusting certain detection property settings in the post-processing Echoview software package only imposes more difficulties. One option to deal with turbulence is to assign turbulence zones and eliminate them from the processed water column range. This choice is, however, not unambiguously.

A difference in total amount of detected fish tracks between the water column recordings, collected on different locations in the BPNS, presumes an influence of these locations on the detection capabilities. However, because not all survey locations are represented by water column recordings from the same season, time of the day and sea conditions, they cannot be compared statistically. The difference in detection capabilities of the two sampled echosounder tools, on the other hand, appears to be not significant. This is, however, announced with care, as the representation of both echosounder tools in the total dataset was not equally divided.

Based on the explorative study of the three echosounder tools, discussed in this thesis, the IXBlue SeaPix 3D sonar proves to be the most promising echosounder system. The combination of the several stability systems which improve the resolution, the simplified in situ calibration, the opportunity to simultaneously transmit multiple swaths to increase the detection range and obtain a 3D visualization of the detected targets, creates benefits which cannot be met by the other investigated echosounder tools. These arguments should, however, still be proven by a demonstration in situ and a processing and post-processing of the obtained water column recordings.

The Kongsberg EM2040 MBES is owned by VLOOT dab and currently mounted on the RV Simon Stevin. Even though this MBES is not calibrated for water column recordings, it has proven to provide water column recordings which can be interpreted and processed by the use of post-processing software packages such as Echoview or Fledermaus (including FMMidwater). In combination with the Echoview software package, fish counts are provided by the built-in fish track variable. The output of this variable raises some concerns, however, regarding the reliability as there is a high uncertainty in the precision of the used detection parameters.

76

In general, currently developed calibrated multibeam echosounder systems, specifically designed for fisheries research seem the better choice in comparison with single and split-beam echosounders, regarding the usability in the BPNS. Low abundances of fish species demand a widening of the ensonified water volume to magnify the extent of the sampling, while the high resolution preserves the precise grain, to detect accurately different targets in the water colum.

77

Future perspectives

Technological developments within the field of hydroacoustics in fisheries research are fast growing. Compared to the echosounder tools brought on the market 10 years ago, current models have much wider and or deeper detection ranges, a higher resolution, faster ping speeds providing high-speed recordings, etc.. These improvements will continue to occur at a faster pace. Consequently, echosounder tools will become essentiel to perform accurate fish stock assessment, in order to tackle global issue of overexploitation. By improving the knowledge on the densities of these fish species, the most suitable fish quota can be advised to policy makers. By the implementation of echosounder tools in fisheries research in Flanders, more knowledge will be obtained regarding the fish stocks in the BPNS. This can be of great importance in the monitoring of certain fish species which are under pressure of past and or current commercial fisheries. Besides this, more knowledge will be obtained regarding the communitie structures in some areas which are inaccessable for classical trawl surveys, such as shipwrecks and wind turbine farms. In the expectation of the demonstration of the IXBlue SeaPix 3D sonar, a continuation of acoustics surveys with the Kongsberg EM2040 MBES can be done, to investigated the detection capabilities further into depth. As a recommendation for these surveys, a fixed protocol in which the necessary survey conditions are stated should be created. This way, the comparability of data from the different surveys will improve. For practical reasons, the time duration of the recordings should be reduced, to obtain smaller sized data files which are easier to process during the post-processing analysis. Currently, this time duration is set to a limit of 30 min, which provides datasets of a size up to 4 GB. The post-processing of these large datafiles requires strong computer systems. The Echoview post-processing software package is constantly updated to support an even wider range of echosounder tools and implement revised algorithms to improve the detection capabilities, in general. All of this, predicts a promising future for the use of echosounder tools in fisheries research in the Belgian part of the southern North Sea.

78

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Addendum

1. Data tables

1)

ECHO SOUNDER

SURVEY ID SAMPLE ID

Sample duration

(s)

Average vessel speed (kn)

Covered distance

(m)

Fan angle

(°)

Water column depth

(m)

