Neurostereology

Contributors ix

Preface xiii

1 Stereological Estimation of Brain Volume and Surface Area from MR Images 3
Niyazi Acer and Mehmet Turgut

Background 3

The Cavalieri Principle 3

Volume Estimation Using Spatial Grid of Points 7

Surface Area Estimation 8

Isotropic Cavalieri Design 14

Sections Analyzed with Independent Grid Design 14

Surface Area Using the Invariator 16

Volume and Surface Area Estimation Using Segmentation Method 17

Discussion 18

References 19

Webliography 21

Appendix A: R Commands for Point Counting Method 21

Appendix B: R Commands for Vertical Section to Estimate Surface Area 23

2 Cell Proliferation in the Brains of Adult Rats Exposed to Traumatic Brain Injury 27
Sandra A. Acosta, Naoki Tajiri, Paula C. Bickford, and Cesar V. Borlongan

Background 27

Materials and Methods 28

Results 29

Discussion 33

Acknowledgments 37

References 37

3 Age Effects in Substantia Nigra of Asian Indians 39
Phalguni Anand Alladi

Background 39

Materials and Methods 40

Discussion 43

Acknowledgments 48

References 49

4 Design-Based Stereology in the Brain Bank Setting 53
Mark W. Burke

Background 53

Specimen Preparation 53

A Practical Application of Design-Based Stereology 57

Results 59

Conclusion 60

References 61

5 Practical Stereology for Preclinical Neurotoxicology 63
Mark T. Butt

Background 63

Specimen Quality 64

Practical Stereology 70

Software Validation/Verifi cation 70

References 72

6 An Overabundance of Prefrontal Cortex Neurons Underlies Early Brain Overgrowth in Autism 73
Eric Courchesne, Peter R. Mouton, Michael E. Calhoun, Clelia Ahrens-Barbeau, Melodie J. Hallet, Cynthia Carter Barnes, Karen Pierce, and Katarina Semendeferi

Background 73

Methods 74

Results 78

Discussion 80

Acknowledgments 81

References 82

7 Order in Chaos: Stereological Studies of Nervous Tissue 85
Peter Dockery

Background 85

The Stereological Approach 85

Axonal Number and Composition in the Murine Optic Nerve 91

Axonal and Fiber Size Distributions 92

The Myelin Sheath 93

Conclusion 94

References 95

8 Comparative Stereology Studies of Brains from Marine Mammals 99
Nina Eriksen and Bente Pakkenberg

Background 99

Description of Different Marine Mammalian Brains 99

Parts of the Brain 102

References 109

Appendix: Cited Stereological Approaches 110

9 Quantitative Assessment of Hippocampus Architecture Using the Optical Disector 113
Shozo Jinno

Background 113

The Hippocampus 114

Conclusion 123

References 123

10 The Possible Applications (and Pitfalls!) of Stereological Analysis in Postmortem Brain Research 129
Ahmad A. Khundakar and Alan J. Thomas

Background 129

The Legacy of Two-Dimensional (2D) Analysis 129

Density: A Necessary Evil 130

"Come on, Feel the Noise": Recognizing Confounding Factors 130

"I Am Not a Number": The Importance of Sound Patient Clinical History 131

Lessons Learned from Stereology: Toward a More Unifi ed Approach to Brain Banking and Postmortem Tissue Research (and Beyond!) 132

Obtain the Full Reference Volume or "Make Do and Mend" 133

Turn Down the "Noise" 134

"Check the Information, Expand the Knowledge" 135

Show Your Work! 135

Conclusion 136

Acknowledgments 136

References 136

11 Visualization of Blood Vessels in Two-Dimensional and Three-Dimensional Environments for Vascular Stereology in the Brain 139
Zerina Lokmic

Background 139

Vascular Stereology of Tissue Sections 139

Visualization of Brain Blood Vessels 142

Conclusion 149

Acknowledgment 149

References 149

12 Blood Flow Analysis in Epilepsy Using a Novel Stereological Approach 153
Rocio Leal-Campanario, Luis Alarcon-Martinez, Susana Martinez-Conde, Michael Calhoun, and Stephen Macknik

Background 153

Materials and Methods 155

Results 166

Discussion 172

References 173

13 AD-Type Neuron Loss in Transgenic Mouse Models 177
Kebreten F. Manaye and Peter R. Mouton

Background 177

Materials and Methods 179

Results 182

Discussion 185

Acknowledgments 187

References 188

14 Quantification in Populations of Nonuniformly Distributed Cells in the Human Cerebral Cortex 191
William L. Maxwell

Background 191

Materials and Methods 191

Results 196

Discussion 205

References 208

15 The Effects of High-Fat Diet on the Mouse Hypothalamus: A Stereological Study 211
Mohammad Reza Namavar, Samira Raminfard, Zahra Vojdani Jahromi, and Hassan Azari

Background 211

Materials and Methods 212

Results 213

Discussion 215

Acknowledgments 217

References 218

16 2D and 3D Morphometric Analyses Comparing Three Rodent Models 221
JiHyuk Park and S. Omar Ahmad

Background 221

Materials and Methods 221

Results 226

Discussion 230

References 235

17 A Stereologic Perspective on Autism Neuropathology 237
Neha Uppal and Patrick R. Hof

Background 237

Cortical Areas 237

Hippocampus 248

Noncortical Areas 249

Conclusions 253

References 254

Index 257