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Identification
of Diatoms: From Subjectivity to
Objectivity Species Identification
Discrete and Continuous Variables
Recognition, Identification,
Classification From Subjectivity to
Objectivity References Preface
Acknowledgements Contents Contributors
Part I Fundamentals 1 Overview:
Antecedents, Motivation and Necessity 1.1
Introduction 1.2 Organization of the Book
Chapters 1.3 Other Diatom-Related
Resources 1.3.1 Databases and Software
1.3.2 Journals and Reference Books 1.3.3
Conferences/Societies 1.3.4 Research
Projects 1.3.5 Diatom Collections/Catalogs
1.4 Diatom Drawings 1.5 Social
Impact/Educational Projects 1.6
Conclusions References 2 Diatom
Classifications: What Purpose Do They
Serve? 2.1 Introduction 2.2 Diatoms 2.3
Scientific Classification 2.4 Diatoms:
Classification and Identification 2.5
Artificial Diatom Classifications 2.5.1
Three Randomly Selected Identification
Guides 2.5.2 Three Non-Randomly Selected
Identification Guides 2.6 Natural Diatom
Classifications 2.6.1 Two Non-randomly
Selected “Natural” Classifications 2.7
Automatic Identification 2.8 Numbers of
Species 2.8.1 What Do We (Think We) Know?
2.8.2 What Would We Like to Know? 2.8.3
What Do We Know? 2.9 Specimens 2.10
Conclusions References 3 Diatom Taxonomy
and Identification Keys 3.1 The Value of
Taxonomic Keys for Applied Diatomology 3.2
Overview on Diatom Morphology 3.3 Diatom
Illustrations: From Drawings to Electron
Microscopy 3.4 Conclusions A.1 Annex A.1.1
Quick Guide to Common Diatom Genera in
Freshwaters References 4 Naturally and
Environmentally Driven Variations in
Diatom Morphology: Implications for
Diatom-Based Assessment of Water Quality
4.1 Teratology in Algae, with a Special
Focus on Diatoms 4.2 The Effect of
Overriding Diatom Teratology on Water
Quality Diagnosis 4.3 Intra- and
Interpopulational Variations in Diatom
Frustule Size and Shape 4.4 The Sample
Size of Type Populations: Implications for
Taxonomic Diagnoses 4.5 Conclusions
References Part II Sensing 5 Microscopic
Modalities and Illumination Techniques 5.1
Introduction 5.2 Principles and Optical
Basics in Light Microscopy 5.2.1 Light
Pathway of a Compound Microscope 5.2.2
Optical Components in General 5.2.2.1
Light Source 5.2.2.2 Condenser 5.2.2.3
Objective 5.2.2.4 Tube Lens 5.2.2.5
Eyepiece 5.3 Standard Illumination
Techniques 5.3.1 Bright-Field 5.3.2
Eccentric Oblique Bright-Field 5.3.3
Concentric Oblique Bright-Field (Circular
Oblique Lighting) 5.3.4 Dark-Field 5.3.4.1
Dark-Field Based on Peripheral Light
5.3.4.2 Dark-Field Based on Central Light
5.3.5 Rheinberg Illumination 5.3.6 Phase
Contrast 5.3.7 Polarized Light Microscopy
5.3.8 Differential Interference Contrast
5.3.9 Fluorescence Microscopy 5.3.10
Incident Light Microscopy
(Epi-illumination) 5.4 Modifications of
Standard Illumination Techniques and
Variable Multimodal Techniques 5.4.1
Apodized Phase Contrast 5.4.2 Relief Phase
Contrast 5.4.3 Aperture Reduction Phase
Contrast 5.4.4 Aperture Reduction
Dark-Field 5.4.5 Digital Dark-Field 5.4.6
Digital Phase Contrast 5.4.7 Luminance
Contrast 5.4.8 Fluorescence Luminance
Contrast 5.4.9 Variable Bright-Dark-Field
Contrast 5.4.10 Variable Phase-Dark-Field
Contrast 5.4.11 Axial Phase-Dark-Field
Contrast 5.4.12 Variable
Phase-Bright-Field Contrast 5.4.13
Variable Combinations of DIC with Phase
Contrast and Dark-Field 5.4.13.1 Variable
Interference-Phase Contrast 5.4.13.2
Variable Interference-Dark-Field Contrast
5.5 Conclusions References 6 Light
Filtering in Microscopy 6.1 Introduction
6.2 Neutral Colorless Filters 6.2.1 UV–IR
Cutters 6.2.2 Diffusers 6.2.3 Neutral Gray
