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Klaipėda University KLAIPĖDA UNIVERSITY ALEKSEJ ŠAŠKOV APPLICATION OF UNDERWATER REMOTE IMAGERY AND ACOUSTIC DATA FOR QUANTITATIVE BENTHIC BIOTOPES IDENTIFICATION, PREDICTIVE MAPPING AND BUILDING OF EXPLANATORY MODELS Doctoral dissertation Biomedical sciences, ecology and environmental sciences (03B) Klaipėda, 2014 Dissertation prepared in 2009–2014 in Klaipėda University. Supervisor: prof. habil. dr. Sergej Olenin (Klaipėda University; Biomedical Sciences, Ecology and Environmental Sciences – 03B). The dissertation will be defended at the Research Board for ecology and environmental sciences: Chairman: prof. dr. Albertas Bitinas (Klaipėda University, physical science, geology, 05P). Members: dr. Anastasija Zaiko (Klaipėda University, biomedical sciences, ecology and environmental sciences, 03B); dr. Juris Aigars (Latvian Water Ecology Institute, biomedical sciences, ecology and environmental sciences, 03B); dr. Ali Ertürk (Stambul University, biomedical sciences, ecology and environmental sciences, 03B); prof. dr. Vitalij Denisov (Klaipėda University, technological science, informatics ingineering, 07T). Opponents: habil. dr. Maria Włodarska-Kowalczuk (Oceanology Institute of Poland Academy of Science, biomedical sciences, Ecology and environmental Sciences, 03B); dr. Linas Ložys (Nature Research Centre, biomedical sciences, ecology and environmental sciences, 03B). The defence of dissertation will take place on 26th of November 2014, at 2 p.m., at the Klaipėda University Aula Magna Conference room. Address: Herkaus Manto 84, LT-92294, Klaipėda, Lithuania The summary of doctoral dissertation sent on 26th of October, 2014. The dissertation is available at the Library of the Klaipėda University. 2 Table of Content 1. INTRODUCTION ................................................................. 6 1.1 Relevance of the thesis ............................................................................ 6 1.2 Objectives and main tasks of the study ................................................. 8 1.3 Novelty of the study ................................................................................ 8 1.4 Scientific and applied significance of the results .................................. 9 1.5 Defensible statements ............................................................................. 9 1.6 Scientific approval ................................................................................ 10 1.7 Thesis structure ..................................................................................... 12 1.8 Acknowledgements ............................................................................... 12 1.9 Abbreviations ........................................................................................ 13 2 LITERATURE ANALYSIS ................................................ 14 2.1 Benthic biotopes .................................................................................... 14 2.1.1 Concept of benthic biotopes in benthic ecology and marine management.............................................................................................. 14 2.1.2 Methods used to distinguish biotopes .............................................. 15 2.2 Underwater remote sensing methods: imagery and acoustic ............ 16 2.2.1 Underwater imagery in benthic ecology .......................................... 16 2.2.2 Qualitative and quantitative approaches to the imagery analysis .... 17 2.2.3 Acoustical data in benthic ecology and associated difficulties ........ 19 3 MATERIALS AND METHODS ........................................ 21 3.1 Underwater imagery ............................................................................. 21 3.1.1 Filming procedures and data collected ............................................ 21 3.1.1.1 Baltic Sea, coastal area ............................................................. 21 3.1.1.2 Baltic Sea, offshore area .......................................................... 23 3.1.1.3 Norwegian Sea ......................................................................... 24 3.1.1.4 Benthic macrofauna samples for ground truthing .................... 25 3.1.2 Analysis of underwater imagery ...................................................... 27 3.1.2.1 Tools and software ................................................................... 27 3.1.2.2 Video samples .......................................................................... 28 3.1.2.3 Video mosaicing of underwater imagery ................................. 29 3.1.2.4 Criteria for identification of visual features ............................. 30 3.1.2.5 Absolute counts ........................................................................ 31 3.1.2.6 Benthic cover estimation approaches ....................................... 33 3.1.2.7 Data for comparison of video analysis methods ....................... 39 3.2 Acoustical methods ............................................................................... 42 3 3.2.1 Acoustical data collected ................................................................. 42 3.2.2 Analysis of acoustical data .............................................................. 44 3.3 Herring spawning grounds data collection ......................................... 47 3.4 Statistical methods ................................................................................ 51 3.4.1 Procedure of quantitative benthic biotope identification ................. 51 3.4.2 Statistical modelling ........................................................................ 54 3.5 Methods and materials summary ........................................................ 56 4. RESULTS ............................................................................ 58 4.1 Assessment of the accuracy, reliability and cost effectiveness of used video analysis methods ............................................................................... 58 4.1.1 Comparison of absolute counts and cover estimations from raw video and video mosaics .................................................................................... 58 4.1.2. Cost-effectiveness analysis of underwater imagery processing approaches ................................................................................................ 65 4.2 Quantitative identification of benthic biotopes based on underwater video ............................................................................................................. 67 4.2.1 Biotopes identified in the coastal area of the Baltic Sea .................. 67 4.2.2 Biotopes identified in the offshore area of the Baltic Sea ............... 77 4.3 Explanatory models for wind farm impact assessment on the rocky Norwegian Sea coast ................................................................................... 85 4.4 Determination of factors shaping the Baltic herring spawning grounds distribution ................................................................................... 87 4.4.1 Bottom profiles ................................................................................ 88 4.4.2 Herring spawning beds spatial modelling ........................................ 90 5. DISCUSSION ...................................................................... 95 5.1. Manual and semi-automatic methods of underwater imagery analysis: advantages and limitations ......................................................... 95 5.1.1 Using underwater imagery for quantitative assessments: what is the influence of a human error? ...................................................................... 95 5.1.2 Semi-automatic method performance: better, but some drawbacks remain ....................................................................................................... 97 5.2 How suitable is underwater video for the benthic biotope identification? .............................................................................................100 5.2.1 Particularities of benthic biotope identification from underwater video ........................................................................................................100 5.2.2 Comparison of the biotopes identified from video with existing classification systems ..............................................................................101 5.3. When underwater imagery is not enough: adding acoustical data .104 4 5.3.1 Explanatory models ........................................................................104 5.3.2 Predictive model .............................................................................106 5.4. Gaps and future perspectives .............................................................109 CONCLUSION ..................................................................... 113 REFERENCES ...................................................................... 116 TECHNICAL ANNEX ......................................................... 131 5 1. Introduction 1.1 Relevance of the thesis Remote sensing methods in recent decades play an increasingly important role in sea bed researches. In hard bottom environment and depths not reachable by SCUBA divers the remote sensing is the only practical method to obtain quantitative benthic biological data (Christie, 1983). Underwater imagery became a standard tool in benthic ecology (Solan et al., 2003), while acoustical surveys data is intensively used for sea bed mapping (McRea et al., 1999; Kostylev et al., 2001; Lurton, 2002; Brown et al., 2002, 2004a, 2004b; Pickrill & Todd, 2003; Allen et al., 2005; Riegl &
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