Computer techniques in neuroanatomy:
Gespeichert in:
| Format: | Buch |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
New York u.a.
Plenum Press
1989
|
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XX, 483 S. Ill., graph. Darst. |
| ISBN: | 0306432633 |
Internformat
MARC
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| 245 | 1 | 0 | |a Computer techniques in neuroanatomy |c Joseph J. Capowski ... |
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| 300 | |a XX, 483 S. |b Ill., graph. Darst. | ||
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| 650 | 4 | |a Computer Systems | |
| 650 | 4 | |a Neuroanatomy | |
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Datensatz im Suchindex
| _version_ | 1804117096772141056 |
|---|---|
| adam_text | Computer
Techniques in
Neuroanatomy
Joseph J Capowski
Eutectic Electronics, Inc
Raleigh, North Carolina
and The University of North Carolina
Chapel Hill, North Carolina
Plenum Press • New York and London
Contents
Glossary l
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
131 Medium 25
132 Perspective 27
133 Magnification 27
134 Contrast 27
135 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 J_ 38
1 10 What This Book Presents 38
Chapter 2 Laboratory Computer Hardware
2 1 Introduction 39
2 2 Overview of Key Components 39
221 Bus 39
222 Central Processing Unit 40
223 Memory 40
224 Disks 41
225 Disk Drives 42
ix
x CONTENTS
226 Keyboard 42
227 Terminal 42
228 Graphics Board 42
229 Ports 42
2 2 10 Analog-to-Digital Converter 42
2 3 Concepts and Definitions 43
231 Forms of Data 43
232 Analog and Digital Values 43
233 Storage of Digital Data 43
2 4 Computing Hardware Described in Some Depth 44
241 Central Processing Unit 44
242 Math Coprocessors 44
243 Random Access Memory 45
244 Disks 46
245 Magnetic Tapes 46
246 Graphics Display Cards 46
247 Computer Speeds 47
248 Bus 48
249 Plotters 48
2 4 10 Printers 49
2 4 11 Analog-to-Digital Converter 51
2 4 12 Digital-to-Analog Converter 51
2 4 13 Modem 51
2 4 14 Graphics Display Systems 52
2 4 15 Data Tablets 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
261 IBM PC 7: 65
262 IBM XT 65
263 IBM AT 65
264 80386 Machines 66
265 IBM Personal System/2 66
266 Apple II 66
267 Macintosh 67
268 Macintosh II 67
269 VME-Bus Machines 67
2 6 10 DEC PDP-11 67
2 6 11 DEC VAX 68
2 7 Purchasing a Computer 68
CONTENTS xi
271 Clones 68
272 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
321 Source Files 72
322 Translation and Execution 72
3 3 System Software 74
331 Operating Systems 74
332 Time-Sharing (Multiuser) Operating Systems 75
333 Language Translators 76
334 Text Editors (Word Processors) 78
3 4 Applications Software 78
341 Specific Laboratory Tasks 78
342 General Laboratory Tasks 78,
3 5 Common Programming Languages 79
351C 79
352 FORTRAN 79
353 BASIC 80
354 Other Programming Languages 80
355 High-Level Proprietary Languages 81
3 6 Software Costs and Productivity 81
361 Software Costs Related to Hardware Costs 82
362 Software Costs Related to Software Level 82
363 Programs and Program Products 83
364 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
421 The Marriage of the Researcher to the Computer 89
422A Single Pass over the Data 89
423 Identify Different Structures in Their Environment 89
424 Feedback 89
425 Work from the Best Image 90
xii CONTENTS
4 3 The UNC Neuron-Tracing System 90
431 Hardware of the UNC Neuron-Tracing System 90
432 Control of the Stage 92
433 Coordinate System and Origins in the UNC Neuron-Tracing
System 94
434 Outlining a Soma with the UNC System 94
435 Tracing a Dendrite with the UNC System 96
436 Locating and Outlining Other Structures 101
437 The Storage of Traced Data 102
438 Advantages of Vector Graphics in Neuron Tracing 103
4 4 Other Neuron-Tracing Techniques 104
441 Alternatives to Motorizing the Stage 104