and Double Polarizing Filters 6.3 Color
Modulating Filters 6.3.1 Blue “Daylight”
Filters 6.3.2 Green Filters 6.3.3 Warming
Filters for Blue LEDs 6.3.4 “Vario-Color”
and “Pol-Color” Polarizing Filters 6.3.5
Monochromatic Interference Filters 6.3.6
RGB Filter Sets (Three-Shot Techniques)
6.3.7 RGB-Intensifying Filters 6.4 LED
Versus Halogen (Bulb) Light 6.5
Conclusions References 7 Automatization
Techniques. Slide Scanning 7.1
Introduction 7.2 Materials and Methods
7.2.1 Optical and Mechanical Performance
7.3 Programmable Illumination 7.3.1 Light
Intensity Control 7.3.2 Programmable
Illumination Modes 7.4 Image Calibration
7.4.1 Usage with ImageJ 7.5 Slide Scanning
7.5.1 Platform Motorization 7.5.2
Automatic Slide Scanning 7.5.2.1
Sequential Scanning 7.5.2.2 Random
Scanning 7.5.2.3 Scanning Based on Regions
of Interest 7.5.3 Autofocusing 7.5.3.1
Criteria to Measure the Focus Level
7.5.3.2 Autofocus Strategies 7.6
Preprocessing 7.6.1 Noise Reduction 7.6.2
Background Correction 7.6.2.1 Division by
Blank Image 7.6.2.2 Division by Unfocused
Image 7.6.2.3 Division by Polynomial
Approximated Image 7.6.2.4 Division by
Rolling Ball Background Image 7.6.2.5
Usage with ImageJ 7.6.2.6 Batch Processing
7.6.3 Contrast Enhancement 7.7 Conclusions
Appendix Microscope Control Application
General Configuration Stage Control
Scanning and Processing Functions
References Part III Analysis 8
Segmentation Techniques 8.1 Introduction
8.2 Classical Methods 8.2.1 Region- and
Contour-Based Methods 8.2.1.1 Thresholding
8.2.1.2 Gradient-Based Methods 8.2.1.3
Deformable Models 8.2.2 Featured Based on
Methods 8.2.2.1 Phase Congruency 8.2.2.2
Scale and Curvature Invariant 8.2.2.3
Viola–Jones 8.3 Deep Learning Techniques
8.3.1 Neural Networks 8.3.2 Convolutional
Neural Networks 8.3.2.1 CNN Components
8.3.3 R-CNN 8.3.3.1 Post-processing 8.3.4
You Only Look Once 8.3.5 Semantic
Segmentation 8.3.6 Instance Segmentation
8.4 Conclusions References 9 Diatom
Feature Extraction and Classification 9.1
Introduction 9.2 Classification Using
Machine Learning Hand-Crafted Techniques
9.2.1 Feature Extraction 9.2.1.1
Morphological Descriptors 9.2.1.2
Statistical Descriptors 9.2.1.3 Local
Binary Patterns 9.2.1.4 Hu Moments 9.2.1.5
Log Gabor Transform 9.2.1.6 Elliptical
Fourier Descriptors 9.2.1.7 Phase
Congruency Descriptors 9.2.2 Feature
Discriminant Analysis and Dimensionality
Reduction 9.2.2.1 Correlation-Based
Feature Selection 9.2.2.2 Sequential
Forward Feature Selection 9.2.2.3
Principal Component Analysis (PCA) 9.2.2.4
Linear Discriminant Analysis (LDA) 9.2.3
Classifiers 9.2.3.1 Supervised Classifiers
9.2.3.2 Unsupervised Classifiers 9.2.4
Classification Performance 9.3
Classification Using Deep Learning
Techniques 9.3.1 Learning Process 9.3.2
Parameters 9.3.3 Insights Visualization
9.4 Diatom Classification Results 9.5
Conclusions Appendix References 10
Multifocus and Multiexposure Techniques
10.1 Introduction 10.2 Multifocus Fusion
Methods 10.2.1 Two-Scale Decomposition
(TSD) 10.2.2 Detection of a Focused Region
and Weight Map Computation 10.2.3 Weight
Map Refinement 10.2.4 Weighted Average
Fusion of BL and DL 10.3 Exposure Fusion
(EF) vs High Dynamic Range (HDR) 10.3.1
HDR and Tone-Mapping 10.3.2 Exposure
Fusion 10.4 Depth Map and 3-D Surface
Visualization of Fusion Results 10.5
Fusion Quality Metrics 10.5.1
Gradient-Based Fusion Performance (QAB/F)
10.5.2 Image Fusion Metric Based on
Spatial Frequency (QSF) 10.5.3 Average
Gradient-Based Fusion Metric (QAG) 10.5.4
Entropy-Based Fusion Metric (QH) 10.6
Efficient Implementations 10.7 Discussion
and Conclusions References 11 Stereoscopic
