|
1 Overview of the Fish4Knowledge Project |
|
|
1 | (18) |
|
|
|
|
|
1 | (2) |
|
1.2 A Quick Tour of the Project |
|
|
3 | (7) |
|
1.3 Background Information About the Studied Marine Environments |
|
|
10 | (4) |
|
1.4 Project Context, Objectives and Achievements |
|
|
14 | (1) |
|
|
15 | (1) |
|
|
16 | (3) |
|
|
16 | (3) |
|
|
19 | (12) |
|
|
|
|
19 | (1) |
|
2.2 Information Needs for Ecology Research on Fish Populations |
|
|
20 | (2) |
|
2.3 Data Collection Techniques |
|
|
22 | (3) |
|
|
25 | (2) |
|
2.5 Uncertainty Factors Impacting the Potential Biases |
|
|
27 | (2) |
|
|
29 | (2) |
|
|
29 | (2) |
|
3 Supercomputing Resources |
|
|
31 | (10) |
|
|
|
|
|
|
31 | (2) |
|
3.2 Computational Platform |
|
|
33 | (1) |
|
3.2.1 Supercomputing Platform |
|
|
33 | (1) |
|
3.2.2 The Virtual Machine Cluster Platform |
|
|
34 | (1) |
|
3.3 Process Execution Interface |
|
|
34 | (4) |
|
3.3.1 Distributed Resource Management System |
|
|
35 | (3) |
|
|
38 | (3) |
|
|
39 | (2) |
|
4 Marine Video Data Capture and Storage |
|
|
41 | (10) |
|
|
|
|
|
41 | (1) |
|
4.2 Enhanced Video Capturing System |
|
|
42 | (2) |
|
4.2.1 Better Video Server Management |
|
|
42 | (1) |
|
|
43 | (1) |
|
4.3 Massive Storage System |
|
|
44 | (1) |
|
4.3.1 Assembly of Storage Drives |
|
|
45 | (1) |
|
4.4 Improvement of Data Retrieval Efficiency |
|
|
45 | (5) |
|
4.4.1 Universally Unique Identifier |
|
|
46 | (2) |
|
|
48 | (2) |
|
|
50 | (1) |
|
|
50 | (1) |
|
5 Logical Data Resource Storage |
|
|
51 | (8) |
|
|
|
51 | (2) |
|
|
53 | (2) |
|
|
53 | (1) |
|
|
54 | (1) |
|
|
54 | (1) |
|
|
55 | (2) |
|
|
57 | (2) |
|
|
57 | (2) |
|
6 Software Architecture with Flexibility for the Data-Intensive Fish4Knowledge Project |
|
|
59 | (14) |
|
|
|
59 | (2) |
|
|
61 | (3) |
|
6.2.1 Grand Design of Interaction |
|
|
61 | (1) |
|
6.2.2 Problem Verification of the Grand Design |
|
|
61 | (1) |
|
6.2.3 Practical Issues in Design Concerning the Database... |
|
|
62 | (1) |
|
6.2.4 Software Components Within the Fish4Knowledge Project |
|
|
62 | (2) |
|
6.3 Individual Software Components and Their Relations |
|
|
64 | (3) |
|
6.3.1 Fish Detection/Tracking Component |
|
|
64 | (1) |
|
|
64 | (1) |
|
|
65 | (1) |
|
|
65 | (1) |
|
|
65 | (1) |
|
|
66 | (1) |
|
6.3.7 Final Overview of the System |
|
|
66 | (1) |
|
6.4 Software Development Process Given the Architecture |
|
|
67 | (2) |
|
6.4.1 First Prototype System |
|
|
67 | (1) |
|
|
68 | (1) |
|
6.4.3 Data Processing Status |
|
|
68 | (1) |
|
6.5 Lessons Learned with Current Architecture |
|
|
69 | (2) |
|
6.5.1 Database Definitions |
|
|
69 | (1) |
|
|
70 | (1) |
|
|
70 | (1) |
|
|
71 | (2) |
|
|
71 | (2) |
|
7 Fish4Knowledge Database Structure, Creating and Sharing Scientific Data |
|
|
73 | (10) |
|
|
|
73 | (1) |
|
7.2 Relational Datastore Schema |
|
|
74 | (2) |
|
|
76 | (2) |
|
7.3.1 Direct Mapping to RDF |
|
|
76 | (1) |
|
7.3.2 Taiwanese Coral Reef Fish Taxonomy in SKOS |
|
|
77 | (1) |
|
7.3.3 Interlinking and Alternative Representations of Direct Mapping Data |
|
|
78 | (1) |
|
7.4 Current Accessibility of Data |
|
|
