Computer Techniques in Neuroanatomy

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.

Table of Contents:
1. The History of Quantitative Neuroanatomy.- 1.1. Introduction.- 1.2. Early History of Drawing Neurons.- 1.3. How the Microscope Handicaps the User.- 1.4. 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.- 2.3. Concepts and Definitions.- 2.4. Computing Hardware Described in Some Depth.- 2.5. Physical Construction of Laboratory Computers.- 2.6. Common Laboratory Computers.- 2.7. Purchasing a Computer.- 2.8. For Further Reading.- 3. Software in the Neuroanatomy Laboratory.- 3.1. Introduction.- 3.2. How Software is Written.- 3.3. System Software.- 3.4. Applications Software.- 3.5. Common Programming Languages.- 3.6. Software Costs and Productivity.- 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.- 4.3. The UNC Neuron-Tracing System.- 4.4. Other Neuron-Tracing Techniques.- 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.- 5.5. The Storage of Data.- 5.6. Editing of Data.- 5.7. Displays and Plots of Serial Section Reconstructions.- 5.8. Statistical Summarizations of Serial Section Reconstructions.- 5.9. For Further Reading.- 6. Video Input Techniques.- 6.1. Introduction.- 6.2. A Video-Based Anatomic Data-Collecting System.- 6.3. Extracting Vector Information from a Televised Image.- 6.4.Extracting Optical-Density Information.- 6.5. Masking of Images.- 6.6. Particle Counting.- 6.7. Automatic Focusing.- 6.8. Video Input Compared to Directly Viewed Input.- 6.9. For Further Reading.- 7. Intermediate Computations of Reconstructed Data.- 7.1. Introduction.- 7.2. Focus-Axis Problems.- 7.3. Merging of Multiple-Section Dendrites.- 7.4. Aligning One Tissue Section with Another.- 7.5. Editing.- 7.6. Mathematical Testing of the Data Base.- 7.7. Serial Inspection of Structures.- 7.8. Reordering of Trees.- 7.9. Filtering.- 7.10. Storage of Data on Disk.- 7.11. Conclusion.- 7.12. For Further Reading.- 8. Three-Dimensional Displays and Plots of Anatomic Structures.- 8.1. Introduction.- 8.2. Three-Dimensional Displays on a Two-Dimensional Screen.- 8.3. Vector Display of Structure.- 8.4. Raster Display of Structures.- 8.5. Three-Dimensional Plots of Neuroanatomical Structure.- 8.6. For Further Reading.- 9. Mathematical Summarizations of Individual Neuron Structures.- 9.1. Introduction.- 9.2. Numeric Summaries of a Cell.- 9.3. Graphing Summaries.- 9.4. For Further Reading.- 10. Topological Analysis of Individual Neurons.- 10.1. Introduction.- 10.2. Classification of Tree Types.- 10.3. Classification Based on Different Topological Features.- 10.4. Comparison of Measures for Asymmetry of Trees.- 10.5. Ordering Systems for Segments.- 10.6. Analysis of Incomplete Trees.- 10.7. In Conclusion.- 10.8. Summary.- 10.9. Appendix.- 11. Statistical Analysis of Neuronal Populations.- 11.1. Introduction.- 11.2. Metrics of Somatic Size and Dendritic Segments.- 11.3. Angular Metrics of Bifurcations.- 11.4. Spatial Orientation of Trees.- 11.5. Statistical Evaluation of Groups of Neurons.- 11.6. In Conclusion.- 11.7. Summary.- 12. Controlling the Computer System: The User Interface.- 12.1. Introduction.- 12.2. Principles of User Interface Design.- 12.3. Selecting Commands.- 12.4. Using Interactive Devices to Control Tracing.- 12.5. Data Storage.- 12.6. Error Handling.- 12.7. Presentation of Output.- 12.8. Subroutine Libraries.- 12.9. User Manuals and Other Documentation.- 13. Video Enhancement Techniques.- 13.1. Introduction.- 13.2. Hardware.- 13.3. Software.- 13.4. Enhancing the Image.- 13.5. Is Image Processing Legitimate?.- 13.6. For Further Reading.- 14. The Analysis of Immunohistochemical Data.- 14.1. Introduction.- 14.2. Hardware for Image Analysis.- 14.3. Characteristics of Image Analyzers.- 14.4. How to Evaluate and Resolve Problems with an Image-Analysis System.- 14.5. How to Measure Immunocytochemically Labeled Tissue.- 14.6. Analysis of Immunocytochemistry Data.- 14.7. Histochemistry Procedures and Controls.- 14.8. Summary and Additional Information.- 14.9. For Further Reading.- 15. Fully Automatic Neuron Tracing.- 15.1. Introduction.- 15.2. The Automatic Reconstruction Problem.- 15.3. A Standard of Comparison.- 15.4. The Current Art of Automatic Tracing.- 15.5. For Future Work.- 15.6. Conclusion.- 15.7. For Further Reading.- 16. Commercially Available Computer Systems for Neuroanatomy.- 16.1. Introduction.- 16.2. Companies and Their Products.- References.- Selected Reading.