442 Alternatives to the Computer-Generated Overlay 105
443 Alternative Stage Control Methods 105
4 5 For Further Reading 107
Chapter 5 Input from Serial Sections
JOSEPH J CAPOWSKI and ELLEN M JOHNSON
5 1 Introduction 109
5 2 History 110
5 3 Purpose of Serial Section Reconstruction 112
5 4 Entering Serial Sections into the Computer 113
541 Using a Data Tablet 113
542 Types of Images 113
543 Calibrating the Data Tablet 114
544 Entering the Data 116
545 Aligning Traced Sections 119
5 5 The Storage of Data 121
551 Compressing the Data 122
552 Organizing the Data 123
5 6 Editing of Data 77 124
5 7 Displays and Plots of Serial Section Reconstructions 125
5 8 Statistical Summarizations of Serial Section Reconstructions 125
5 9 For Further Reading 125
Chapter 6 Video Input Techniques
6 1 Introduction 129
62A Video-Based Anatomic Data-Collecting System 130
6 3 Extracting Vector Information from a Televised Image 130
631 Tracing a Dendrite 133
632 Outlining a Structure 135
CONTENTS xiii
6 4 Extracting Optical-Density Information 136
6 5 Masking of Images 141
6 6 Particle Counting 143
6 7 Automatic Focusing 144
6 8 Video Input Compared to Directly Viewed Input 145
681 Advantages of Television-Based Data Collection 145
682 Disadvantages of Television-Based Systems 146
6 9 For Further Reading 146
Chapter 7 Intermediate Computations of Reconstructed Data
7 1 Introduction 149
7 2 Focus-Axis Problems 149
7 3 Merging of Multiple-Section Dendrites 152
7 4 Aligning One Tissue Section with Another 154
7 5 Editing 155
7 6 Mathematical Testing of the Data Base 157
7 7 Serial Inspection of Structures 158
7 8 Reordering of Trees 159
7 9 Filtering 159
7 10 Storage of Data on Disk 161
7 11 Conclusion 163
7 12 For Further Reading 163
Chapter 8 Three-Dimensional Displays and Plots of Anatomic
Structures
8 1 Introduction 165
8 2 Three-Dimensional Displays on a Two-Dimensional Screen 167
821 Smooth Rotation and Kinesthesia 167
822 Clipping n- 169
823 Projection onto the Two-Dimensional Screen 170
824 Zooming and Magnification 172
825 Variation of Intensity 173
826 Hidden-Line and Hidden-Surface Removal 173
827 Stereo Pairs 175
828 Line Generation 176
8 3 Vector Display of Structure 177
831 Time Constraint to Avoid Flicker 177
832 Only Wire-Frame Stick Figures without Thickness 178
833 Smooth Rotation 178
834 Spatial Resolution and Aliasing 178
835 Highlighting Vector Displays by Varying Brightness 179
836 Color Vector Graphics Systems 180
xiv CONTENTS
8 4 Raster Display of Structures 181
841 The Aliasing Problem in Raster Displays 182
842 Spatial Resolution 183
843 Surface-Filled Raster Displays 184
844 Current Sophisticated Image-Generation Techniques 184
845 Enriched Raster Displays 187
846 Time and Costs of Raster Displays of Anatomic Data 188
8 5 Three-Dimensional Plots of Neuroanatomical Structure 189
851 Felt-Tip Pen Plotter 189
852 Plots on a Laser Printer 190
8 6 For Further Reading 191
Chapter 9 Mathematical Summarizations of Individual Neuron
Structures
9 1 Introduction 193
9 2 Numeric Summaries of a Cell 193
921 Counting Measurements 194
922 Length-Based Measurements 195
923 Area-Based Measurements 195
924 Volume-Based Measurements 196
925 The Region of Influence of the Neuron 197
926 Measurements of the Neuron s Center 198
927 Orientations of the Neuron 199
928 Point-Type Densities 199
929 Analysis of Dendritic Spines 200
9 3 Graphing Summaries 200
931 Distributions of Point Types 201
932 Distributions of Dendritic Length 202
933 Analysis of Branch Segments 202
934 Analysis of Branch Points 207
935 Sholl Sphere Analysis 208
936 Directional Analysis 77 210
937 Cluster Analysis 213
9 4 For Further Reading 213
Chapter 10 Topological Analysis of Individual Neurons
HARRY B M UYLINGS, JAAP VAN PELT, and
RONALD W H VERWER
10 1 Introduction 215
10 2 Classification of Tree Types 217
