MATLAB for Neuroscientists by Wallisch, Pascal -- Read -- Imperial Library of Trantor

Index

Cover image Title page Table of Contents Copyright Preface to the Second Edition Preface to the First Edition About the Authors How to Use this Book

Structural and Conceptual Considerations Layout and Style Companion Web Site

Part I: Fundamentals

Chapter 1. Introduction Chapter 2. MATLAB Tutorial

2.1 Goal of this Chapter 2.2 Purpose and Philosophy of MATLAB 2.3 Graphics and Visualization 2.4 Function and Scripts 2.5 Data Analysis 2.6 A Word on Function Handles 2.7 The Function Browser 2.8 Summary MATLAB Functions, Commands, and Operators Covered in This Chapter

Chapter 3. Mathematics and Statistics Tutorial

3.1 Introduction 3.2 Linear Algebra 3.3 Probability and Statistics MATLAB Functions, Commands, and Operators Covered in This Chapter

Chapter 4. Programming Tutorial: Principles and Best Practices

4.1 Goals of this Chapter 4.2 Organizing Code 4.3 Organizing More Code: Bigger Projects 4.4 Taming Errors MATLAB Functions, Commands, and Operators Covered in This Chapter

Chapter 5. Visualization and Documentation Tutorial

5.1 Goals of This Chapter 5.2 Visualization 5.3 Documentation MATLAB Functions, Commands, and Operators Covered in This Chapter

Part II: Data Collection with MATLAB

Chapter 6. Collecting Reaction Times I: Visual Search and Pop Out

6.1 Goals of this Chapter 6.2 Background 6.3 Exercises 6.4 Project MATLAB Functions, Commands, and Operators Covered in this Chapter

Chapter 7. Collecting Reaction Times II: Attention

7.1 Goals of this Chapter 7.2 Background 7.3 Exercises 7.4 Project MATLAB Functions, Commands, and Operators Covered in this Chapter

Chapter 8. Psychophysics

8.1 Goals of this Chapter 8.2 Background 8.3 Exercises 8.4 Project MATLAB Functions, Commands, and Operators Covered in this Chapter

Chapter 9. Psychophysics with GUIs

Abstract 9.1 Goals of This Chapter 9.2 Introduction and Background 9.3 GUI Basics 9.4 Using a GUI to Track an IP Address 9.5 Using a GUI for Psychophysics 9.6 Project MATLAB Functions, Commands, and Operators Covered in This Chapter

Chapter 10. Signal Detection Theory

10.1 Goals of This Chapter 10.2 Background 10.3 Exercises 10.4 Project MATLAB Functions, Commands, and Operators Covered in This Chapter

Part III: Data Analysis with MATLAB

Chapter 11. Frequency Analysis Part I: Fourier Decomposition

11.1 Goals of this Chapter 11.2 Background 11.3 Exercises 11.4 Project MATLAB Functions, Commands, and Operators Covered in this Chapter

Chapter 12. Frequency Analysis Part II: Nonstationary Signals and Spectrograms

12.1 Goal of this Chapter 12.2 Background 12.3 Exercises 12.4 Project MATLAB Functions, Commands, and Operators Covered in this Chapter

Chapter 13. Wavelets

13.1 Goals of This Chapter 13.2 Background 13.3 Exercises 13.4 Project MATLAB Functions, Commands, and Operators Covered in This Chapter

Chapter 14. Introduction to Phase Plane Analysis

14.1 Goal of this Chapter 14.2 Background 14.3 Exercises 14.4 Project MATLAB Functions, Commands, and Operators Covered in this Chapter

Chapter 15. Exploring the Fitzhugh-Nagumo Model

15.1 Goal of this Chapter 15.2 Background 15.3 Exercises 15.4 Project MATLAB Functions, Commands, and Operators Covered in this Chapter

Chapter 16. Convolution

16.1 Goals of this Chapter 16.2 Background 16.3 Exercises 16.4 Project MATLAB Functions, Commands, and Operators Covered in this Chapter

Chapter 17. Neural Data Analysis I: Encoding

17.1 Goals of this Chapter 17.2 Background 17.3 Exercises 17.4 Project MATLAB Functions, Commands, and Operators Covered in this Chapter

Chapter 18. Neural Data Analysis II: Binned Spike Data

18.1 Goals of this Chapter 18.2 Background 18.3 Exercises 18.4 Project MATLAB Functions, Commands, and Operators Covered in this Chapter

Chapter 19. Principal Components Analysis

19.1 Goals of this Chapter 19.2 Background 19.3 Exercises 19.4 Project MATLAB Functions, Commands, and Operators Covered in this Chapter

Chapter 20. Information Theory

20.1 Goals of this Chapter 20.2 Background 20.3 Exercises 20.4 Project MATLAB Functions, Commands, and Operators Covered in This Chapter

