Computer Techniques in Neuroanatomy

496 Pages·1989·20.853 MB·English

by  Joseph J. Capowski (auth.)

Computer
Techniques in
Neuroanatomy
CONTRIBUTORS
Ellen M. Johnson
Department of Physiology
The University of North Carolina
Chapel Hill, North Carolina
R. Ranney Mize
Department of Anatomy and Neurobiology
University of Tennessee Health Science Center
Memphis, Tennessee
David G. Tieman
Department of Biological Sciences
State University of New York
Albany, New York
Harry B. M. Uylings, Jaap van Pelt,
Ronald W. H. Verwer, and Patricia McConnell
Netherlands Institute for Brain Research
Amsterdam, The Netherlands
Computer
Techniques in
Neuroanatomy
Joseph J. Capowski
Eutectic Electronics, Inc.
Raleigh, North Carolina
and The University oj North Carolina
Chapel Hill, North Carolina
Plenum Press • New York and London
Library of Congress Cataloging in Publication Data
Capowski, Joseph J.
Computer techniques in neuroanatomy I Joseph J. Capowski.
p. cm.
Bibliography: p.
Includes index.
ISBN-13: 978-1-4684-5693-6 e-ISBN-13: 978-1-4684-5691-2
DOl: 10.1007/978-1-4684-5691-2
1. Neuroanatomy-Data processing. I. Title.
[DNLM: 1. Computer Systems. 2. Neuroanatomy. WL 101 C245c]
QM451.C36 1989
591.4'8'0285 - dc20
DNLM/DLC 89-16046
for Library of Congress CIP
Cover illustration: HRP-filled spinocervical tract neuron from the spinal cord of an
adult cat. The cell was identified and stained by L. M. Mendell and M. J. Sedivec of the
Department of Anatomy and Neurobiology, SUNY, Stony Brook, New York. The
reconstruction was performed by J. J. Capowski of the Department of Physiology, The
University of North Carolina, Chapel Hill, North Carolina. Reproduced with permis
sion from Oxford University Press, New York, New York.
© 1989 Plenum Press, New York
Softcover reprint of the hardcover 1st edition 1989
A Division of Plenum Publishing Corporation
233 Spring Street, New York, N.Y. 10013
All rights reserved
No part of this book may be reproduced, stored in a retrieval system, or transmitted
in any form or by any means, electronic, mechanical, photocopying, microfilming,
recording, or otherwise, without written permission from the Publisher
Preface
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.
The data may be entered from tissue directly mounted in a microscope or from drawings,
photographs, or televised images of the tissue. Errors are made during data entry, both by
the person entering the data and because of optical constraints of the microscope. Tech
niques to correct these errors are found in Chapter 7. Chapter 8 presents techniques for
building displays of the data that are superior to the original microscope image. These
displays form one of the two major reasons for using a computer to assist in the study of
neuroanatomy.
The second major reason for using a computer in neuroanatomy is to summarize
statistically a structure, perhaps to compare one popUlation of structures to another. These
statistical methods are covered in Chapters 9, 10, and 11 by Harry Uylings, his col
leagues, and me.
In Chapter 12, Ellen Johnson describes functions that should be included in a com
puterized data collection system to make it easy to use. This chapter especially will help
v
vi PREFACE
you design your own programs, instruct your own programmer more intelligently, or
survey the marketplace with more insight.
Imaging systems that combine computers and television devices offer you new ways
to look at structures. Dave Tieman in Chapter 13 explains their basics, and Ranney Mize
follows in Chapter 14 with a complete treatment of their use in the analysis of immu
nocytochemically treated tissue. Television also offers the potential to automate the
tedious data entry process, especially when used in conjunction with the laser-scanning
microscope. Chapter 15 closes the text portion of the book by describing the current
capabilities and the future of such automation.
The final chapter compiles commercially available products for computer-assisted
neuroanatomy. These are presented side by side, as a shopping mall.
Why do you need to know the material in this book? In the last 20 years, computers
have been applied successfully to many fields, reducing tedium and increasing knowledge
and productivity. Often the initiative for applying this technology comes as much from the
computer manufacturers as it does from the users. When the marketplace is large, comput
er companies are willing to invest their people and financial resources in solving its
problems. Unfortunately, the neuroscience community does not form a large market, and
the neuroanatomy marketplace is even smaller. So the burden of applying the new tech
nology falls primarily you with some help from smaller companies.
