Imaging marine life: macrophotography and microscopy approaches for marine biology
Gespeichert in:
| Format: | Buch |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
Weinheim
Wiley-VCH
2014
|
| Schlagworte: | |
| Online-Zugang: | Inhaltstext Inhaltsverzeichnis |
| Beschreibung: | Literaturangaben |
| Beschreibung: | XXI, 253 S. zahlr. Ill., graph. Darst., Kt. |
| ISBN: | 3527327444 9783527327447 |
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Datensatz im Suchindex
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CONTENTS
PREFACE
XIII
LIST OF CONTRIBUTORS
XVII
1 UNDER THE EYE OF NEPTUNE: AN HISTORICAL PERSPECTIVE OF MARINE
CREATURE IMAGERY 3
EMMANUEL G. REYNAUD
1.1 INTRODUCTION 3
1.2 ANCIENT USES OF THE OCEANS 5
1.2.1 SEAFARERS 5
1.2.2 THE MEDITERRANEAN SEA: THE CRADLE OF MARINE BIOLOGY 6
1.2.2.1 ARISTOTLE AND PLINY THE ELDER, THE FOUNDING FATHERS 6
1.2.2.2 UNDERSTANDING THE OCEANS 7
1.3 FROM NEPTUNE TO ANIMALCULES 8
1.3.1 AGE OF EUROPEAN DISCOVERY AND EXPLORATION 8
1.3.2 VOYAGES OF EXPLORATION AND FINALLY SCIENCE 9
1.3.3 A GLIMPSE AT THE INVISIBLE 9
1.4 THE BIRTH OF OCEANOGRAPHY (THE NINETEENTH CENTURY) 10
1.4.1 DRAWING THE JELLYFISH 10
1.4.2 THE H.M.S. CHALLENGER EXPEDITION 11
1.4.3 STATIONS AND INSTITUTIONS 14
1.5 THE TWENTIETH CENTURY: INSTITUTIONS AND MOVING IMAGES 15
1.5.1 NEW TOOLS - NEW IMAGES: 15
1.5.2 JEAN PAINLEVE 16
1.5.3 THE WRITERS AND THE EXPLORERS 16
1.5.4 THE FUTURE 18
1.6 TIME LINE OF OCEAN IMAGERY 18
FURTHER READING 20
BASIC TEXTS 20
SOURCE BOOKS 20
SHIPS AND EXPEDITIONS 21
INSTITUTIONS 21
HTTP://D-NB.INFO/1034510789
VII
CONTENTS
2 NEW SOLUTIONS IN UNDERWATER IMAGING AND VISION SYSTEMS 23
FRANCISCO BONIN-FONT, ANTONI BURGUERA, AND GABRIEL OLIVER
2.1 INTRODUCTION 23
2.2 UNDERWATER OPTICAL IMAGE FORMATION 25
2.3 ILLUMINATION TECHNIQUES 27
2.3.1 ILLUMINATION SOURCES 27
2.3.2 SELECTION OF THE LIGHT SOURCE POSITION 28
2.3.3 ILLUMINATING SYSTEMS 30
2.4 LASER-BASED TECHNIQUES 32
2.4.1 LASER RANGE-GATING (LRG) METHODS 32
2.4.2 LASER LINE SCAN (LLS) METHODS 33
2.4.3 SCATTERED LIGHT REJECTION USING MODULATION/DEMODULATION
TECHNIQUES 33
2.5 UNDERWATER IMAGING INFRASTRUCTURES 34
2.6 IMAGE IMPROVEMENT VIA POLARIZATION 35
2.6.1 EXTENDED RANGE USING POLARIZATION 36
2.6.2 HOUSING 36
2.6.3 EXPERIMENTAL EVALUATION 37
2.7 A VISION SYSTEM FOR UNDERWATER APPLICATIONS 39
2.7.1 THE FUGU VISION SYSTEM 40
2.8 CONCLUSION 42
ACKNOWLEDGEMENTS 44
REFERENCES 44
3 HOLOGRAPHIC MICROSCOPY OF MARINE ORGANISMS 49
STEFAN K. JERICHO, MANFRED H. JERICHO, AND HANS J. KREUZER
3.1 INTRODUCTION 49
3.2 ADVANTAGES OF HOLOGRAPHIC MICROSCOPY 50
3.3 PAST ATTEMPTS TO IMAGE MICROPLANKTON 51
3.4 POINT SOURCE DIGITAL IN-LINE HOLOGRAPHIC MICROSCOPY 54
3.4.1 INSTRUMENTS 55
3.4.2 IMAGE RECONSTRUCTION 56
3.4.3 IMAGE EXAMPLES 58
3.4.4 RESOLUTION 60
