QUANTIFYING THE EFFECT OF ENVIRONMENTS ON CROP EMERGENCE, DEVELOPMENT AND YIELD USING SENSING AND DEEP LEARNING TECHNIQUES _______________________________________ A Dissertation presented to the Faculty of the Graduate School at the University of Missouri-Columbia __________________________________________________ In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy _____________________________________________________ by AIJING FENG Dr. Jianfeng Zhou, Dissertation Supervisor MAY 2021 The undersigned, appointed by the dean of the Graduate School, have examined the dissertation entitled QUANTIFYING THE EFFECT OF ENVIRONMENTS ON CROP EMERGENCE, DEVELOPMENT AND YIELD USING SENSING AND DEEP LEARNING TECHNIQUES presented by Aijing Feng, a candidate for the degree of doctor of philosophy, and hereby certify that, in their opinion, it is worthy of acceptance. ______________________________ Dr. Jianfeng Zhou ______________________________ Dr. Gang Yao ______________________________ Dr. Kenneth A. Sudduth ______________________________ Dr. Toni Kazic ______________________________ Dr. Earl D. Vories ACKNOWLEDGEMENTS I would like to express my sincere appreciation to my advisor and committee chair Dr. Jianfeng Zhou. Dr. Zhou constantly offers me great support and excellent suggestions during the period of my Ph.D. study. Without his mentoring, I could not have completed this dissertation. I not only regard him as my academic advisor but also as a respected elder. He taught me how to think critically, how to do things meticulously, and how to deal with the trivial things in life wisely. I would like to thank my committee members Dr. Kenneth A. Sudduth and Dr. Earl D. Vories for the help with my experiments as well as all the wonderful suggestions and the review of my publications. They help me improve my writing skills a lot and I learn how to think deeper on a research topic. I would also like to thank my committee members Dr. Gang Yao and Dr. Toni Kazic for all their guidance and suggestions through this long- term process. I appreciate the great support from my colleagues Jing Zhou and Chin Nee Vong from the Precision and Automated Agriculture Lab at the University of Missouri. They created an excellent environment for research in our lab. I enjoy working with them. They always try their best to help me with the data collection and gave me useful suggestions in my research. We are best friends in life and no matter in life or study, they have helped me a lot. In the end, I would like to thank the China Scholarships Council fellowship support. ii TABLE OF CONTENTS ACKNOWLEDGEMENTS ................................................................................................ ii LIST OF FIGURES ........................................................................................................... vi LIST OF TABLES ........................................................................................................... xiii LIST OF ABBREVIATIONS .......................................................................................... xiv ABSTRACT ..................................................................................................................... xvi Chapter 1. INTRODUCTION ............................................................................................. 1 1.1 Problem Statement ................................................................................................... 1 1.2 Literature review ...................................................................................................... 4 Soil and weather affect crop emergence, development and yield ....................... 4 Sensor networks for crop monitoring .................................................................. 5 1.3 Problems not been solved......................................................................................... 8 The need for rapid and accurate emergence assessment in early stage ............... 8 The need of quantifying the effects of soil, water and weather on plant growth and yield ............................................................................................................ 10 Evaluation of high-resolution spatiotemporal crop, soil and weather ............... 10 Integration of emerging data analysis techniques: machine learning and deep learning .............................................................................................................. 11 1.4 Goals of the study .................................................................................................. 11 1.5 Literature cited ....................................................................................................... 12 Chapter 2. GROUND DATA COLLECTION AND EXPERIMENT DESIGN .............. 20 2.1 Experimental field .................................................................................................. 20 2.2 Soil, field elevation and weather data .................................................................... 21 2.3 Crop management and cotton yield data ................................................................ 23 2.5 Literature cited ....................................................................................................... 24 Chapter 3. COTTON EMERGENCE EVALUATION AND THE SOIL EFFECTS ON EMERGENCE ............................................................................................................. 26 3.1 Abstract .................................................................................................................. 26 3.2 Introduction ............................................................................................................ 27 3.3 UAV system and experimental design ................................................................... 31 3.4 UAV image pre-processing .................................................................................... 33 Distortion calibration ......................................................................................... 33 Quantification of cotton row spacing ................................................................ 34 Geo-referencing cotton rows ............................................................................. 37 Evaluation of distortion correction and estimated row spacing ........................ 39 3.5 Evaluation of cotton stand count and canopy size ................................................. 40 Introduction to convolutional neural networks ................................................. 40 Deployment of transform learning model using resnet18 ................................. 41 Data set preparation ........................................................................................... 44 Performance of deep learning model resnet18 .................................................. 46 Comparison of resnet18 and other deep learning models ................................. 50 3.6 Development of a framework for evaluation of cotton emergence ........................ 51 Stand count and canopy size mapping .............................................................. 53 The use of the data processing framework ........................................................ 56 3.7 Conclusion ............................................................................................................. 59 iii 3.8 Future work ............................................................................................................ 60 3.9 Literature cited ....................................................................................................... 61 Chapter 4. SOIL AND ELEVATION EFFECTS ON COTTON EMERGENCE............ 69 4.1 Abstract .................................................................................................................. 69 4.2 Introduction ............................................................................................................ 70 4.3 Emergence row register from individual RGB frame ............................................ 73 Feature detection and matching ......................................................................... 73 Removal of false matches ................................................................................. 73 Calculation of the geometric transformation matrix ......................................... 75 Crop rows alignment based on the geometric transformation matrix ............... 76 Image frame positions within each entire crop row .......................................... 77 Emergence mapping based on the image alignment ......................................... 78 4.4 Limitation of the crop row alignment algorithm .................................................... 79 Low overlapping of the image frames ............................................................... 79 Incorrect image alignment when changing UAV batteries ............................... 81 4.5 GPS accuracy ......................................................................................................... 82 4.6 Factors affected the stand count and canopy size .................................................. 83 The emergence maps ......................................................................................... 83 Soil and elevation effects on the stand count and canopy size .......................... 84 Emergence and the crops’ subsequent development ......................................... 89 4.7 Conclusion ............................................................................................................