10 3 Classification Based on Different Topological Features 221
CONTENTS xv
10 3 1 Classification according to the Degree of Subtree Pairs 221
10 3 2 Classification Based on Topological Distance from the Root 228
10 4 Comparison of Measures for Asymmetry of Trees 232
10 4 1 Trees with Bifurcations Only (Strictly Binary Trees) 232
10 4 2 Multifurcating Trees 234
10 5 Ordering Systems for Segments 235
10 6 Analysis of Incomplete Trees 236
10 7 In Conclusion 237
10 8 Summary 238
10 9 Appendix 239
Chapter 11 Statistical Analysis of Neuronal Populations
HARRY B M UYLINGS, JAAP VAN PELT,
RONALD W H VERWER, and PATRICIA McCONNELL
11 1 Introduction 241
11 2 Metrics of Somatic Size and Dendritic Segments 242
11 2 1 Somatic Size 242
11 2 2 The Size of a Dendritic Tree 243
11 2 3 Metric Analysis of Segments 244
11 3 Angular Metrics of Bifurcations 246
11 4 Spatial Orientation of Trees 247
11 4 1 Spherical and Circular Orientation Methods 247
11 4 2 Cubic Orientation Methods 250
11 4 3 Principal-Axes Method 253
11 4 4 Cartesian Grid Analysis for Dendritic Orientation and Density 254
11 4 5 Comparison of Orientation Methods 255
11 5 Statistical Evaluation of Groups of Neurons 257
11 5 1 Parametric and Nonparametric Testing 260
11 5 2 Geometric Dendritic Size and Body Size 262
11 5 3 Multivariate Comparison of Sets of Dendritic Variables 262
11 6 In Conclusion ,-rr 263
11 7 Summary 263
Chapter 12 Controlling the Computer System: The User
Interface
ELLEN M JOHNSON
12 1 Introduction 265
12 2 Principles of User Interface Design 266
12 3 Selecting Commands 268
12 3 1 Introduction 268
12 3 2 Menus 268
xvi CONTENTS
12 3 3 Command-Line Interfaces 271
12 3 4 Direct-Manipulation Systems 273
12 3 5 Command Operands, Default Values, and Parameters 275
12 4 Using Interactive Devices to Control Tracing 276
12 4 1 Introduction 276
12 4 2 Tracing with a Data Tablet 276
12 4 3 Tracing by Moving the Microscope Stage 277
12 4 4 Tracing on a Digitized Video Image 278
12 5 Datastorage 278
12 5 1 Introduction 278
12 5 2 Disk Files 278
12 5 3 Backup 279
12 6 Error Handling 280
12 7 Presentation of Output 281
12 8 Subroutine Libraries 282
12 9 User Manuals and Other Documentation 282
Chapter 13 Video Enhancement Techniques
DAVID G TIEMAN
13 1 Introduction 285
13 2 Hardware 287
13 2 1 Image-Processing Boards 287
13 2 2 The Video Input 292
13 2 3 Video Displays 294
13 2 4 True Color Systems 295
13 2 5 Storage of Images 295
13 3 Software 296
13 4 Enhancing the Image 296
13 4 1 Analog Adjustments of the Gray Scale 297
13 4 2 Digital Manipulation of the Gray Scale 299
13 4 3 Decreasing the Noise ~ T 305
13 4 4 Delimiting the Object 314
13 4 5 Fourier Analysis of Images 321
13 4 6 Combining Images 326
13 5 Is Image Processing Legitimate? 330
13 6 For Further Reading 331
Chapter 14 The Analysis of Immunohistochemical Data
R RANNEY MIZE
14 1 Introduction 333
14 2 Hardware for Image Analysis 334
CONTENTS **»
14 2 1 Image-Acquisition Devices 334
14 2 2 Image Memory and Processor Boards 336
14 2 3 General Information 336
14 3 Characteristics of Image Analyzers 337
14 3 1 Spatial Resolution 337
14 3 2 Gray-Scale Resolution 338
14 3 3 Dynamic Range 338
14 3 4 Image Input and Processing Speed 338
14 4 How to Evaluate and Resolve Problems with an Image-Analysis
System 339
14 4 1 Photometric Uniformity in Space 339
14 4 2 Photometric Uniformity in Time 341
14 4 3 System Sensitivity and Linearity 343
14 4 4 Evaluation of Measurement Algorithms 343
14 5 How to Measure Immunocytochemically Labeled Tissue 344
14 5 1 Setting up the System 344
14 5 2 Collecting Data 346
14 6 Analysis of Immunocytochemistry Data 355
14 6 1 Field Measurements 356
14 6 2 Cell Measurements 35 6
14 6 3 Fiber Measurements 358
14 7 Histochemistry Procedures and Controls 360
14 7 1 Factors Affecting Labeling 360
14 7 2 Controls 363
14 7 3 Quantitative Standards 364