OD
Many journal articles that describe the application of computers and ancillary hard
ware (e.g., television cameras, video digitizers, computer graphics display devices) have
been published in the last two decades, though scattered among neuroscience research
journals, neuroscience techniques journals, microscope journals, and computer journals.
Very few books have consolidated this information. This one does, and in it techniques
and principles are presented broadly enough so that the book will maintain its relevance
well past the lifespan of anyone computer system.
We use the book at UNC as a text in the course "The Computer in the Laboratory,"
but it is more likely that you will read it to learn more about the subject. You will probably
not read the book from cover to cover; rather, you will read the individual chapters that
discuss the particular problem that interests you. I have attempted to make each chapter
stand alone, even though this means that some repetition does occur.
The marriage of computers and neuroanatomy, like all marriages, does have some
strings attached, however. Using or programming computers can be a fascinating and
captivating hobby with never-ending challenges. My 16-year-old stepson spends un
counted hours in front of our home computer programming video games; he won't come
to the dinner table in the same way that young Pete Rose wouldn't come in from the
baseball diamond for lunch. The neuroscientist who discovers computers and doesn't use
them effectively can also miss lunch, that is, his neuroscience. It takes discipline to
remain a neuroscientist and not become a technologist interested more in the means of
solving a neuroscience problem than in its solution.
I came to the Physiology Department of the University of North Carolina as a
computer design engineer in 1972. The department was a leader in computer use in
neuroscience at that time, although its hardware consisted only of a PDP-ll computer,
which many people signed up to use. It was attached to a large IBM 370 computer owned
by our university. With the help of many people, I designed hardware and software for
neuron reconstruction, serial section reconstruction, silver grain counting, and other now
PREFACE vii
standard neuroanatomical measurement tasks. Since that time, many improvements have
been made to all these tasks, and new ones have been added. The work was not done in a
vacuum; many neuroscientists at UNC and at other schools contributed their suggestions,
and several computer engineers who had neuroscience interest at other institutions have
also been very helpful.
I must personally thank Edward R. Perl, the chairman of the UNC Department of
Physiology, for his moral support over 12 years. Miklos Rethelyi, 2nd Department of
Anatomy, Semmelweis University Medical School, Budapest, and a frequent visitor to
our department, has contributed much time and expertise in critiquing my efforts. William
L. R. Cruce, Department of Neurobiology, Northeastern Ohio Universities College of
Medicine, has been most helpful and has been a cheerleader. Ellen M. Johnson and C.
William Davis, both of our Department of Physiology, have been wonderful backboards
for technical discussions on how to solve problems.
The writing effort of this book has also been shared. I want to thank my wife Carolyn
W. Capowski, who is an instructional developer, and her colleagues, technical editors
David Carozza, Judy Clark, Connie Cowell, Craig Henkle, and Kim Miller for their
efforts, especially in the face of my umeasonable demands.
I am delighted to acknowledge multiyear financial support from a National Institutes
of Health program project grant on the effects of spinal cord injury, number NS-14899.
Most recently, I am indebted to Eutectic Electronics, Inc., Raleigh, NC, for seeing
enough potential marketplace for a neuron-tracing system and a serial section reconstruc
tion system to provide me laboratory grant support for their continued development.
I hope that the book helps you. Please call or write me if there are any issues you
wish to discuss. Good luck with your reading.