Number of fish

tracks per 1000 m3 volume

(#) Kongsberg_EM2040

13FEB_MRU

0000_20130213_SimonStevin 76.00 12.50 488.72 140.00 10.00 9.32

Kongsberg_EM2040

13FEB_MRU

0001_20130213_SimonStevin 41.00 12.50 263.65 140.00 19.00 5.54

Kongsberg_EM2040

13FEB_MRU

0002_20130213_SimonStevin 39.00 12.50 250.79 140.00 21.00 2.38

Kongsberg_EM2040

13FEB_MRU

0003_20130213_SimonStevin 168.00 7.50 648.20 140.00 24.50 2.69

Kongsberg_EM2040

13FEB_MRU

0004_20130213_SimonStevin 141.00 7.00 507.76 140.00 25.00 4.06

Kongsberg_EM2040

13FEB_MRU

0005_20130213_SimonStevin 154.00 7.00 554.57 140.00 25.00 3.74

Kongsberg_EM2040

13FEB_MRU

0006_20130213_SimonStevin 155.00 7.00 558.17 140.00 24.50 3.30

Kongsberg_EM2040

13FEB_MRU

0007_20130213_SimonStevin 120.00 9.50 586.47 140.00 25.00 2.38

Kongsberg_EM2040

13FEB_MRU

0008_20130213_SimonStevin 188.00 6.00 580.29 140.00 25.00 2.30

Kongsberg_EM2040

13FEB_MRU

0009_20130213_SimonStevin 175.00 11.00 990.31 140.00 25.00 1.32

Kongsberg_EM2040

13FEB_OCTANS

0000_20130213_SimonStevin 188.00 6.00 580.29 140.00 25.50 1.60

Kongsberg_EM2040

13FEB_OCTANS

0001_20130213_SimonStevin 151.00 8.50 660.29 140.00 25.50 1.32

Kongsberg_EM2040

13FEB_OCTANS

0002_20130213_SimonStevin 180.00 6.00 555.60 140.00 25.50 1.60

Kongsberg_EM2040

13FEB_OCTANS

0003_20130213_SimonStevin 187.00 6.00 577.21 140.00 26.00 2.06

Kongsberg_EM2040

13FEB_OCTANS

0004_20130213_SimonStevin 192.00 6.00 592.64 140.00 26.00 2.39

Kongsberg_EM2040

13FEB_OCTANS

0005_20130213_SimonStevin 182.00 6.00 561.77 140.00 26.00 2.00

Kongsberg_EM2040

13FEB_OCTANS

0006_20130213_SimonStevin 168.00 9.00 777.84 140.00 26.00 1.28

Kongsberg_EM2040

13FEB_SIDENOISE

0000_20130213_SimonStevin 161.00 11.50 952.49 140.00 29.00 0.59

84

Kongsberg_EM2040

13FEB_SIDENOISE

0001_20130213_SimonStevin 135.00 12.00 833.40 140.00 26.00 0.33

Kongsberg_EM2040

13FEB_SIDENOISE

0002_20130213_SimonStevin 114.00 12.50 733.08 140.00 19.50 0.71

Kongsberg_EM2040

13FEB_SIDENOISE

0003_20130213_SimonStevin 109.00 12.00 672.89 140.00 19.50 2.55

Kongsberg_EM2040 120917

0000_20120917_SimonStevin 1444.00 0.50 371.43 140.00 2.00 6.73

Kongsberg_EM2040 120917

0001_20120917_SimonStevin 1168.00 1.00 600.87 140.00 5.00 1797.68

Kongsberg_EM2040 120917

0003_20120917_SimonStevin 1799.00 5.00 4627.43 140.00 25.00 10.20

Kongsberg_EM2040 120917

0004_20120917_SimonStevin 1799.00 9.00 8329.37 140.00 25.00 6.84

Kongsberg_EM2040 120917

0005_20120917_SimonStevin 1799.00 10.00 9254.86 140.00 25.00 5.46

Kongsberg_EM2040 120917

0006_20120917_SimonStevin 1799.00 10.00 9254.86 140.00 25.00 6.29

Kongsberg_EM2040 120917

0007_20120917_SimonStevin 1799.00 10.50 9717.60 140.00 25.00 4.71

Kongsberg_EM2040 120917

0009_20120917_SimonStevin 1799.00 5.00 4627.43 140.00 25.00 10.75

Kongsberg_EM2040 120917

0011_20120917_SimonStevin 1799.00 10.00 9254.86 140.00 25.00 4.14

Kongsberg_EM2040 120917

0013_20120917_SimonStevin 1799.00 9.00 8329.37 140.00 25.00 7.67

Kongsberg_EM2040 120917

