USING AIRBORNE HYPERSPECTRAL IMAGERY TO ESTIMATE CHLOROPHYLL A AND PHYCOCYANIN IN THREE CENTRAL INDIANA MESOTROPHIC TO EUTROPHIC RESERVOIRS Rebecca Elizabeth Sengpiel Submitted to the faculty of the University Graduate School in partial fulfillment of the requirements for the degree Master of Science in the Department of Earth Sciences, Indiana University August 2007 Accepted by the Faculty of Indiana University, in partial fulfillment of the requirements for the degree of Master of Science Lin Li, Ph.D., Chair Lenore P. Tedesco, Ph.D. Master’s Thesis Committee Jeffrey S. Wilson, Ph.D. ii Acknowledgements I wish to thank my committee members for allowing me the opportunity to accomplish this goal. Furthermore, I would like to thank all of the graduate students and faculty in the Department of Earth Sciences, IUPUI and the staff of CEES who participated in the September 6 and 7, 2005 sampling excursion and who assisted in the lab analyses. I also want to wish to thank the Veolia Water Indianapolis, LLC White River Laboratories for all of their assistance with sample analyses; the University of Nebraska CALMIT laboratory for acquiring the AISA imagery; IndyParks and Eagle Creek Park for dock space and launch access; and Kent Duckwell for launch access to Geist and Morse Reservoirs. And last, but not least, I would like to thank my husband, my family and friends, and University of the Pacific Geology Professors for all of their help, support and inspiration. This project was funded by the Indiana Department of Natural Resources LARE Grant and Veolia Water Company LLC, Central Indiana Water Resources Partnership. iii Abstract Rebecca Elizabeth Sengpiel USING AIRBORNE HYPERSPECTRAL IMAGERY TO ESTIMATE CHLOROPHYLL A AND PHYCOCYANIN IN THREE CENTRAL INDIANA MESOTROPHIC TO EUTROPHIC RESERVOIRS This thesis presents the results of an analysis of predicting phytoplankton pigment concentrations (chlorophyll a and phycocyanin) from remotely sensed imagery. Hyperspectral airborne and hand-held reflectance spectra were acquired on three reservoirs (Geist, Morse and Eagle Creek) in Central Indiana, USA. Concurrent with the reflectance acquisition, in situ samples were collected and analyzed in laboratories to quantify the pigment concentration and other water quality parameters. The resultant concentration was then linked to Airborne Imaging Spectrometer for Applications (AISA) reflectance spectra for the sampling stations to develop predictive models. AISA reflectance spectra were extracted from the imagery which had been processed for radiometric calibration and geometric correction. Several previously published algorithms were examined for the estimation of pigment concentration from the spectra. High coefficients of determination were achieved for predicting chlorophyll a in two of the three reservoirs (Geist R2 = 0.712, Morse R2 = 0.895 and Eagle Creek Reservoir R2 = 0.392). This situation was similar for PC prediction, where two of the three reservoirs had high coefficients of determination between pigment concentration and reflectance (Geist R2 = 0.805, Morse R2 = 0.878 and Eagle Creek Reservoir R2 = 0.316). The results of this study show that reflectance spectra collected with an airborne hyperspectral imager are statistically significant, p < 0.03, in predicting chlorophyll a and phycocyanin pigment concentration in all three reservoirs in this study without the consideration of other parameters. The algorithms were then applied to the AISA image to generate high spatial resolution (1 m2) maps of Chlorophyll a and Phycocyanin distribution for each reservoir. Lin Li, Ph.D., Chair iv Table of Contents List of Tables .............................................................................................................................................................. ix List of Figures ............................................................................................................................................................ xi 1.0 Introduction.................................................................................................................................................. 1 Adverse effects of Cyanobacteria in Limnitic Ecosystems ................................................................ 1 Ecological Degradation ............................................................................................................................... 1 Aesthetic Degradation .................................................................................................................................. 2 Human Health Effects ................................................................................................................................... 2 Introduction of the Study ................................................................................................................................ 3 Objective of the Research ............................................................................................................................ 3 Significance of the Research ....................................................................................................................... 3 Overview of Study ........................................................................................................................................... 4 Overview of research directly related to problem................................................................................ 4 2.0 Background ................................................................................................................................................... 7 A Brief Overview of Cyanobacteria ............................................................................................................. 7 Cyanobacteria Systematics ......................................................................................................................... 7 Cyanobacterial Ecological Diversity ....................................................................................................... 7 Cyanobacterial Morphology ....................................................................................................................... 8 Bloom Formation ........................................................................................................................................... 9 Photosynthetic Pigments of Phytoplankton .......................................................................................... 11 Chlorophylls .................................................................................................................................................... 11 Carotenoids..................................................................................................................................................... 12 Biliproteins ..................................................................................................................................................... 12 A Brief Introduction of Cyanobacterial Toxins ..................................................................................... 13 Hepatotoxins .................................................................................................................................................. 13 Neurotoxins .................................................................................................................................................... 14 Other Cyanobacterial Toxins.................................................................................................................... 15 Nature of Electromagnetic Radiation and light .................................................................................... 15 Wave Model/Particle Theory ................................................................................................................... 15 Remote Sensing of Water quality ............................................................................................................... 17 Radiance, Irradiance and Reflectance .................................................................................................. 17 Energy-Matter Interactions...................................................................................................................... 18 Extraterrestrial Solar Radiation............................................................................................................. 19 v Remote Sensing Above Water ..................................................................................................................... 20 Light Paths ...................................................................................................................................................... 20 Considerations for Airborne Remote Sensing .................................................................................... 21 3.0 Review of Remote Sensing of Inland Waters ............................................................................... 23 Spectral Characteristics of Inland Waters .............................................................................................. 23 Case I vs. Case II ............................................................................................................................................ 23 Approximate Absorption Maxima of Pigments found in Cyanobacteria .................................. 23 Sample of Above Water Reflectance Spectra ....................................................................................