Chapter 21. Neural Decoding I: Discrete Variables

21.1 Goals of this Chapter 21.2 Background 21.3 Exercises 21.4 Project MATLAB Functions, Commands, and Operators Covered in this Chapter

Chapter 22. Neural Decoding II: Continuous Variables

22.1 Goals of This Chapter 22.2 Background 22.3 Exercises 22.4 Project MATLAB Functions, Commands, and Operators Covered in This Chapter

Chapter 23. Local Field Potentials

23.1 Goals of This Chapter 23.2 Background 23.3 Exercises 23.4 Project MATLAB Functions, Commands, and Operators Covered in this Chapter

Chapter 24. Functional Magnetic Resonance Imaging

24.1 Goals of This Chapter 24.2 Background 24.3 Exercises 24.4 Project MATLAB Functions, Commands, and Operators Covered in This Chapter

Part IV: Data Modeling with MATLAB

Chapter 25. Voltage-Gated Ion Channels

25.1 Goal of This Chapter 25.2 Background 25.3 Exercises 25.4 Project Matlab Functions, Commands, and Operators Covered in This Chapter

Chapter 26. Synaptic Transmission

26.1 Goals of This Chapter 26.2 Background 26.3 Exercises 26.4 Project MATLAB Functions, Commands, and Operators Covered in This Chapter

Chapter 27. Modeling a Single Neuron

27.1 Goal of This Chapter 27.2 Background 27.3 Exercises 27.4 Project MATLAB Functions, Commands, and Operators Covered in This Chapter

Chapter 28. Models of the Retina

28.1 Goal of This Chapter 28.2 Background 28.3 Exercises 28.4 Project MATLAB Functions, Commands, and Operators Covered in This Chapter

Chapter 29. Simplified Model of Spiking Neurons

29.1 Goal of This Chapter 29.2 Background 29.3 Exercises 29.4 Project MATLAB Functions, Commands, and Operators Covered in This Chapter

Chapter 30. Fitzhugh-Nagumo Model: Traveling Waves

30.1 Goals of This Chapter 30.2 Background 30.3 Exercises 30.4 Project MATLAB Functions, Commands, and Operators Covered in This Chapter

Chapter 31. Decision Theory

31.1 Goals of this Chapter 31.2 Background 31.3 Simple Accumulation of Evidence 31.4 Free Response Tasks 31.5 Multiple Iterators: The Race Model 31.6 Cortical Models 31.7 Project MATLAB Functions, Commands, and Operators Covered in this Chapter

Chapter 32. Markov Models

32.1 Goal of this Chapter 32.2 Introduction 32.3 Finding the Most Probable Path: The Viterbi Algorithm 32.4 Hidden Markov Models 32.5 Training an HMM: The Baum-Welch Algorithm 32.6 A Simple Example 32.7 Project MATLAB Functions, Commands, and Operators Covered in This Chapter

Chapter 33. Modeling Spike Trains as a Poisson Process

33.1 Goals of this Chapter 33.2 Background 33.3 The Bernoulli Process: Events in Discrete Time 33.4 The Poisson Process: Events in Continuous Time 33.5 Picking Random Variables Without the Statistics Toolbox 33.6 Non-Homogeneous Poisson Processes: Time-Varying Rates of Activity 33.7 Project MATLAB Functions, Commands, and Operators Covered in This Chapter

Chapter 34. Exploring the Wilson-Cowan Equations

34.1 Goal of This Chapter 34.2 Background 34.3 The Model 34.4 Exercises 34.5 Projects MATLAB Functions, Commands, and Operators Covered in This Chapter

Chapter 35. Neural Networks as Forest Fires: Stochastic Neurodynamics

35.1 Goals of This Chapter 35.2 Background 35.3 Exercises 35.4 Projects MATLAB Functions, Commands, and Operators Covered in This Chapter

Chapter 36. Neural Networks Part I: Unsupervised Learning

36.1 Goals of This Chapter 36.2 Background 36.3 Exercises 36.4 Project MATLAB Functions, Commands, and Operators Covered in This Chapter

Chapter 37. Neural Networks Part II: Supervised Learning

37.1 Goals of This Chapter 37.2 Background 37.3 Exercises 37.4 Project MATLAB Functions, Commands, and Operators covered in This Chapter

Appendix A. Creating Publication-Quality Figures

A.1 Introduction A.2 Figure Makeovers A.3 Saving Figures in the Desired Format A.4 How to Make Animated GIFs MATLAB Functions, Commands, and Operators Covered in This Appendix

Appendix B. Relevant Toolboxes

B.1 The Concept of Toolboxes B.2 Neural Network Toolbox B.3 Parallel Computing Toolbox B.4 Statistics Toolbox B.5 MATLAB Compiler B.6 Database Toolbox B.7 Signal Processing Toolbox B.8 Data Acquisition Toolbox B.9 Image Processing Toolbox B.10 Psychophysics Toolbox and MGL B.11 Chronux B.12 Mathworks File Exchange

References Index

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