Portable Microscope Group 27 Austin Bryant - Computer Scientist Adam Bush - Computer Engineer Cayla Gill - Electrical Engineer Hannah Pierson - Photonic Engineer 2019-04-22 Table of Contents 1.0 Executive Summary 1 2.0 Project Description 3 2.1 Motivation 3 2.2 Goals and Objectives 4 2.3 Requirements and Specifications 5 2.4 Anticipated Obstacles 6 2.5 House of Quality 8 2.6 System Block Diagrams 9 2.6.1 Original Hardware and Software Diagrams 10 2.6.2 Alternative Hardware and Software Diagrams 13 3.0 Research 13 3.1 Existing Microscopes 16 3.1.1 Resolution vs. Magnification 16 3.1.2 Microscopes Used for Research 16 3.1.2.1 Pocket Microscope 16 3.1.2.2 Digital USB Microscope 17 3.1.3 Results of Research 17 3.2 Microscopy 18 3.2.1 Chromatic Aberration 19 3.2.1.1 Correcting Chromatic Aberration 19 3.2.2 Spherical Aberration 19 3.2.3 Types of Microscopy 19 3.2.4 Conjugate Planes 20 3.3 Image Sensors 20 3.3.1 CMOS Image Sensors 21 3.3.2 Charge-Coupled Devices 21 3.3.3 Image Sensing Schemes 21 3.4 Image Processing Approaches 22 3.4.1 Image Processing Techniques 22 3.5 Microcontrollers 23 3.5.1 A Dual-Core Approach 23 3.5.2 An Embedded JPEG Codec 24 3.6 Database Management on Android 24 3.6.1 SQLite 24 3.7 Communications Methods 25 3.7.1 Choosing Wi-Fi over NFC and Bluetooth 25 3.7.2 Transmission Control Protocol 25 3.7.3 User Datagram Protocol 26 3.8 Printed Circuit Board 27 3.8.1 Chip Package Designs 27 3.8.2 Layers of Printed Circuit Board 28 3.8.3 Circuitry Design Process 29 3.8.4 Eagle Program 29 3.9 Power Supply Options 30 i 3.9.1 Batteries 30 3.9.1.1 Single-Use Alkaline Batteries 30 3.9.1.2 Rechargeable Alkaline Batteries 31 3.9.1.3 Single-Use Lithium Batteries 32 3.9.1.4 Rechargeable Lithium Batteries 33 3.9.1.5 Battery Design Choice 34 3.9.2 Voltage Regulators 35 3.9.2.1 Types of Regulators 35 3.9.2.2 Voltage Regulator Design 36 3.9.2.3 Voltage Regulator Design Comparison 37 3.9.2.4 Voltage Regulator Design Alterations 39 3.10 Body 40 3.10.1 Project Body Concepts 41 3.10.1.1 Lighting Design 44 3.10.2 Plastic Enclosure 45 3.10.3 Body Construction 45 3.10.3.1 3D Printing 45 3.10.3.2 Machining 46 3.10.3.3 Diffusion Filter Construction 46 3.11 Mobile App Cross-Platform Considerations 47 3.12 Parts and Components Selection 48 4.0 Standards and Constraints 51 4.1 Constraints 51 4.1.1 Economic Constraints 51 4.1.2 Environmental Constraints 51 4.1.3 Social Constraints 52 4.1.4 Political Constraints 52 4.1.5 Ethical Constraints 53 4.1.6 Health and Safety Constraints 53 4.1.7 Manufacturability Constraints 53 4.1.8 Time Constraints 54 4.1.9 Testing and Presentation Constraints 54 4.2 Standards 55 4.2.1 Power Supply Standards 55 4.2.2 IEEE 802.11 56 4.2.3 Other Wireless Communication Standards 57 4.2.4 Standard for Tests for Flammability of Plastic Materials for Parts in Devices and Appliances 57 4.2.5 IPC PCB Standards 57 4.2.6 Software Project Management 58 4.2.7 Physical and Inter-Chip Communication Formats 58 4.2.7.1 Universal Asynchronous Receiver/Transmitter 58 4.2.7.2 Other Relevant Serial Interfaces 59 4.2.7.3 Common Parallel Interfaces 60 4.2.7.4 Camera Parallel Interface 60 5.0 System Design 62 ii 5.1 System Architecture 62 5.2 STM32H753ZI Microcontroller Operations and Details 65 5.2.1 Development Environment 65 5.2.1.1 STMCube32 65 5.2.1.2 The NUCLEO-H743ZI Development Kit 66 5.2.1.3 Arm’s Keil MDK 66 5.2.2 Memory Management 66 5.2.2.1 Direct Memory Access 67 5.2.2.2 Managing Uncompressed Single-Frame Transfers 67 5.2.3 Included Libraries and Initializations 68 5.2.3.1 DCMI Setup 69 5.2.3.2 RGB to YCbCr Conversion 69 5.2.3.3 JPEG Codec Setup 69 5.2.4 Parallelizable Data Flows 69 5.3 Microscope Design 71 5.3.1 Microscope Optical Design 72 5.3.1.1 Illumination System 72 5.3.1.1.1 Our Illumination System vs. Traditional 72 5.3.1.1.2 Ideas for