This book is the story of the marriage of a new techl}ology, computers, with an old problem, the study of neuroanatomical structures using the light microscope. It is aimed toward you, the neuroanatomist, who until now have used computers primarily for word processing but now wish to use them also to collect and analyze your laboratory data. Mter reading the book, you will be better equipped to use a computer system for data collection and analysis, to employ a programmer who might develop a system for you, or to evaluate the systems available in the marketplace. To start toward this goal, a…mehr
This book is the story of the marriage of a new techl}ology, computers, with an old problem, the study of neuroanatomical structures using the light microscope. It is aimed toward you, the neuroanatomist, who until now have used computers primarily for word processing but now wish to use them also to collect and analyze your laboratory data. Mter reading the book, you will be better equipped to use a computer system for data collection and analysis, to employ a programmer who might develop a system for you, or to evaluate the systems available in the marketplace. To start toward this goal, a glossary first presents commonly used terms in computer assisted neuroanatomy. This, on its own, will aid you as it merges the jargon of the two different fields. Then, Chapter 1 presents a historical review to describe the manual tasks involved in presenting and measuring anatomic structures. This review lays a base line of the tasks that were done before computers and the amount of skill and time needed to perform the tasks. In Chapters 2 and 3, you will find basic information about laboratory computers and programs to the depth required for you to use the machines easily and talk with some fluency to computer engineers, programmers, and salesmen. Chapters 4, 5, and 6 present the use of computers to reconstruct anatomic structures, i.e., to enter them into a computer memory, where they are later displayed and analyzed.
1. The History of Quantitative Neuroanatomy.- 1.1. Introduction.- 1.2. Early History of Drawing Neurons.- 1.3. How the Microscope Handicaps the User.- 1.3.1. Medium.- 1.3.2. Perspective.- 1.3.3. Magnification.- 1.3.4. Contrast.- 1.3.5. Measurement.- 1.4. Drawing with the Camera Lucida.- 1.5. The Pantograph: A Plotter for the Microscope.- 1.6. Physical Model Building.- 1.7. Early Attempts at Statistical Summaries.- 1.8. How the Computer Helps Visualizing and Summarizing.- 1.9. For Further Reading.- 1.10. What This Book Presents.- 2. Laboratory Computer Hardware.- 2.1. Introduction.- 2.2. Overview of Key Components.- 2.2.1. Bus.- 2.2.2. Central Processing Unit.- 2.2.3. Memory.- 2.2.4. Disks.- 2.2.5. Disk Drives.- 2.2.6. Keyboard.- 2.2.7. Terminal.- 2.2.8. Graphics Board.- 2.2.9. Ports.- 2.2.10. Analog-to-Digital Converter.- 2.3. Concepts and Definitions.- 2.3.1. Forms of Data.- 2.3.2. Analog and Digital Values.- 2.3.3. Storage of Digital Data.- 2.4. Computing Hardware Described in Some Depth.- 2.4.1. Central Processing Unit.- 2.4.2. Math Coprocessors.- 2.4.3. Random Access Memory.- 2.4.4. Disks.- 2.4.5. Magnetic Tapes.- 2.4.6. Graphics Display Cards.- 2.4.7. Computer Speeds.- 2.4.8. Bus.- 2.4.9. Plotters.- 2.4.10. Printers.- 2.4.11. Analog-to-Digital Converter.- 2.4.12. Digital-to-Analog Converter.