14 8 Summary and Additional Information 365
14 8 1 Hardware Considerations 365
14 8 2 Choice of Image Analyzer 366
14 8 3 Biological Measures 368
14 8 4 Biological Utility of the Measures 369
14 9 For Further Reading 371
Chapter 15 Fully Automatic Neuron Tracing
15 1 Introduction 373
15 2 The Automatic Reconstruction Problem 373
15 3 A Standard of Comparison 375
15 4 The Current Art of Automatic Tracing 375
15 4 1 Automatic Neuron Tracing with a Vidisector 376
15 4 2 Automatic Neuron Tracing with a Television Camera 377
15 5 For Future Work 380
15 5 1 Bigger and Faster Computers 380
15 5 2 Better Image-Enhancement Techniques 381
15 5 3 The Confocal Microscope 381
15 6 Conclusion 386
15 7 For Further Reading 386
xviii CONTENTS
Chapter 16 Commercially Available Computer Systems for
Neuroanatomy
16 1 Introduction 387
16 2 Companies and Their Products 387
16 2 1 American Innovision, Inc 387
16 2 2 Analytical Imaging Concepts, Inc 388
16 2 3 Axon Instruments, Inc 389
16 2 4 Biographies, Inc 390
16 2 5 Bio Image—A Kodak Company 391
16 2 6 Bio-Rad 392
16 2 7 Burleigh Instruments, Inc 394
16 2 8 Dage-MTI, Inc 397
16 2 9 Dapple Systems 398
16 2 10 Eikonix 399
16 2 11 Eutectic Electronics, Inc 400
16 2 12 General Imaging Corporation 403
16 2 13 Image Data Systems 404
16 2 14 Imaging Research, Inc 406
16 2 15 INDEC Systems 407
16 2 16 Jandel Scientific 409
16 2 17 Joyce-Loebl 411
16 2 18 Media Cybernetics 412
16 2 19 Microscience, Inc 413
16 2 20 Olympus Corporation 414
16 2 21 Quantex Corporation 415
16 2 22 R amp;M Biometrics, Inc 416
16 2 23 Sarastro, Inc 416
16 2 24 Southern Micro Instruments 417
16 2 25 SPEX Industries, Inc 418
16 2 26 Technology Resources, Inc 419
16 2 27 Universal Imaging Corporation 420
16 2 28 Wild Leitz UJS A , Inc 421
References 425
Selected Reading 445
Index 447
|
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| spelling | Computer techniques in neuroanatomy Joseph J. Capowski ... New York u.a. Plenum Press 1989 XX, 483 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Anatomie gtt Computers gtt Neuroanatomie - Système informatique Zenuwstelsel gtt Datenverarbeitung Computer Systems Neuroanatomy Neuroanatomy Data processing Datenverarbeitung (DE-588)4011152-0 gnd rswk-swf Neuroanatomie (DE-588)4171577-9 gnd rswk-swf Neuroanatomie (DE-588)4171577-9 s Datenverarbeitung (DE-588)4011152-0 s DE-604 Capowski, Joseph J. Sonstige oth HEBIS Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=001754314&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Computer techniques in neuroanatomy Anatomie gtt Computers gtt Neuroanatomie - Système informatique Zenuwstelsel gtt Datenverarbeitung Computer Systems Neuroanatomy Neuroanatomy Data processing Datenverarbeitung (DE-588)4011152-0 gnd Neuroanatomie (DE-588)4171577-9 gnd |
| subject_GND | (DE-588)4011152-0 (DE-588)4171577-9 |
| title | Computer techniques in neuroanatomy |
| title_auth | Computer techniques in neuroanatomy |
| title_exact_search | Computer techniques in neuroanatomy |
| title_full | Computer techniques in neuroanatomy Joseph J. Capowski ... |
| title_fullStr | Computer techniques in neuroanatomy Joseph J. Capowski ... |
| title_full_unstemmed | Computer techniques in neuroanatomy Joseph J. Capowski ... |
| title_short | Computer techniques in neuroanatomy |
| title_sort | computer techniques in neuroanatomy |
| topic | Anatomie gtt Computers gtt Neuroanatomie - Système informatique Zenuwstelsel gtt Datenverarbeitung Computer Systems Neuroanatomy Neuroanatomy Data processing Datenverarbeitung (DE-588)4011152-0 gnd Neuroanatomie (DE-588)4171577-9 gnd |
| topic_facet | Anatomie Computers Neuroanatomie - Système informatique Zenuwstelsel Datenverarbeitung Computer Systems Neuroanatomy Neuroanatomy Data processing Neuroanatomie |
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