Even Distribution of Light 73 5.3.1.1.3 Diffusion Filters 73 5.3.1.1.4 Light Position 75 5.3.1.1.5 Controlling Amount of Light 75 5.3.1.2 Light Sources 75 5.3.1.3 Apertures 76 5.3.1.4 Objective Lens 76 5.3.1.4.1 Achromat Objective Lenses 78 5.3.1.4.2 Fluorite Objective Lenses 79 5.3.1.4.3 Apochromatic Objective Lenses 79 5.3.1.4.4 Optical Design Choice 79 5.3.1.5 Resolution, Field of View, and Focal Length 80 5.3.1.5.1 Resolution 80 5.3.1.5.2 Field of View 81 5.3.1.5.3 Focal Length 82 5.3.1.6 Cover Slip or Slide 82 5.3.1.7 Tube Lens 83 5.3.2 Image Sensor 85 5.3.2.1 Pixels 85 5.4 Software Architecture and Design 86 5.4.1 Raspberry Pi 86 5.4.2 Interfacing with the OmniVision OV5647 Image Sensor 87 5.4.3 Displaying Video using OpenCV 87 5.4.4 Data Storage 89 5.4.4.1 Naming Convention for Files 91 5.4.4.2 Organizing Images 91 5.4.4.3 Data Recall 93 5.4.5 Data Transmission 95 iii 5.4.5.1 Sockets 95 5.4.5.2 Control Signals 96 5.4.5.3 Internet Protocol Choice 96 5.4.6 Google’s Android Design Guidelines 97 5.4.7 User Interface Design 98 5.4.7.1 Mobile Interface for Connecting Devices 99 5.4.8 Software Development Methodology 100 5.4.9 Remote Code Repository Usage 101 5.4.9.1 GitHub 101 5.4.9.2 GitHub Issue Tracker 102 5.5 Power Systems 102 5.6 Hardware Design 105 5.7 Printed Circuit Board Design 107 5.7.1 Completed Main PCB Design 107 5.7.2 Voltage Regulator PCB Design 109 5.7.3 Lighting PCB Design 111 5.8 The GS2101 Wi-Fi Chip 113 5.8.1 Summarized Feature Set 114 5.8.2 Interfacing 114 5.8.2.1 UART and SDIO Connections 114 5.8.2.2 AT Commands 115 5.8.3 Wi-Fi Initialization 115 5.8.3.1 Wi-Fi Direct 115 5.8.3.1.1 Group Formation and Election Process 116 5.8.3.1.2 Group Owner vs. Client 117 5.8.3.1.3 Android Implementation 117 5.8.3.1.4 Authorization 120 5.8.3.2 Wireless Access Point 121 5.8.3.2.1 Why WAP over Wi-Fi Direct? 121 5.8.3.2.2 WAP Hosting on Raspberry Pi 122 5.8.3.2.3 Hostapd 122 5.8.3.2.4 Dnsmasq 122 5.8.4 Development Environment 123 5.8.5 Support for TCP 124 6.0 Integration and Testing 125 6.1 Standalone Testing 125 6.1.1 Mobile Application 125 6.1.1.1 Unit Testing 127 6.1.1.2 Embedded-Facing Components 127 6.1.1.3 Espresso Testing Framework 128 6.1.2 Optical Component Testing 129 6.1.2.1 Objective Lens Testing 129 6.1.2.2 Results – Objective Lens 130 6.1.2.3 Additional Testing and Results – Objective Lens 130 6.1.2.4 Light Source Testing 132 6.1.2.5 LED Results 132 iv 6.1.2.6 Additional Testing and Results – LED 133 6.1.2.7 Optical Testing – Camera 134 6.2 Breadboard Testing 135 6.2.1 LED Testing 135 6.2.2 Breadboard Testing Plan 136 6.3 Integration Testing 137 6.3.1 Microcontroller and Image Sensor Interoperation 137 6.3.2 Microcontroller and Wi-Fi Chip Communications 137 6.3.3 Mobile and Embedded Communications 137 6.3.3.1 Accessing Data Stream 137 6.4 Second Semester Optical Testing 139 7.0 Administrative Content 142 7.1 Estimated Budget & Financing 142 7.2 Milestones 144 8.0 Project Summary and Conclusion 146 Appendices I Appendix A. References I Appendix B. Copyright Permission IV v List of Figures Figure 1. Alternate Design 2 Figure 2. House of Quality 9 Figure 3. Hardware Block Diagram Original Design 10 Figure 4. Software Block Diagram Original Design 12 Figure 5. Alternate Hardware Diagram 14 Figure 6. Alternate Software Diagram 15 Figure 7. Ray Diagram 18 Figure 8. Three-Way Handshake 26 Figure 9. Voltage Regulator Design Schematic 38 Figure 10. 5V Regulator Schematic 39 Figure 11. 2.8V Regulator Schematic 39 Figure 12. 1.8V Regulator Schematic 40 Figure 13. 5V Alternate Regulator 40 Figure 14. Example of Existing Portable Microscope 41 Figure 15. Focusing System 42 Figure 16. Body Implementation 43 Figure 17. Panel for Electronics 43 Figure 18. LED Layout around Objective Lens 44 Figure 19. Overall Design of Body 45 Figure 20.