Imaging of Diatoms in Light and Electron
Microscopy 11.1 Introduction 11.1.1
Stereoscopy: Basic Concepts and Brief
History 11.1.2 Physical Principles of
Stereoscopy 11.1.3 Types of Stereo Images
and Viewing Techniques 11.2
Three-Dimensional Imaging in LM 11.2.1
Basic Visualization Techniques 11.2.2
Stereoscopic LM Images of Diatoms 11.3
Three-Dimensional Imaging in EM 11.3.1
Basic Visualization Techniques 11.3.2
Stereoscopic SEM Images of Diatoms 11.4
Conclusion: Role of 3D Imaging in Diatom
Research A.1 Appendix References 12
Geometric Morphometrics and the Shape of
Microscopic Organisms 12.1 Introduction
12.2 Theory of Shape and Morphospaces 12.3
Geometric Morphometrics' Tools 12.3.1
Landmark-Based Methods 12.3.2
Outline-Based Methods 12.3.3 Eigenshape
Analysis 12.3.4 Legendre Polynomials
(Orthogonal Polynomial Regression) 12.4
Image Acquisition 12.5 Visualization of
Shape Variation 12.5.1 Landmark-Based
Methods 12.5.2 Outline-Based Methods 12.6
Quantification of Shape Variation 12.7
What Information Conveys the Analysis of
Microscopic Imagery? 12.8 Conclusions
Appendix: Software Available References
Part IV Applications 13 Water Quality
Assessment 13.1 Introduction 13.2 Sampling
and Analytical Protocols 13.2.1 EU
Standards 13.2.2 Automatic Diatom
Identification 13.2.3 Diatom DNA
Metabarcoding 13.3 Distribution and
Frequency of Diatoms in the Iberian
Peninsula 13.3.1 River Typologies:
Siliceous and Calcareous 13.3.2 Reference
Conditions 13.4 Diatom-Based Bioassessment
Tools 13.4.1 European Autoecological
Indexes: SPI, TDI, Rott, and ICM
(Intercalibration Common Metric) 13.4.1.1
SPI (Specific Pollution Sensitivity Index)
13.4.1.2 TDI (Trophic Diatom Index)
13.4.1.3 Rott's Index 13.4.1.4 ICM
(Intercalibration Common Metric) 13.4.2
Diatom Indexes Developed for the Iberian
Peninsula 13.4.2.1 Multimetric Index:
MDIAT 13.4.2.2 Autoecological Index: DDI
13.4.2.3 Ecological Distance Index:
iDIAT-ES 13.4.3 Complementary Metrics
Based on Diatoms (Growth Forms, Ecological
Guilds, Teratologies) 13.5 ID-TAX:
Identification Key for Biological Quality
Elements Used in Routine Biological
Monitoring in Spain 13.6 Conclusions
References 14 Diatoms in Forensic Analysis
14.1 Introduction 14.1.1 Diatom Test in
Drowning 14.1.2 Other Applications of
Diatoms 14.1.2.1 Drowning Site 14.1.2.2
Suspects 14.1.2.3 Time of Death 14.2
Sample Preparation: A Review of Techniques
for Diatom Analysis in Forensics 14.2.1
Acid Digestion Method 14.2.2 Acid
Digestion in Disorganization Can 14.2.3
Soluene-350 Method 14.2.4 Enzymatic
Digestion 14.2.5 Membrane Filter 14.2.6
Novel Techniques 14.2.7 Suspect
Identification Methods 14.2.8 Evaluation
of Methods for Extracting Diatoms in
Tissues 14.3 Diatom Analysis 14.3.1 Diatom
Identification 14.3.2 Water Analysis
14.3.2.1 Protocols 14.4 Histological
Findings in Drowning 14.4.1 Skin
Histological Findings 14.4.2 Lung
Histological Findings 14.4.3 Muscle
Histological Findings 14.5 Discussion and
Conclusions 14.5.1 Main Controversies of
Diatom Test 14.5.1.1 False Positives
14.5.1.2 False Negatives 14.5.2
Quantitative and Qualitative Analysis
14.5.2.1 Quantitative Analysis 14.5.2.2
Qualitative Analysis 14.5.3 Conclusions
References 15 Benthic Foraminifera and
Diatoms as Ecological Indicators 15.1
Introduction to Benthic Foraminifera and
Diatoms: Basic Aspects of Biology and
Ecology 15.2 Sampling and Foraminifera
Analysis 15.3 Benthic Foraminifera and
Diatoms as Modern and Past Ecological
Indicators 15.4 Multiproxy Analysis 15.5
Conclusions and Implications Illustration
Plates of Foraminifera Glossary
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