3.4.5 VOLUME IMAGING CHALLENGES 63
3.5 FUTURE OUTLOOK 64
REFERENCES 65
4 CONFOCAL LASER SCANNING MICROSCOPY - DETAILED THREE-DIMENSIONAL
MORPHOLOGICAL IMAGING OF MARINE ORGANISMS 69
JAN MICHELS
4.1 INTRODUCTION 69
4.2 TECHNICAL AND METHODOLOGICAL ASPECTS OF CONFOCAL LASER SCANNING
MICROSCOPY 69
CONTENTS I VII
4.3 PREREQUISITES FOR GENERATING HIGH-QUALITY CONFOCAL LASER SCANNING
MICROGRAPHS 73
4.4 USING AUTOFLUORESCENCES FOR DETAILED THREE-DIMENSIONAL
MORPHOLOGICAL IMAGING 76
4.5 APPLICATION OF FLUORESCENCE DYES 80
4.6 SURFACE TOPOGRAPHY ANALYSES 85
4.7 FUTURE PERSPECTIVES
88
ACKNOWLEDGEMENTS 89
REFERENCES 89
5 OPTICAL PROJECTION TOMOGRAPHY 93
KARL GAFF, LUKE MCCORMAC PARKER, DEE LAWLOR, AND
EMMANUEL G. REYNAUD
5.1 INTRODUCTION 93
5.2 WHAT IS OPTICAL PROJECTION TOMOGRAPHY? 94
5.2.1 ASSEMBLY OF AN OPT SYSTEM 98
5.2.1.1 DETECTION UNIT 98
5.2.1.2 ILLUMINATION UNITS 98
5.2.1.3 SAMPLE MANIPULATION UNIT 98
5.2.2 ILLUMINATION SOURCES 99
5.2.3 SYSTEM CAPABILITIES AND LIMITATIONS 99
5.3 COMPARISON WITH OTHER 3D MICROSCOPY TECHNIQUES 100
5.3.1 CONFOCAL MICROSCOPY 101
5.3.2 TWO-PHOTON MICROSCOPY 102
5.4 SAMPLE PREPARATION 102
5.5 IMAGE PROCESSING AND ANALYSIS 104
5.6 MARINE BIOLOGY APPLICATIONS 104
ACKNOWLEDGMENTS 108
REFERENCES 108
6 ELECTRON MICROSCOPY TECHNIQUES FOR IMAGING MARINE
PHYTOPLANKTON 111
GUSTAAF HALLEGRAEFF
6.1 INTRODUCTION 111
6.2 COLLECTING AND PROCESSING SPECIMENS 112
6.3 LIGHT MICROSCOPY 113
6.4 SEDIMENT CYST SURVEYS 113
6.5 TRANSMISSION ELECTRON MICROSCOPY 114
6.6 SCANNING ELECTRON MICROSCOPY 116
ACKNOWLEDGEMENTS 121
REFERENCES 121
VIII
| CONTENTS
7 LOOKING INSIDE MARINE ORGANISMS WITH MAGNETIC RESONANCE AND X-RAY
IMAGING 123
IRENE ZANETTE, GHEYLEN DAGHFOUS, TIMM WEITKAMP, BRIGITTE GILLET,
DOMINIQUE ADRIAENS, MAX LUNGER, PETER CLOETENS, LUKAS HELFEN,
ALBERTO BRAVIN, FRANQOISE PEYRIN, TILO BAUMBACH, JEAN-MICHEL DISCHLER,
DENIS VAN LOO, TOMAS PRAET, MARIE POIRIER-QUINOT, AND RENAUD BOISTEL
7.1 INTRODUCTION 123
7.2 MAGNETIC RESONANCE IMAGING 124
7.2.1 EXPERIMENTAL SETUP 124
7.2.2 HARDWARE IMPROVEMENTS 128
7.2.3 CONTRAST 128
7.2.4 APPLICATIONS 129
7.2.4.1 ANATOMICAL MRI 129
7.2.4.2 FUNCTIONAL MRI 129
7.2.4.3 DIFFUSION TENSOR IMAGING OR DIFFUSION MRI (DTI) 129
7.2.4.4 MEMRI OR MANGANESE-ENHANCED MAGNETIC RESONANCE
IMAGING 131
7.3 X-RAY MICROTOMOGRAPHY 132
7.3.1 SOURCES 133
7.3.1.1 LABORATORY-BASED SETUPS 133
7.3.1.2 SYNCHROTRON-BASED SETUPS 135
7.3.2 SAMPLE STAGE 138
7.3.3 DETECTOR 138
7.3.4 FORWARD PROBLEM (CONTRAST FORMATION) 140
7.3.5 TOMOGRAPHIC RECONSTRUCTION 142
7.3.5.1 2D FILTERED BACK-PROJECTION 142
7.3.5.2 IMAGE QUALITY AND ARTIFACTS 144
7.3.5.3 3D IMAGE RECONSTRUCTION 145
7.4 SYNCHROTRON LAMINOGRAPHY 146
7.4.1 INTRODUCTION 146
7.4.2 IMAGE RECONSTRUCTION 149
7.4.3 EXAMPLE APPLICATIONS 151
7.5 ABSORPTION IMAGING 151
7.5.1 NATURAL CONTRAST 151
