Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2013 Raman spectroscopic characterization and analysis of agricultural and biological systems Qi Wang Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Agriculture Commons, Biomedical Commons, Bioresource and Agricultural Engineering Commons, and the Biostatistics Commons Recommended Citation Wang, Qi, "Raman spectroscopic characterization and analysis of agricultural and biological systems" (2013). Graduate Theses and Dissertations. 13019. https://lib.dr.iastate.edu/etd/13019 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Raman spectroscopic characterization and analysis of agricultural and biological systems by Qi Wang A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Agricultural Engineering Program of Study Committee: Chenxu Yu, Major Professor Jacek Adam Koziel Kenneth J Koehler Lie Tang Sinisa Grozdanic Iowa State University Ames, Iowa 2013 Copyright © Qi Wang, 2013. All rights reserved. ii TABLE OF CONTENTS LIST OF FIGURES………………………………………………………………………………...…..v LIST OF TABLES.................................................................................................................................vi ABSTRACT ....................................................................................................................................... viii Chapter 1. GENERAL INTRODUCTION ...................................................................................... 1 1.1 Introduction ............................................................................................................................ 1 1.1.1 Raman spectroscopy and its instrumentation .................................................................. 1 1.1.2 Application of Raman spectroscopy ............................................................................... 5 1.1.3 Raman spectra pre-processing ...................................................................................... 14 1.1.4 Classification of samples based on spectral signatures................................................. 30 1.2 Research Objectives ............................................................................................................. 41 1.3 Dissertation Overview .......................................................................................................... 42 1.4 References ............................................................................................................................ 43 Chapter 2. EXPLORING RAMAN SPECTROSCOPY FOR THE EVALUATION OF GLAUCOMATOUS RETINAL CHANGES ............................................................... 51 2.1 Abstract ................................................................................................................................ 51 2.2 Introduction .......................................................................................................................... 52 2.3 Materials and Methods ......................................................................................................... 54 2.3.1 Animals and tissue collection ....................................................................................... 54 2.3.2 Acquisition of Raman spectrum from retinal tissues .................................................... 55 2.3.3 Spectral data processing ............................................................................................... 56 2.3.4 PCA and data compression for SVM discriminant modeling ....................................... 57 2.4 Results .................................................................................................................................. 58 2.4.1 Spectroscopic characterization of retinal ganglion cells from the retinal tissues ......... 58 2.4.2 Discriminant classification of glaucomatous versus healthy spectra using support vector machine .............................................................................................................. 61 2.4.3 Effect of spectral data processing for the classification accuracy ................................ 62 2.4.4 Classification differences between different breeds of dogs ........................................ 64 2.5 Conclusions .......................................................................................................................... 67 2.6 Acknowledgments ................................................................................................................ 71 2.7 References ............................................................................................................................ 71 Chapter 3. DETECTION AND CHARACTERIZATION OF GLAUCOMA-LIKE CANINE RETINAL TISSUES USING RAMAN SPECTROSCOPY ........................................ 74 iii 3.1 Abstract ................................................................................................................................ 74 3.2 Introduction .......................................................................................................................... 75 3.3 Materials and Methods ......................................................................................................... 77 3.3.1 Acute elevation of the intraocular pressure in beagles ................................................. 77 3.3.2 Dog model for compressive optic neuropathy .............................................................. 78 3.3.3 Animals and tissue collection ....................................................................................... 80 3.3.4 Acquisition of Raman spectrum from retinal tissues .................................................... 81 3.3.5 Spectral data processing ............................................................................................... 81 3.3.6 Principal component analysis ....................................................................................... 81 3.3.7 Cross-validation, independent validation and discriminant modeling .......................... 83 3.3.8 Pattern electroretinography (pERG) characterization of the disease status of AEIOP dogs .................................................................................................................. 84 3.4 Results .................................................................................................................................. 84 3.4.1 Spectroscopic difference between the RGCs of Acute Elevation of Intraocular Pressure (AEIOP), Compressive Optic Neuropathy (CON) and healthy beagles ........ 84 3.4.2 Spectroscopic differences between AEIOP/CON beagles and advanced glaucoma in basset hounds ............................................................................................................ 86 3.4.3 Discriminant classification using support vector machine ........................................... 88 3.4.4 Limitations and future directions .................................................................................. 93 3.5 Conclusions .......................................................................................................................... 95 3.6 Acknowledgments ................................................................................................................ 96 3.7 References ............................................................................................................................ 96 Chapter 4. RAPID DETERMINATION OF PORK SENSORY QUALITY USING RAMAN SPECTROSCOPY ........................................................................................................ 99 4.1 Abstract ................................................................................................................................ 99 4.2 Introduction .......................................................................................................................... 99 4.3 Materials and Methods ....................................................................................................... 104 4.3.1 Animals and sample collection ................................................................................... 104 4.3.2 Meat sensory quality and star probe value assessments ............................................. 104 4.3.3 Sample preparation and Raman measurements .......................................................... 105 4.3.4 Spectral data processing ............................................................................................. 106 4.4 Results and Discussion ....................................................................................................... 108 4.4.1 Sensory tenderness, star probe, sensory chewiness, and sensory juiciness ................ 108 4.4.2 Raman spectroscopic analysis .................................................................................... 109 iv 4.4.3 Predication of sensory tenderness, chewiness and juiciness values based on PLS regression model ........................................................................................................