Development of Accessible Hyperspectral Imaging Architectures Towards Biomedical Applications by C. Harrison Brodie A Thesis presented to The University of Guelph In partial fulfilment of requirements for the degree of Master of Applied Science in Engineering Guelph, Ontario, Canada © C. Harrison Brodie, December, 2018 ABSTRACT DEVELOPMENT OF ACCESSIBLE HYPERSPECTRAL IMAGING ARCHITECTURES TOWARDS BIOMEDICAL APPLICATIONS C. Harrison Brodie Advisor: University of Guelph, 2018 Dr. Christopher M. Collier Hyperspectral imaging combines the attributes of imaging (detecting physical features) and spectroscopy (detecting chemical features) and is a technology with great potential in many applications. However, to facilitate widespread adoption of hyperspectral imaging, such systems require enhanced accessibility (i.e., being inexpensive and upcomplicated) and can be developed as novel hyperspectral imaging instrumentation architectures. This thesis presents, designs, develops, and evaluates an accessible hyperspectral imaging instrumentation architecture, with snapshot operation, based on the integration of readily-available components and frequency multiplexing with Fourier analyses. This is achieved through the identification of incident spatial image channels with frequency encoding from unique dynamic binary codes. Comparison to data from a commercial spectrometer reveals the performance of the hyperspectral imaging instrumentation architecture. Overall, the hyperspectral imaging instrumentation architecture compares favourably to commercially available products and can be adapted for two-dimensional operation. The presented hyperspectral imaging instrumentation architecture can provide benefit for regions of the world that have limited financial resources and have a need for accessible hyperspectral imaging technologies. iii ACKNOWLEDGEMENTS I wish to extend my sincere gratitude to my advisor, Dr. Christopher Collier. Thank you for your guidance and leadership. Your encouraging mentorship has been a positive influence on my life. Jasen Devasagayam, thank you for your enthusiasm and collaboration on this project. Thank you to my parents, Donna and Keith. You have loved and supported me throughout my entire life. iv TABLE OF CONTENTS Abstract ........................................................................................................................................... ii Acknowledgements ........................................................................................................................ iii Table of Contents ........................................................................................................................... iv 1 Introduction ............................................................................................................................. 1 1.1 Hyperspectral Imaging Background................................................................................. 1 1.1.1 Optoelectronic Devices ............................................................................................. 1 1.1.2 Imaging ..................................................................................................................... 2 1.1.3 Spectroscopy ............................................................................................................. 2 1.2 Hyperspectral Imaging ..................................................................................................... 4 1.2.1 Hyperspectral Imaging Applications ........................................................................ 5 1.2.2 Hyperspectral Imaging Development ....................................................................... 5 1.2.3 Photonic Innovations and Low-cost Opportunities for Hyperspectral Imaging ..... 10 1.3 Contributions of this Thesis ........................................................................................... 11 1.4 Thesis Scope ................................................................................................................... 12 1.5 Dissemination of Results ................................................................................................ 12 2 Background Scientific Knowledge ....................................................................................... 13 2.1 Fourier Series and Transform ......................................................................................... 13 2.1.1 Fourier Series .......................................................................................................... 13 2.1.2 Fourier Transform ................................................................................................... 16 2.2 Temporal Fourier Transform: Lock-in Detection .......................................................... 17 2.3 Spatial Fourier Transform: Diffraction and Fourier Optics ........................................... 18 3 Instrumentation Development ............................................................................................... 20 3.1 Instrumentation Design .................................................................................................. 20 3.2 Instrumentation Analysis................................................................................................ 25 4 Results ................................................................................................................................... 27 v 4.1 Instrumentation Evaluation ............................................................................................ 27 4.2 Comparison to Other Instrumentation ............................................................................ 35 5 Conclusions ........................................................................................................................... 38 5.1 Hyperspectral Imaging Instrumentation Architecture .................................................... 38 5.2 Future Work ................................................................................................................... 40 Copyright Notice ........................................................................................................................... 41 Bibliography ................................................................................................................................. 42 Appendix ....................................................................................................................................... 52 APPENDIX A: Component Selection and Experimental Challenges ....................................... 52 APPENDIX B: MATLAB Script for HSI Instrumentation Architecture .................................. 56 vi LIST OF FIGURES Figure 1: The electromagnetic spectrum is shown with decreasing wavelength and increasing frequency progressing over radio, microwaves, terahertz, infrared, visible light, ultraviolet, X-rays, and gamma-rays (-rays). ....................................................................................... 3 Figure 2: Whiskbroom HSI acquisition is shown. To populate the datacube, time must be used. 6 Figure 3: Pushbroom HSI acquisition is shown. To populate the datacube, time must be used. ... 7 Figure 4: Wavelength scan HSI acquisition is shown. To populate the datacube, time must be used. ............................................................................................................................................. 8 Figure 5: Snapshot HSI acquisition is shown. To populate the datacube, time is not required. ..... 9 Figure 6: The Fourier Series approximations (blue) of a periodic square wave function (green), gsw(x), are shown in primary (temporal or spatial) domain in subfigures (a)-(e) for n = 1, 2, 5, 10, and 100. The corresponding frequency domain representations are shown in respective subfigures (f)-(j) for the aforementioned Fourier Series approximations. ...... 15 Figure 7: Periodic and aperiodic time domain signals (a)-(d) are shown along with the corresponding frequency domain representations (e)-(h). ................................................ 16 Figure 8: A standard implementation for an optical chopper is shown. ....................................... 18 Figure 9: Transmission diffraction gratings with (a) large diffraction grating pitch and (b) small diffraction grating pitch are shown. .................................................................................. 19 vii Figure 10: The schematic of the HSI instrumentation architecture is shown. The inset shows scanning electron microscope images of the diffractive element, being the polycarbonate layer of a CD. © 2018 IEEE. ............................................................................................ 21 Figure 11: The dynamic coded aperture is shown. The spatial image channels are identified in the inset. The reference channel is also identified. © 2018 IEEE. ......................................... 24 Figure 12: The Fourier amplitude spectra is shown as a surface plot versus its argument variables, being CCD pixel, j, and frequency, f. The DC Fourier amplitude spectrum can be seen at f = 0 Hz. The pixel Fourier amplitude spectra associated with spatial image channel i = 1, 2, and 3 can be seen at f = F1 = 19.3 Hz, f = F2 = 15.4 Hz, and f = F3 = 11.6 Hz, respectively. © 2018 IEEE. .................................................................................................................... 28 Figure 13: The amplitude of the Fourier spectra for each spatial image channel are shown as