7.5.2 STAINING CONTRAST 152
7.6 PHASE-CONTRAST IMAGING 155
7.6.1 INTRODUCTION 155
7.6.2 FREE-SPACE PROPAGATION METHODS (HOLOTOMOGRAPHY) 157
7.6.3 ANALYZER-BASED IMAGING 160
7.6.3.1 APPLICATIONS 161
7.6.4 X-RAY GRATING INTERFEROMETRY 162
7.6.4.1 INTRODUCTION 162
7.6.4.2 PERFORMANCE CHARACTERISTICS AND APPLICATIONS 165
7.7 APPLICATIONS (POST-TREATMENT) 166
7.7.1 SEGMENTATION - VISUALIZATION METHODS 166
CONTENTS
IIX
7.7.1.1 MAIN VISUALIZATION METHODS 167
7.7.1.2 CLASSIFICATION AND SEGMENTATION 170
7.7.2 NUMERIC SIMULATION - TESTING HYPOTHESES ON ADAPTIVE EVOLUTION IN
MARINE VERTEBRATES USING 3D IMAGING TOOLS 172
7.8 CONCLUSION 173
ACKNOWLEDGEMENTS 175
REFERENCES 175
8 IMAGING MARINE LIFE WITH A THIN LIGHT-SHEET 187
J6R6MIE CAPOULADE, EMMANUEL C. REYNAUD, AND
MALTE WACHSMUTH
8.1 INTRODUCTION 187
8.2 FLUORESCENCE MICROSCOPY METHODS 188
8.2.1 FLUORESCENCE 188
8.2.2 EPI-FLUORESCENCE WIDE-FIELD MICROSCOPY 189
8.2.3 CONFOCAL LASER SCANNING FLUORESCENCE MICROSCOPY 191
8.2.4 OTHER APPROACHES FOR OPTICAL SECTIONING 191
8.3 LIGHT-SHEET FLUORESCENCE MICROSCOPY 192
8.3.1 CONCEPT 192
8.3.2 IMPLEMENTATIONS AND INSTRUMENTS 193
8.3.2.1 ILLUMINATION UNIT 194
8.3.2.2 DETECTION UNIT 194
8.3.2.3 SAMPLE CHAMBER AND MOVEMENT UNIT 195
8.3.3 SPATIAL RESOLUTION 196
8.3.4 SAMPLE MOUNTING 196
8.3.5 UPRIGHT LSFM: AN ALTERNATIVE CONFIGURATION WITH SIMPLIFIED SAMPLE
MOUNTING 197
8.4 ADVANTAGES OF LSFM 198
8.5 HOW TO IMPROVE LSFM IMAGING 200
8.6 DIFFERENT WAYS TO GENERATE A LIGHT-SHEET 201
8.6.1 DIGITAL SCANNED LIGHT-SHEET MICROSCOPE 201
8.6.2 INCOHERENT STRUCTURED ILLUMINATION 201
8.6.3 TWO-PHOTON EXCITATION 202
8.6.4 BESSEL BEAMS 203
8.7 APPLICATION EXAMPLES 203
8.8 LSFM COMBINED WITH OTHER FLUORESCENCE TECHNIQUES 204
8.9 LIGHT-SHEET FLUORESCENCE MICROSCOPY FOR MARINE BIOLOGY 204
8.10 SUMMARY AND OUTLOOK 206
REFERENCES 207
9 EX-SITU MACRO PHOTOGRAPHY OF MARINE LIFE 211
MATTIAS ORMESTAD, ALDINE AMIEL, AND ERIC ROTTINGER
9.1 INTRODUCTION 211
9.2 THE EXPOSURE 213
X
I
CONTENTS
9.2.1 SHUTTER SPEED 213
9.2.2 APERTURE 215
9.2.3 ISO VALUE 215
9.2.4 DEPTH OF FIELD (DOF) 216
9.2.5 CAMERA SETTINGS 217
9.2.6 WHAT IS A GOOD EXPOSURE? 217
9.3 USING FLASHES 220
9.3.1 CONTROLLING EXPOSURE 220
9.3.2 POSITIONING AND SHAPING THE LIGHT 220
9.4 EQUIPMENT 222
9.4.1 CAMERA 222
9.4.2 LENSES 222
9.4.3 FLASHES 223
9.4.4 FLASH ACCESSORIES AND LIGHTING GEAR 224
9.4.5 AQUARIUM SETUP 224
9.4.6 OTHER ACCESSORIES 225
9.5 MACRO PHOTOGRAPHY OF MARINE LIFE 226
9.5.1 SETTING UP THE CAMERA 226
9.5.2 POSITIONING THE FLASHES 227
9.5.2.1 LIGHTING SMALL ANIMALS 227
9.5.2.2 LIGHTING BIGGER ANIMALS 228
9.5.2.3 WATER QUALITY 228
9.6 AFTER THE PHOTOGRAPHIC SHOOT 228
9.6.1 FILE FORMATS 229
9.6.2 POST-PROCESSING WORKFLOW 230
9.6.3 SELECTING IMAGES 231
9.7 ANIMAL CARE 232
9.7.1 COLLECTING 232
9.7.2 HANDLING AND IMAGING 232
