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An Evaluation of the Along Track Reef Imaging System (ATRIS) for Efficient Reef Monitoring and Rapid Groundtruthing of EAARL Lidar

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An Evaluation of the Along Track Reef Imaging System (ATRIS) for Efficient Reef Monitoring and Rapid Groundtruthing of EAARL Lidar
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  An Evaluation of the Along Track Reef Imaging System (ATRIS) for Efficient Reef Monitoring and Rapid Groundtruthing of EAARL Lidar  by  Nicole O. Caesar A thesis submitted in partial fulfillment of the requirements for the degree of Marine Science College of Marine Science University of South Florida Major Professor: Pamela Hallock Muller, Ph. D. John Brock, Ph. D. Deby Cassill, Ph. D. David Mann, Ph. D. Date of Approval: April 7, 2006 Keywords: patch reef, Biscayne National Park, rugosity, digital camera, Florida Keys © Copyright 2006, Nicole O. Caesar   ACKNOWLEDGEMENTS I would like to acknowledge my major professor, Dr. Pamela Hallock Muller, for her commitment to her students and to her role as a research scientist. I thank Dr. Muller for the guidance and support provided to me during the course of my degree. I also thank my committee members: John Brock, Deby Cassill and David Mann. Many thanks to W. Wright, the Principal Investigator for the NASA EAARL, for his very significant contributions to the success of this research project. V. Rabine is thanked for his dedication and skill as the Chief Pilot of the Cessna 310 aircraft used during the NASA EAARL lidar overflights of the northern Florida Keys reef tract. The substantial contributions from R. Curry to field investigations within Biscayne National Park are greatly appreciated. Special thanks to P. Thompson for the development of the ATRIS, and D. Hickey for his professionalism in handling the boat operations undertaken within this study. I would also like to thank my family, N. Piehl and T. Wood for their support and encouragement. The U.S. Geological Survey Coastal and Marine Geology Program funded this investigation as a component of the Geologic Studies of Coral Reefs Project. My stipends were provided by the University of South Florida/U.S. Geological Survey 2003  – 2006 cooperative agreement.   i TABLE OF CONTENTS LIST OF TABLES ............................................................................................................iii LIST OF FIGURES ..........................................................................................................iv ABSTRACT ......................................................................................................................vi 1. INTRODUCTION ..........................................................................................................1 The Along-Track Reef Imaging System (ATRIS) ..................................................2 Experimental Advanced Airborne Research Lidar (EAARL) ................................5 Topographic Complexity ........................................................................................7 Biscayne National Park ...........................................................................................7 Objectives ...............................................................................................................9 2. METHODS ...................................................................................................................10 Study Sites ............................................................................................................10   Transects ...............................................................................................................10 ATRIS Data Acquisition........................................................................................12 Diver-acquired Data...............................................................................................13 Image Post-processing...........................................................................................13 Benthic Classification and Calculation of Percent Cover......................................15 EAARL Data Acquisition......................................................................................16 Statistical Analyses................................................................................................17 3. RESULTS .....................................................................................................................18 Percent Cover of Benthic Categories.....................................................................18 Comparison of ATRIS and Diver-acquisition Methods .......................................22 Relationship between Benthic Class, Depth and Rugosity Index .........................24 4. DISCUSSION ...............................................................................................................29   iiComparison of ATRIS and Diver-acquisition Methods .......................................30 Benthic Class and Rugosity Index ........................................................................31 5. CONCLUSIONS ...........................................................................................................34 REFERENCES .................................................................................................................35 APPENDICES ..................................................................................................................39 Appendix I Diver-acquired benthic category frequencies for each transect on each of the five reef sites ............................................40 Appendix II ARIS-acquired benthic category frequencies for each transect on each of the five reef sites ............................................41 Appendix III Data utilized to create lower, mean and upper quartile  benthic category distributions for ATRIS and diver- acquired data sets combined; Figure 14 ........................................42 Appendix IV Raw data used for regression analysis of benthic category and depth versus rugosity indices .................................................43   iii LIST OF TABLES Table 1. Summary of data collected with ATRIS and by a Scuba diver.................13 Table 2. Original and reclassified benthic categories identified for ATRIS and diver-acquired images.........................................................................16 Table 3. Summarized results of the Kolmogorov-Smirnov Goodness-of-fit test comparing the maximum differences  between the ATRIS and diver-acquired datasets; significant differences differences noted by asterisk (*)................................................................23 Table 4. Results of linear regressions of point-count data for each  benthic category and each image, compared with the rugosity index for the index of the GPS coordinates of each image; significant correlations (p ) (p ≤  0.05) are noted by asterisk (*)...........................................................24 Table 5. Results of linear regressions of water depths recorded during the ATRIS surveys over each of four reefs, against the rugosity indices for  indices for those GPS coordinates; significant correlations (p ≤  0.05) noted (p ≤  0.05) noted by asterisk (*)..................................................................25 Table 6. Comparisons of relative advantages and disadvantages of image-data acquisition using ATRIS and diver-acquired video................30
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