- 2.4.13. Modem.- 2.4.14. Graphics Display Systems.- 2.4.15. Data Tablets.- 2.4.16. Mouse.- 2.4.17. Joysticks.- 2.4.18. Trackball.- 2.4.19. Stepping Motors.- 2.4.20. Components Used for Sensing Position and Motion.- 2.4.21. Ports.- 2.5. Physical Construction of Laboratory Computers.- 2.6. Common Laboratory Computers.- 2.6.1. IBM PC.- 2.6.2. IBM XT.- 2.6.3. IBM AT.- 2.6.4. 80386 Machines.- 2.6.5. IBM Personal System/2.- 2.6.6. Apple II.- 2.6.7. Macintosh.- 2.6.8. Macintosh II.- 2.6.9. VME-Bus Machines.- 2.6.10. DEC PDP-11.- 2.6.11. DEC VAX.- 2.7. Purchasing a Computer.- 2.7.1. Clones.- 2.7.2. Compatibility.- 2.8. For Further Reading.- 3. Software in the Neuroanatomy Laboratory.- 3.1. Introduction.- 3.2. How Software is Written.- 3.2.1. Source Files.- 3.2.2. Translation and Execution.- 3.3. System Software.- 3.3.1. Operating Systems.- 3.3.2. Time-Sharing (Multiuser) Operating Systems.- 3.3.3. Language Translators.- 3.3.4. Text Editors (Word Processors).- 3.4. Applications Software.- 3.4.1. Specific Laboratory Tasks.- 3.4.2. General Laboratory Tasks.- 3.5. Common Programming Languages.- 3.5.1. C.- 3.5.2. FORTRAN.- 3.5.3. BASIC.- 3.5.4. Other Programming Languages.- 3.5.5. High-Level Proprietary Languages.- 3.6. Software Costs and Productivity.- 3.6.1. Software Costs Related to Hardware Costs.- 3.6.2. Software Costs Related to Software Level.- 3.6.3. Programs and Program Products.- 3.6.4. How to Get the Job Done.- 3.7. The Vendor's Dilemma.- 3.8. For Further Reading.- 4. Semiautomatic Entry of Neuron Trees from the Microscope.- 4.1. Introduction.- 4.2. Principles of Semiautomatic Neuron Tracing.- 4.2.1. The Marriage of the Researcher to the Computer.- 4.2.2. A Single Pass over the Data.- 4.2.3. Identify Different Structures in Their Environment.- 4.2.4. Feedback.- 4.2.5. Work from the Best Image.- 4.3. The UNC Neuron-Tracing System.- 4.3.1. Hardware of the UNC Neuron-Tracing System.- 4.3.2. Control of the Stage.- 4.3.3. Coordinate System and Origins in the UNC Neuron-Tracing System.- 4.3.4. Outlining a Soma with the UNC System.- 4.3.5. Tracing a Dendrite with the UNC System.- 4.3.6. Locating and Outlining Other Structures.- 4.3.7. The Storage of Traced Data.- 4.3.8. Advantages of Vector Graphics in Neuron Tracing.- 4.4. Other Neuron-Tracing Techniques.- 4.4.1. Alternatives to Motorizing the Stage.- 4.4.2. Alternatives to the Computer-Generated Overlay.- 4.4.3. Alternative Stage Control Methods.- 4.5. For Further Reading.- 5. Input from Serial Sections.- 5.1. Introduction.- 5.2. History.- 5.3. Purpose of Serial Section Reconstruction.- 5.4. Entering Serial Sections into the Computer.- 5.4.1. Using a Data Tablet.- 5.4.2. Types of Images.
1. The History of Quantitative Neuroanatomy.- 1.1. Introduction.- 1.2. Early History of Drawing Neurons.- 1.3. How the Microscope Handicaps the User.- 1.3.1. Medium.- 1.3.2. Perspective.- 1.3.3. Magnification.- 1.3.4. Contrast.- 1.3.5. Measurement.- 1.4. Drawing with the Camera Lucida.- 1.5. The Pantograph: A Plotter for the Microscope.- 1.6. Physical Model Building.- 1.7. Early Attempts at Statistical Summaries.- 1.8. How the Computer Helps Visualizing and Summarizing.- 1.9. For Further Reading.- 1.10. What This Book Presents.- 2. Laboratory Computer Hardware.- 2.1. Introduction.- 2.2. Overview of Key Components.- 2.2.1. Bus.- 2.2.2. Central Processing Unit.- 2.2.3. Memory.