78 | (3) |
|
7.5 Data Usage and Future Possibilities |
|
|
81 | (1) |
|
|
82 | (1) |
|
|
82 | (1) |
|
8 Intelligent Workflow Management for Fish4Knowledge Using the SWELL System |
|
|
83 | (20) |
|
|
|
|
|
83 | (1) |
|
|
84 | (10) |
|
|
86 | (2) |
|
|
88 | (2) |
|
8.2.3 Workflow Evaluation |
|
|
90 | (4) |
|
8.3 F4K Domain Ontologies |
|
|
94 | (7) |
|
|
95 | (2) |
|
8.3.2 Video Description Ontology |
|
|
97 | (1) |
|
8.3.3 Capability Ontology |
|
|
98 | (3) |
|
|
101 | (2) |
|
|
101 | (2) |
|
|
103 | (20) |
|
|
|
|
|
103 | (2) |
|
|
105 | (2) |
|
9.3 The Fish Detection Approaches |
|
|
107 | (5) |
|
|
107 | (2) |
|
9.3.2 A Texton-Based Kernel Density Estimation for Video Object Segmentation |
|
|
109 | (3) |
|
9.4 Improving Detection Performance |
|
|
112 | (4) |
|
9.4.1 Perceptual Organization Model Features |
|
|
113 | (1) |
|
|
113 | (3) |
|
|
116 | (4) |
|
9.5.1 Fish Segmentation in Underwater Videos |
|
|
116 | (4) |
|
|
120 | (1) |
|
|
120 | (3) |
|
|
121 | (2) |
|
|
123 | (18) |
|
|
|
|
|
123 | (1) |
|
10.2 Literature on Fish Tracking |
|
|
124 | (1) |
|
10.3 Underwater Object Tracking |
|
|
125 | (2) |
|
10.4 Tracking with Covariance Modeling |
|
|
127 | (5) |
|
10.4.1 Covariance-Based Tracker (COV) |
|
|
127 | (3) |
|
10.4.2 Covariance-Based Particle Filter (COVPF) |
|
|
130 | (2) |
|
10.5 Assessing Tracking Quality Online |
|
|
132 | (3) |
|
|
135 | (3) |
|
|
138 | (3) |
|
|
139 | (2) |
|
11 Hierarchical Classification System with Reject Option for Live Fish Recognition |
|
|
141 | (20) |
|
|
|
141 | (2) |
|
|
143 | (1) |
|
|
144 | (3) |
|
11.3.1 Image Pre-processing |
|
|
144 | (2) |
|
11.3.2 Feature Extraction |
|
|
146 | (1) |
|
|
147 | (5) |
|
11.4.1 The Balance Guaranteed Optimized Tree Method |
|
|
148 | (2) |
|
11.4.2 Trajectory Voting Method |
|
|
150 | (1) |
|
11.4.3 Gaussian Mixture Model For Reject Option |
|
|
150 | (2) |
|
11.5 Fish Recognition Experiments |
|
|
152 | (4) |
|
11.5.1 Fish Recognition Experiments Using Ground Truth Data |
|
|
152 | (3) |
|
11.5.2 BGOTR Application to New Real Fish Videos |
|
|
155 | (1) |
|
|
156 | (5) |
|
|
157 | (4) |
|
12 Fish Behavior Analysis |
|
|
161 | (20) |
|
|
|
161 | (1) |
|
12.2 Problem Description, Definitions and Challenges |
|
|
162 | (1) |
|
12.3 Literature Review on Fish Behavior Understanding |
|
|
163 | (1) |
|
|
164 | (13) |
|
12.4.1 A Rule Based Method for Filtering Normal Fish Trajectories |
|
|
164 | (2) |
|
12.4.2 Detecting Unusual Fish Trajectories Using Clustered and Labeled Data: Flat Classifier |
|
|
166 | (4) |
|
12.4.3 Detecting Unusual Fish Trajectories Using Hierarchical Decomposition |
|
|
170 | (4) |
|
12.4.4 Experiments and Results |
|
|
174 | (3) |
|
|
177 | (4) |
|
|
177 | (4) |
|
13 Understanding Uncertainty Issues in the Exploration of Fish Counts |
|
|
181 | (26) |
|
|
|
|
181 | (1) |
|
13.2 Evaluating Uncertainty Due to Computer Vision Algorithms |
|
|
182 | (6) |
|
13.3 Visualizing Uncertainty Due to Computer Vision Algorithms |
|
|
188 | (7) |
|
13.3.1 Usability Issues with Computer Vision Evaluations |
|
|
189 | (1) |
|
13.3.2 Preliminary User Study |
