Towards Intelligent Aquaculture - Development of an early Biological Warning System to monitor ...

176 Pages·2016·6.52 MB·English

University of the Basque Country UPV/EHU
Department of Zoology and Animal Cell Biology
Research Center for Experimental Marine Biology and
Biotechnology - Plentzia Marine Station (PiE)
Marine Environment and Resources Erasmus Mundus PhD Program
Towards Intelligent Aquaculture - Development
of an early Biological Warning System to monitor
exposure to contaminants and fish welfare: from
artificial vision to systems modelling
International PhD Thesis submitted by
HARKAITZ EGUIRAUN MARTINEZ
For the degree of
Philosophiae Doctor
Under the supervision of Prof Iciar Martinez and Dr Karmele Lopez de Ipiña.
Plentzia, December 2015
(cc)2016 HARKAITZ EGUIRAUN MARTINEZ (cc by-nc 4.0)

For Edur,
for Berta,
and for Aitite Cesar (in memoriam).
CONTENTS
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CONTENTS
Image from http://www.ehu.eus/PIE
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CONTENTS
CONTENTS
List of figures .............................................................................................................v
List of tables ............................................................................................................vii
Preface ......................................................................................................................1
Acknowledgements ...................................................................................................3
Financial support .......................................................................................................5
Abstract .....................................................................................................................7
Chapter 1. Introduction ............................................................................................11
1.1. General Context ........................................................................................13
1.2. Fish welfare and fish welfare monitoring ...................................................14
1.3. Challenges in the monitoring of chemical contaminants ...........................19
1.4. Malicious contaminants ............................................................................21
1.5. Emergent chemical contaminants .............................................................22
1.6. The need for a paradigm shift in seafood safety assurance .......................25
1.6.1. Introduction to Biological Warning Systems (BWSs) .........................26
1.7. Understanding, defining and dealing with a system ..................................27
1.8. Biological systems and fish farming ..........................................................31
1.9. Hypothesis ................................................................................................31
1.10. Objectives and contributions ....................................................................31
1.11. Ethical statements ....................................................................................32
1.12. Scientific output ........................................................................................33
1.12.1. JCR peer reviewed scientific journals .................................................33
1.12.2. Refereed published conference proceeding ......................................33
1.12.3. International conferences ..................................................................34
1.12.4. Grants................................................................................................36
Chapter 2. Research methodology ..........................................................................37
2.1. Introduction ..............................................................................................39
2.2. Research questions ...................................................................................39
2.3. Research plan ...........................................................................................40
2.3.1. Informational phase ..........................................................................40
2.3.2. Propositional phase ..........................................................................40
2.3.3. Analytical phase ................................................................................40
2.3.4. Evaluative phase ...............................................................................41
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CONTENTS
2.4. Benefits of the research plan ....................................................................41
2.5. Specific research methods used in this Thesis ..........................................42
2.5.1. Image processing ..............................................................................42
2.5.2. Cluster estimation .............................................................................43
2.5.3. Trajectory magnitude normalization by z-score .................................44
2.5.4. Fractal dimension ..............................................................................44
2.5.5. Entropy ..............................................................................................47
2.5.5.1. Shannon entropy ......................................................................48
2.5.5.2. Permutation entropy .................................................................49
2.5.6. Descriptive statistics. Mean and standard deviation .........................50
2.5.7. Boxplots ............................................................................................50
2.5.8. Curve fitting and goodness of the fit .................................................51
2.5.9. Modelling ..........................................................................................52
2.5.10. Programming ....................................................................................54
2.6. Limitations of the study ............................................................................54
2.6.1. Limitations of the research methods used .........................................54
2.6.2. Limitations of the case studies ..........................................................55
2.6.3. Limitations of the model....................................................................55
Chapter 3. State of the art .......................................................................................57
Chapter 4. Application of entropy and fractal dimension analyses to the pattern
recognition of contaminated fish responses in aquaculture ............................63
4.1. Introduction ..............................................................................................65
4.2. Materials and Methods .............................................................................66
4.2.1. Experimental cases ............................................................................66
4.2.2. Image acquisition and processing .....................................................66
4.2.3. Object detection and motion estimation ...........................................68
4.2.4. Clustering and trajectory generation .................................................70
4.3. Results and Discussion .............................................................................73
4.4. Conclusions ..............................................................................................78
Chapter 5. Variation in the Shannon entropy of the trajectory of a European seabass
(Dicentrarchus labrax) system in relation to the number of fish .....................79
5.1. Introduction ..............................................................................................81
5.2. Materials and methods .............................................................................83
5.2.1. Animals and acclimation conditions ..................................................83
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CONTENTS
5.2.2. Experimental conditions ....................................................................84
5.2.3. Experimental setup ...........................................................................85
5.2.3.1. Experiment A - Decreasing the density ......................................86
5.2.3.2. Experiment B - Increasing density .............................................86
5.2.4. Data acquisition ................................................................................87
5.2.5. Image processing ..............................................................................87
5.2.6. Trajectory Estimation ........................................................................88
5.2.7. Non Linear Trajectory Analysis ..........................................................89
5.3. Results ......................................................................................................89
5.3.1. Experiment A .....................................................................................89
5.3.2. Experiment B .....................................................................................89
5.4. Discussion ................................................................................................94
Chapter 6. Application of the tool to an experimental case: variation of the Shannon
entropy in a European seabass (Dicentrarchus labrax) system exposed to
sodium selenite (Na2SeO3) and/or methylmercury chloride (CH3ClHg) ..........97
6.1. Introduction ..............................................................................................99
6.2. Phase A - Na2SO3 exposure ....................................................................100
6.2.1. Biological material and water/environmental conditions ................100
6.2.2. Experimental setup and exposure to Na2SeO3 ......................................101
6.2.3. Image acquisition, processing, trajectory estimation and non linear
trajectory analysis ..........................................................................................101
6.2.4. Results and Discussion ....................................................................101
6.3. Phase B - Exposure to MeHg ...................................................................104
6.3.1. Biological material, water/environmental conditions, experimental
setup and exposure to MeHg .........................................................................104
6.3.2. Results and discussion ....................................................................104
6.4. Phase C - Recovery period ......................................................................105
6.4.1. Biological material, water/environmental conditions, image acquisition,
processing, trajectory estimation and non linear trajectory analysis ..............105
6.4.2. Results and discussion ....................................................................105
6.5. Overall conclusion...................................................................................109
Chapter 7. Modelling .............................................................................................111
7.1. Introduction ............................................................................................113
7.2. Parameters of the model .........................................................................113
7.3. Construction of the model .......................................................................114
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7.3.1. Basal-state reference sub-models ...................................................116
7.3.2. Response to the stochastic event reference sub-models .................118
7.3.3. Basal/Event response reference sub-models ..................................120
7.4. Integrated model ....................................................................................122
7.5. Discussion ..............................................................................................125
Chapter 8. General discussion, Conclusions, Thesis and Future prospects ..........127
8.1. General discussion ..................................................................................129
8.2. Conclusions ............................................................................................132
8.3. Thesis .....................................................................................................133
8.4. Future prospects .....................................................................................133
Laburpena..............................................................................................................135
Bibliography ..........................................................................................................143
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