0015_20120917_SimonStevin 1799.00 9.00 8329.37 140.00 25.00 4.75

Kongsberg_EM2040 120917

0017_20120917_SimonStevin 1799.00 11.00 10180.34 140.00 25.00 3.97

Kongsberg_EM2040 120917

0019_20120917_SimonStevin 1799.00 12.00 11105.83 140.00 25.00 2.47

Kongsberg_EM2040

130226_Lifewatch

0000_20130226_SimonStevin 1800.00 9.00 8334.00 140.00 25.00 0.36

Kongsberg_EM2040

130226_Lifewatch

0001_20130226_SimonStevin 1795.00 8.00 7387.42 140.00 20.00 0.75

Kongsberg_EM2040

130226_Lifewatch

0002_20130226_SimonStevin 689.00 5.00 1772.26 140.00 20.00 25.15

Kongsberg_EM2040

130304_ST13121

0004_20130304_SimonStevin 596.00 3.00 919.83 120.00 3.50 247.81

Kongsberg_EM2040

130304_ST13121

0006_20130304_SimonStevin 806.00 0.15 62.20 120.00 4.00 4558.24

85

Kongsberg_EM2040

130304_ST13121

0008_20130304_SimonStevin 1748.00 0.05 44.96 120.00 4.50 5579.31

Kongsberg_EM2040

130304_ST13121

0010_20130304_SimonStevin 305.00 0.10 15.69 120.00 4.50 466.31

Kongsberg_EM2040

130304_ST13121

0012_20130304_SimonStevin 296.00 0.10 15.23 120.00 4.50 1547.08

Kongsberg_EM2040

130304_ST13121

0014_20130304_SimonStevin 295.00 0.10 15.18 120.00 4.50 4074.19

Kongsberg_EM2040

130304_ST13121

0016_20130304_SimonStevin 317.00 0.10 16.31 120.00 4.50 5980.52

Kongsberg_EM2040

130304_ST13121

0018_20130304_SimonStevin 909.00 0.10 46.76 120.00 5.00 1254.83

Kongsberg_EM2040

130304_ST13121

0019_20130304_SimonStevin 994.00 0.05 25.57 120.00 5.00 1826.35

Kongsberg_EM2040

130304_ST13121

0020_20130304_SimonStevin 1800.00 0.10 92.60 120.00 5.50 827.70

Kongsberg_EM2040

130304_ST13121

0021_20130304_SimonStevin 1800.00 0.05 46.30 120.00 6.00 2225.21

Kongsberg_EM2040

130304_ST13121

0022_20130304_SimonStevin 1800.00 0.15 138.90 120.00 6.50 1540.63

Kongsberg_EM2040

130304_ST13121

0023_20130304_SimonStevin 1800.00 0.15 138.90 120.00 7.00 2167.12

Kongsberg_EM2040

130304_ST13121

0024_20130304_SimonStevin 1800.00 0.15 138.90 120.00 7.50 1013.40

Kongsberg_EM2040

130304_ST13121

0025_20130304_SimonStevin 1800.00 0.10 92.60 120.00 7.50 935.57

Kongsberg_EM2040

130304_ST13121

0026_20130304_SimonStevin 1800.00 0.15 138.90 120.00 7.50 462.42

Kongsberg_EM2040

130304_ST13121

0027_20130304_SimonStevin 1800.00 0.20 185.20 120.00 7.50 256.32

Kongsberg_EM2040

130304_ST13121

0028_20130304_SimonStevin 1800.00 0.15 138.90 120.00 7.00 559.30

Kongsberg_EM2040

130304_ST13121

0030_20130304_SimonStevin 1800.00 0.05 46.30 120.00 6.50 1790.33

86

Kongsberg_EM2040

130304_ST13121

0032_20130304_SimonStevin 1800.00 0.10 92.60 120.00 6.00 721.87

Kongsberg_EM2040

130304_ST13121

0034_20130304_SimonStevin 1800.00 0.10 92.60 120.00 5.00 948.07

Kongsberg_EM2040

130304_ST13121

0036_20130304_SimonStevin 1800.00 0.20 185.20 120.00 4.50 969.88

Kongsberg_EM2040

130304_ST13121

0038_20130304_SimonStevin 1800.00 0.10 92.60 120.00 4.50 1690.56

Kongsberg_EM2040

130304_ST13121

0040_20130305_SimonStevin 1800.00 0.15 138.90 120.00 4.50 1429.78

Kongsberg_EM2040

130304_ST13121

0042_20130305_SimonStevin 1800.00 0.10 92.60 120.00 5.00 2353.99