ACKNOWLEDGEMENTS 233
REFERENCES 233
10 AUTOMATED IMAGE PROCESSING IN MARINE BIOLOGY 235
ROBERT T. KELLY, MAUREEN A. WILLIAMS, AND EMMANUEL G. REYNAUD
10.1 INTRODUCTION 235
10.2 METHODS OF PLANKTONIC COMMUNITY ANALYSIS 236
10.2.1 GENERAL METHODS 236
10.2.2 SEMI-AUTOMATED OPTIONS 237
10.3 SEMI-AUTOMATED PLANKTONIC COMMUNITY ANALYSIS 238
10.3.1 WORK FLOW OF ANALYSIS 238
10.3.1.1 SAMPLE COLLECTION 239
10.3.1.2 IMAGE CAPTURE 239
10.3.1.3 IMPORTATION AND SEGMENTATION 240
10.3.1.4 CLASSIFIER GENERATION 241
CONTENTS | XI
10.3.1.5 CLASSIFICATION 243
10.4 FUTURE DIRECTIONS 245
10.5 CONCLUSION 245
REFERENCES 246
INDEX 249 |
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| spelling | Imaging marine life macrophotography and microscopy approaches for marine biology ed. by Emmanuel G. Reynaud Weinheim Wiley-VCH 2014 XXI, 253 S. zahlr. Ill., graph. Darst., Kt. txt rdacontent n rdamedia nc rdacarrier Literaturangaben Bildgebendes Verfahren (DE-588)4006617-4 gnd rswk-swf Meeresbiologie (DE-588)4169246-9 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Meeresbiologie (DE-588)4169246-9 s Bildgebendes Verfahren (DE-588)4006617-4 s DE-604 Reynaud, Emmanuel G. Sonstige (DE-588)1046682873 oth text/html http://deposit.dnb.de/cgi-bin/dokserv?id=4329619&prov=M&dok_var=1&dok_ext=htm Inhaltstext DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=027078697&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Imaging marine life macrophotography and microscopy approaches for marine biology Bildgebendes Verfahren (DE-588)4006617-4 gnd Meeresbiologie (DE-588)4169246-9 gnd |
| subject_GND | (DE-588)4006617-4 (DE-588)4169246-9 (DE-588)4143413-4 |
| title | Imaging marine life macrophotography and microscopy approaches for marine biology |
| title_auth | Imaging marine life macrophotography and microscopy approaches for marine biology |
| title_exact_search | Imaging marine life macrophotography and microscopy approaches for marine biology |
| title_full | Imaging marine life macrophotography and microscopy approaches for marine biology ed. by Emmanuel G. Reynaud |
| title_fullStr | Imaging marine life macrophotography and microscopy approaches for marine biology ed. by Emmanuel G. Reynaud |
| title_full_unstemmed | Imaging marine life macrophotography and microscopy approaches for marine biology ed. by Emmanuel G. Reynaud |
| title_short | Imaging marine life |
| title_sort | imaging marine life macrophotography and microscopy approaches for marine biology |
| title_sub | macrophotography and microscopy approaches for marine biology |
| topic | Bildgebendes Verfahren (DE-588)4006617-4 gnd Meeresbiologie (DE-588)4169246-9 gnd |
| topic_facet | Bildgebendes Verfahren Meeresbiologie Aufsatzsammlung |
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