|
|
190 | (1) |
|
13.3.3 Visualization Design for Non-expert Users |
|
|
191 | (4) |
|
13.4 Evaluating Uncertainty Due to In-Situ System Deployment |
|
|
195 | (4) |
|
13.5 Visualizing Uncertainty Due to In-Situ System Deployment |
|
|
199 | (3) |
|
13.6 Uncertainty Due to both Computer Vision Algorithms and In-Situ Deployment |
|
|
202 | (2) |
|
|
204 | (3) |
|
|
205 | (2) |
|
14 Data Groundtruthing and Crowdsourcing |
|
|
207 | (22) |
|
|
|
|
|
|
207 | (1) |
|
14.2 Ground Truth for Fish Detection and Tracking |
|
|
208 | (7) |
|
14.2.1 Generating High Quality Annotations Using Collaborative Efforts |
|
|
208 | (4) |
|
14.2.2 Experimental Results |
|
|
212 | (2) |
|
|
214 | (1) |
|
14.3 A Cluster-Based Approach to Fish Recognition |
|
|
215 | (5) |
|
|
215 | (1) |
|
14.3.2 Ground-Truth Annotation Using Automatic Clustering |
|
|
215 | (3) |
|
|
218 | (2) |
|
|
220 | (1) |
|
14.4 Do You Need Experts in the Crowd? A Case Study in Fish Species Verification |
|
|
220 | (6) |
|
|
222 | (2) |
|
14.4.2 Results and Discussion |
|
|
224 | (2) |
|
|
226 | (3) |
|
|
226 | (3) |
|
15 Counting on Uncertainty: Obtaining Fish Counts from Machine Learning Decisions |
|
|
229 | (10) |
|
|
|
229 | (1) |
|
|
230 | (1) |
|
15.3 Method for Estimation of Counts Based on Similarity Scores of a Classifier |
|
|
231 | (3) |
|
|
231 | (1) |
|
15.3.2 Normal Classification Process |
|
|
231 | (1) |
|
15.3.3 Estimating Counts Based on Logistic Regression |
|
|
232 | (1) |
|
15.3.4 Limitation in Estimations |
|
|
233 | (1) |
|
15.4 Counting Fish with Logistic Regression |
|
|
234 | (3) |
|
15.4.1 Experimental Datasets for Counting Fish |
|
|
234 | (1) |
|
15.4.2 Results of Counting Fish with and Without Logistic Regression |
|
|
235 | (2) |
|
|
237 | (1) |
|
|
237 | (2) |
|
|
238 | (1) |
|
16 Experiments with the Full Fish4Knowledge Dataset |
|
|
239 | (22) |
|
|
|
239 | (1) |
|
|
240 | (4) |
|
16.3 Statistics of the Dataset |
|
|
244 | (13) |
|
|
257 | (1) |
|
|
258 | (3) |
|
|
259 | (2) |
|
17 The Fish4Knowledge Virtual World Gallery |
|
|
261 | (8) |
|
|
|
|
261 | (1) |
|
17.2 The Fish4Knowledge Second Life Gallery---Ground Level |
|
|
262 | (3) |
|
17.3 The Fish4Knowledge Second Life Gallery---Underwater Level |
|
|
265 | (1) |
|
17.4 The Fish4Knowledge Virtual World Gallery in OpenSimulator |
|
|
266 | (1) |
|
|
266 | (3) |
|
|
269 | (14) |
|
|
18.1 Summary of Achievements |
|
|
269 | (3) |
|
|
272 | (2) |
|
18.3 What Lies in the Future |
|
|
274 | (1) |
|
18.4 Project Publications |
|
|
275 | (8) |
|
18.4.1 Fish Detection and Tracking |
|
|
276 | (1) |
|
18.4.2 Fish Species Classification and Behavior Analysis |
|
|
276 | (2) |
|
18.4.3 User Needs and Information Presentation |
|
|
278 | (1) |
|
18.4.4 System Architecture and Overview |
|
|
279 | (1) |
|
18.4.5 System Evaluation and Data Ground Truthing |
|
|
280 | (1) |
|
|
281 | (2) |
Glossary |
|
283 | (4) |
Appendix A User Interface and Usage Scenario |
|
287 | (14) |
Appendix B Database Tables Related to F4K Workflow |
|
301 | (2) |
Appendix C F4K Database Schema |
|
303 | (12) |
Index |
|
315 | |