Joseph J. Capowski
Chapel Hill, North Carolina
Contents
Glossary. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Chapter 1. The History of Quantitative Neuroanatomy
1.1. Introduction................................................... 23
1.2. Early History of Drawing Neurons ................................ 23
1.3. How the Microscope Handicaps the User. . . . . . . . . . . . . . . . . . . . . . . . . . . 25
1.3.1. Medium................................................ 25
1.3.2. Perspective ............................................. 27
1.3.3. Magnification ........................................... 27
1.3.4. Contrast................................................ 27
1.3.5. Measurement............................................ 27
1.4. Drawing with the Camera Lucida ................................. 28
1. 5. The Pantograph: A Plotter for the Microscope ....................... 31
1.6. Physical Model Building ........................................ 32
1. 7. Early Attempts at Statistical Summaries ............................ 35
1.8. How the Computer Helps Visualizing and Summarizing. . . . . . . . . . . . . . . 35
1. 9. For Further Reading ............................................ 38
1.10. What This Book Presents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Chapter 2. Laboratory Computer Hardware
2.1. Introduction.................................................... 39
2.2. Overview of Key Components. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
2.2.1. Bus.................................................... 39
2.2.2. Central Processing Unit ................................... 40
2.2.3. Memory................................................ 40
2.2.4. Disks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
2.2.5. Disk Drives 42
ix
x CONTENTS
2.2.6. Keyboard............................................... 42
2.2.7. Terminal ............................................... 42
2.2.8. Graphics Board. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
2.2.9. Ports................................................... 42
2.2.10. Analog-to-Digital Converter. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
2.3. Concepts and Definitions ......................................... 43
2.3.1. Forms of Data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
2.3.2. Analog and Digital Values " . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
2.3.3. Storage of Digital Data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
2.4. Computing Hardware Described in Some Depth ...................... 44
2.4.1. Central Processing Unit ................................... 44
2.4.2. Math Coprocessors ....................................... 44
2.4.3. Random Access Memory. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
2.4.4. Disks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
2.4.5. Magnetic Tapes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
2.4.6. Graphics Display Cards ................................... 46
2.4.7. Computer Speeds ........................................ 47
2.4.8. Bus.................................................... 48
2.4.9. Plotters................................................. 48
2.4.10. Printers ................................................ 49
2.4.11. Analog-to-DigitalConverter ........ ..... ......... .......... 51
2.4.12. Digital-to-Analog Converter. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
2.4.13. Modem ................................................ 51
2.4.14. Graphics Display Systems ................................. 52
2.4.15. DataTablets . .... ................. ............... ....... 57
2.4.16. Mouse................................................. 58
2.4.17. Joysticks............................................... 58
2.4.18. Trackball............................................... 60
2.4.19. Stepping Motors ............... , ............ .... ......... 61
2.4.20. Components Used for Sensing Position and Motion ............ 61
2.4.21. Ports................................................... 62
2.5. Physical Construction of Laboratory Computers. . . . . . . . . . . . . . . . . . . . . . . 63
2.6. Common Laboratory Computers ................................... 65
2.6.1. IBM PC ...... .......... .... .... ..... ... ... ....... ...... 65
2.6.2. IBM XT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
2.6.3. IBM AT. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
2.6.4. 80386 Machines ......................................... 66
2.6.5. IBM Personal System!2 ................................... 66
2.6.6. Apple II . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
2.6.7. Macintosh.............................................. 67
2.6.8. Macintosh II ............................................ 67
2.6.9. VME-Bus Machines. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
2.6.10. DEC PDP-ll ............................................ 67
2.6.11. DEC VAX.............................................. 68
2.7. Purchasing a Computer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
CONTENTS xi
2.7.1. Clones . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
2.7.2. Compatibility............................................ 69
2.8. For Further Reading ............................................. 70
Chapter 3. Software in the Neuroanatomy Laboratory
3. 1. Introduction.................................................... 71
3.2. How Software is Written ......................................... 71
3.2.1. Source Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
3.2.2. Translation and Execution .................................. 72
3.3. System Software. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
3.3.1. Operating Systems ........................................ 74
3.3.2. Time-Sharing (Multiuser) Operating Systems. . . . . . . . . . . . . . . . . . . 75
3.3.3. Language Translators ...................................... 76
3.3.4. Text Editors (Word Processors) ... . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
3.4. Applications Software. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
3.4.1. Specific Laboratory Tasks .................................. 78
3.4.2. General Laboratory Tasks .................................. 78
3.5. Common Programming Languages ................................. 79
3.5.1. C ...................................................... 79
3.5.2. FORTRAN ........•................•...................... 79
3.5.3. BASIC................................................... 80
3.5.4. Other Programming Languages .............................. 80
3.5.5. High-Level Proprietary Languages ........................... 81
3.6. Software Costs and Productivity ................................... 81
3.6.1. Software Costs Related to Hardware Costs. . . . . . . . . . . . . . . . . . . . . 82
3.6.2. Software Costs Related to Software Level ..................... 82
3.6.3. Programs and Program Products ............................. 83
3.6.4. How to Get the Job Done .................................. 84
3.7. The Vendor's Dilemma .......................................... 86
3.8. For Further Reading ............................................. 86
Chapter 4. Semiautomatic Entry of Neuron Trees from the
Microscope
4.1. Introduction.................................................... 87
4.2. Principles of Semiautomatic Neuron Tracing ......................... 87
4.2.1. The Marriage of the Researcher to the Computer. . . . . . . . . . . . . . . . 89
4.2.2. A Single Pass over the Data ................................ 89
4.2.3. Identify Different Structures in Their Environment .............. 89
4.2.4. Feedback................................................ 89
4.2.5. Work from the Best Image. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90