Kongsberg_EM2040

130304_ST13121

0044_20130305_SimonStevin 1800.00 0.10 92.60 120.00 5.50 2401.73

Kongsberg_EM2040

130304_ST13121

0046_20130305_SimonStevin 239.00 0.20 24.59 120.00 6.00 952.71

Kongsberg_EM2040

130304_ST13121

0048_20130305_SimonStevin 1800.00 0.10 92.60 120.00 7.00 1878.14

Kongsberg_EM2040

130304_ST13121

0050_20130305_SimonStevin 1800.00 0.15 138.90 120.00 7.50 1099.67

Kongsberg_EM2040

130304_ST13121

0052_20130305_SimonStevin 1800.00 0.05 46.30 120.00 7.50 754.58

Kongsberg_EM2040

130304_ST13121

0054_20130305_SimonStevin 1800.00 0.15 138.90 120.00 7.50 106.90

Kongsberg_EM2040

130304_ST13121

0056_20130305_SimonStevin 1800.00 0.05 46.30 120.00 7.00 1118.84

Kongsberg_EM2040

130304_ST13121

0058_20130305_SimonStevin 1800.00 0.15 138.90 120.00 6.00 360.12

Kongsberg_EM2040

130304_ST13121

0060_20130305_SimonStevin 1800.00 0.10 92.60 120.00 5.50 1341.53

Kongsberg_EM2040

130304_ST13121

0062_20130305_SimonStevin 1800.00 0.10 92.60 120.00 4.50 675.53

Kongsberg_EM2040

130304_ST13121

0064_20130305_SimonStevin 1800.00 0.15 138.90 120.00 4.00 656.43

87

Kongsberg_EM2040

130304_ST13121

0066_20130305_SimonStevin 1800.00 0.10 92.60 120.00 4.50 1151.35

Kongsberg_EM2040

130304_ST13121

0068_20130305_SimonStevin 1800.00 0.10 92.60 120.00 4.50 1759.16

Kongsberg_EM2040

130304_ST13121

0070_20130305_SimonStevin 1799.00 0.05 46.27 120.00 5.50 2750.85

Kongsberg_EM2040

130304_ST13121

0072_20130305_SimonStevin 1800.00 0.10 92.60 120.00 6.50 1057.47

Kongsberg_EM2040

130306_Circle

0000_20130306_SimonStevin 264.00 6.00 814.88 140.00 12.00 7.03

Kongsberg_EM2040

130306_Circle

0001_20130306_SimonStevin 305.00 5.50 862.98 140.00 13.00 10.98

Kongsberg_EM2040

130306_Circle

0002_20130306_SimonStevin 422.00 6.00 1302.57 140.00 13.50 7.71

Kongsberg_EM2040

130306_Circle

0003_20130306_SimonStevin 75.00 6.00 231.50 140.00 13.50 6.48

Kongsberg_EM2040

131113_WaTuR

0000_20131113_SimonStevin 1148.00 0.20 118.12 120.00 10.00 2331.78

Kongsberg_EM2040

150714_CW

0004_20140731_SimonStevin 1800.00 3.50 3241.00 120.00 28.00 1.93

Kongsberg_EM2040

data_Matthias_Baeye

0046_20121127_SimonStevin 1765.00 0.30 272.40 120.00 6.50 2167.06

Kongsberg_EM2040

data_Matthias_Baeye

0048_20121127_SimonStevin 1800.00 0.20 185.20 120.00 6.00 4304.38

Kongsberg_EM2040

data_Matthias_Baeye

0050_20121127_SimonStevin 967.00 0.15 74.62 120.00 6.00 6532.51

Kongsberg_EM2040

data_Matthias_Baeye

0052_20121127_SimonStevin 85.00 0.20 8.75 120.00 6.00 2187.52

Kongsberg_EM2040

data_Matthias_Baeye

0054_20121127_SimonStevin 1800.00 0.15 138.90 120.00 6.00 3777.06

Kongsberg_EM2040

data_Matthias_Baeye

0056_20121127_SimonStevin 1800.00 0.15 138.90 120.00 6.50 2643.74

Kongsberg_EM2040

Demonstration

0009_20140804_SimonStevin 1799.00 0.05 46.27 140.00 28.00 78.04

Kongsberg_EM2040

Demonstration

0010_20140804_SimonStevin 999.00 0.10 51.39 140.00 29.00 27.96

Kongsberg_EM2040

Demonstration

0012_20140804_SimonStevin 992.00 3.00 1530.99 140.00 30.00 0.80

Kongsberg_EM2040