- 2.2.4. Disks.- 2.2.5. Disk Drives.- 2.2.6. Keyboard.- 2.2.7. Terminal.- 2.2.8. Graphics Board.- 2.2.9. Ports.- 2.2.10. Analog-to-Digital Converter.- 2.3. Concepts and Definitions.- 2.3.1. Forms of Data.- 2.3.2. Analog and Digital Values.- 2.3.3. Storage of Digital Data.- 2.4. Computing Hardware Described in Some Depth.- 2.4.1. Central Processing Unit.- 2.4.2. Math Coprocessors.- 2.4.3. Random Access Memory.- 2.4.4. Disks.- 2.4.5. Magnetic Tapes.- 2.4.6. Graphics Display Cards.- 2.4.7. Computer Speeds.- 2.4.8. Bus.- 2.4.9. Plotters.- 2.4.10. Printers.- 2.4.11. Analog-to-Digital Converter.- 2.4.12. Digital-to-Analog Converter.- 2.4.13. Modem.- 2.4.14. Graphics Display Systems.- 2.4.15. Data Tablets.- 2.4.16. Mouse.- 2.4.17. Joysticks.- 2.4.18. Trackball.- 2.4.19. Stepping Motors.- 2.4.20. Components Used for Sensing Position and Motion.- 2.4.21. Ports.- 2.5. Physical Construction of Laboratory Computers.- 2.6. Common Laboratory Computers.- 2.6.1. IBM PC.- 2.6.2. IBM XT.- 2.6.3. IBM AT.- 2.6.4. 80386 Machines.- 2.6.5. IBM Personal System/2.- 2.6.6. Apple II.- 2.6.7. Macintosh.- 2.6.8. Macintosh II.- 2.6.9. VME-Bus Machines.- 2.6.10. DEC PDP-11.- 2.6.11. DEC VAX.- 2.7. Purchasing a Computer.- 2.7.1. Clones.- 2.7.2. Compatibility.- 2.8. For Further Reading.- 3. Software in the Neuroanatomy Laboratory.- 3.1. Introduction.- 3.2. How Software is Written.- 3.2.1. Source Files.- 3.2.2. Translation and Execution.- 3.3. System Software.- 3.3.1. Operating Systems.- 3.3.2. Time-Sharing (Multiuser) Operating Systems.- 3.3.3. Language Translators.- 3.3.4. Text Editors (Word Processors).- 3.4. Applications Software.- 3.4.1. Specific Laboratory Tasks.- 3.4.2. General Laboratory Tasks.- 3.5. Common Programming Languages.- 3.5.1. C.- 3.5.2. FORTRAN.- 3.5.3. BASIC.- 3.5.4. Other Programming Languages.- 3.5.5. High-Level Proprietary Languages.- 3.6. Software Costs and Productivity.- 3.6.1. Software Costs Related to Hardware Costs.- 3.6.2. Software Costs Related to Software Level.- 3.6.3. Programs and Program Products.- 3.6.4. How to Get the Job Done.- 3.7. The Vendor's Dilemma.- 3.8. For Further Reading.- 4. Semiautomatic Entry of Neuron Trees from the Microscope.- 4.1. Introduction.- 4.2. Principles of Semiautomatic Neuron Tracing.- 4.2.1. The Marriage of the Researcher to the Computer.- 4.2.2. A Single Pass over the Data.- 4.2.3. Identify Different Structures in Their Environment.- 4.2.4. Feedback.- 4.2.5. Work from the Best Image.- 4.3. The UNC Neuron-Tracing System.- 4.3.1. Hardware of the UNC Neuron-Tracing System.- 4.3.2. Control of the Stage.- 4.3.3. Coordinate System and Origins in the UNC Neuron-Tracing System.- 4.3.4. Outlining a Soma with the UNC System.- 4.3.5. Tracing a Dendrite with the UNC System.- 4.3.6. Locating and Outlining Other Structures.- 4.3.7. The Storage of Traced Data.- 4.3.8. Advantages of Vector Graphics in Neuron Tracing.- 4.4. Other Neuron-Tracing Techniques.- 4.4.1. Alternatives to Motorizing the Stage.- 4.4.2. Alternatives to the Computer-Generated Overlay.- 4.4.3. Alternative Stage Control Methods.- 4.5. For Further Reading.- 5. Input from Serial Sections.- 5.1. Introduction.- 5.2. History.- 5.3. Purpose of Serial Section Reconstruction.- 5.4. Entering Serial Sections into the Computer.- 5.4.1. Using a Data Tablet.- 5.4.2. Types of Images.
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