Demonstration

0013_20140804_SimonStevin 992.00 3.00 1530.99 140.00 30.00 0.79

88

Kongsberg_EM2040

MB_CTM_juni2013

0002_20130626_SimonStevin 480.00 11.00 2716.27 80.00 5.00 1114.01

Kongsberg_EM2040

MB_CTM_juni2013

0006_20130626_SimonStevin 1800.00 12.00 11112.00 80.00 6.00 160.66

Kongsberg_EM2040

MB_CTM_juni2013

0008_20130626_SimonStevin 1800.00 1.00 926.00 80.00 8.00 608.58

Kongsberg_EM2040

MB_CTM_juni2013

0010_20130626_SimonStevin 486.00 1.00 250.02 80.00 8.00 1113.34

Kongsberg_EM2040

MB_CTM_juni2013

0012_20130626_SimonStevin 1800.00 0.10 92.60 80.00 8.00 13555.32

Kongsberg_EM2040

MB_CTM_juni2013

0014_20130626_SimonStevin 1089.00 12.00 6722.76 80.00 10.00 92.79

Kongsberg_EM2040

MB_CTM_juni2013

0016_20130626_SimonStevin 693.00 5.00 1782.55 120.00 8.00 301.48

Kongsberg_EM2040

MB_CTM_juni2013

0018_20130626_SimonStevin 1169.00 10.00 6013.86 120.00 8.00 108.64

Kongsberg_EM2040

Wrakken_20150821

0000_20150821_SimonStevin 1016.00 4.00 2090.70 120.00 23.00 17.99

Kongsberg_EM2040

Wrakken_20150821

0001_20150821_SimonStevin 1031.00 0.10 53.04 120.00 21.00 1329.25

Kongsberg_EM2040

Wrakken_20150821

0002_20150821_SimonStevin 941.00 0.05 24.20 120.00 21.00 2579.18

Kongsberg_EM2040

Wrakken_20150821

0004_20150821_SimonStevin 106.00 7.00 381.72 120.00 28.00 8.72

BioSonics_DT-X

BIOSONICS_08102015

20151008_075949 1.00 0.00 0.00 6.70 15.50 0.00

BioSonics_DT-X

BIOSONICS_08102015

20151008_080128 51.00 4.50 118.07 6.70 8.00 1867.29

BioSonics_DT-X

BIOSONICS_08102015

20151008_080512 1269.00 5.50 3590.57 6.70 7.50 1592.81

BioSonics_DT-X

BIOSONICS_08102015

20151008_082727 97.00 5.50 274.46 6.70 9.00 11381.95

BioSonics_DT-X

BIOSONICS_08102015

20151008_083843 94.00 6.00 290.15 6.70 8.50 10096.00

89

BioSonics_DT-X

BIOSONICS_08102015

20151008_124041 35.00 0.50 9.00 6.70 31.50 1052.99

BioSonics_DT-X

BIOSONICS_08102015

20151008_124857 27.00 0.50 6.95 6.70 31.50 546.00

BioSonics_DT-X

BIOSONICS_08102015

20151008_125351 28.00 1.00 14.40 6.70 31.00 1426.99

BioSonics_DT-X

BIOSONICS_08102015

20151008_125440 159.00 0.50 40.90 6.70 31.50 996.70

BioSonics_DT-X

BIOSONICS_08102015

20151008_125801 11.00 0.50 2.83 6.70 31.50 335.04

BioSonics_DT-X

BIOSONICS_08102015

20151008_125822 488.00 0.50 125.52 6.70 31.50 1487.78

BioSonics_DT-X

BIOSONICS_08102015

20151008_130658 118.00 1.00 60.70 6.70 31.50 733.97

BioSonics_DT-X

BIOSONICS_08102015

20151008_131035 537.00 5.00 1381.28 6.70 31.50 39.81

BioSonics_DT-X

BIOSONICS_08102015

20151008_131933 1053.00 1.00 541.71 6.70 31.00 482.44

Addendum: Table 1: Overview of all the obtained parameters from the Echoview post-processing of 105 Kongsberg EM2040 MBES water column recordings and 14 BioSonics DT-X split-beam echosounder water column recordings. From left to right the echosounder tool, survey ID, sample ID, sample duration (s), average vessel speed (kn), covered distance (m), beam fan angle (°), water column depth (m) and total amount of detected fish track per 1000 m³ are represented.

90

2)

SURVEY_ID SAMPLE _ID

Turbulence source

Total amount of fish tracks

(#)

Fish tracks in

turbulence zones (#)

Fish tracks outside

turbulence zones (#)

Turbulence caused fish tracks (%)

Real fish

tracks (%)

BIOSONICS_08102015

20151008_075949 Surface 1 1 0 0.00 100.00

BIOSONICS_08102015

20151008_080128 Surface 15 7 8 53.33 46.67

BIOSONICS_08102015

20151008_080512 Surface 342 117 225 65.79 34.21

BIOSONICS_08102015

20151008_082727 Surface 269 79 190 70.63 29.37

BIOSONICS_08102015

20151008_083843 Surface 225 74 151 67.11 32.89

BIOSONICS_08102015

20151008_124041 Surface 10 9 1 10.00 90.00

BIOSONICS_08102015

20151008_124857 Surface 4 4 0 0.00 100.00

BIOSONICS_08102015

20151008_125351 Surface 21 1 20 95.24 4.76

BIOSONICS_08102015

20151008_125440 Surface 43 33 10 23.26 76.74

BIOSONICS_08102015

20151008_125801 Surface 1 1 0 0.00 100.00

BIOSONICS_08102015

20151008_125822 Surface 197 128 69 35.03 64.97

BIOSONICS_08102015

20151008_130658 Surface 47 43 4 8.51 91.49

BIOSONICS_08102015

20151008_131035 Surface 58 33 25 43.10 56.90

BIOSONICS_08102015

20151008_131933 Surface 267 193 74 27.72 72.28

91

4)

Fish

trac

ks in

tu

rbul

ence

zone

s (#)

Fish

trac

ks o

utsi

de

turb

ulen

ce zo

nes (

#)Fi

sh tr

acks

in

uppe

r zon

e (#

)Fi

sh tr

acks

in

low

er zo

ne (#

)

ST13

121

0022

_201

3030

4_Si

mon

Stev

inbo

ttom

tu

rbul

ence

2568

212

923

1306

750

.319

50.8

8/

//

/

MB_

CTM

_jun

i13

0018

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3062

6_Si

mon

Stev

insu

rfac

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1647

184

1468

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//

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26_L

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atch

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6_09

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evi

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surf

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8885

855

3913

.431

86.7

171

548

9611

.192

8616

276

.643

7069

5

1303

06_C

ircle

0002

_201

3030

6_Si

mon

Stev

in(z

onat

ion)

7112

/69

52/

97.7

515

7953

7322

.201

9122

675

.548

3689

5

SURV

EY_I

DSA

MPL

E_ID

Fish

trac

ks in

tu

rbul

ence

zo

nes (

%)

Fish

trac

ks

(out

side

tu

rbul

ence

) in

upp

er

zone

(%)

Fish

trac

ks

outs

ide

turb

ulen

ce

zone

s (%

)

Fish

trac

ks

(out

side

tu

rbul

ence

) in

low

er

zone

(%)

Zona

tion

(out

side

turb

ulen

ce

zone

s)Tu

rbul

ence

so

urce

Tota

l am

ount

of

dete

cted

fis

h tr

acks

(#

)

Turb

ulen

ce

92

2. SAS-codes proc glm data=Multi; class SURVEY_ID ECHOSOUNDER; model Number_targets_per_1000_m3_volum = SURVEY_ID ; lsmeans SURVEY_ID; run; proc glm data=Multi; class SURVEY_ID ECHOSOUNDER; model Number_targets_per_1000_m3_volum = ECHOSOUNDER; lsmeans ECHOSOUNDER; run; proc glm data=Multi; class SURVEY_ID; model Number_targets_per_1000_m3_volum = SURVEY_ID Distance; run; proc mixed data=Multi; class ECHOSOUNDER SURVEY_ID; model Number_targets_per_1000_m3_volum = ECHOSOUNDER/solution ddfm=satterth; random SURVEY_ID; lsmeans ECHOSOUNDER; run; proc glm data=Biosonics; class Turbulence; model Detected_fish_tracks = Turbulence; run;

93

3. Figures 1)

94

2)

95