Quantitative methods in neuroscience

NeuBeh 545/PBIO 545

Tu/Th 12:30-1:50, G328 HSB (except 1/13 when we meet in E216)

Date Topic and Handouts

Reading and Discussion topics


Linear Algebra

some logistics

linear algebra primer from Eero Simoncelli

Linear transformations on Wikipedia

Column space demo from class (note: requires some files from linear algebra tutorial - get those first)


Linear Algebra part 2


linear algebra tutorial normrnd PlotVector Plot3DVector statsizechk

note: you need all five files; make sure they are all on Matlab's path. You may already have normrnd and statsizechk if you have the statistics toolbox.

Markov chain slides (optional part of tutorial)


Journal club

note: meet in E216



Wandell, Foundations of Vision, Chapter 4 (good intro) or here: https://foundationsofvision.stanford.edu/chapter-4-wavelength-encoding/

Baylor, Nunn and Schnapf (1987) J Physiol 390:145-160. (primary paper)

http://graphics.stanford.edu/courses/cs178/applets/colormatching.html (introduction to color matching)


Class Discussion



Differential equations and neural dynamics

Howard Berg, Random Walks in Biology, Appendix B
Hugh Wilson, Spikes, Decisions and Actions, Chapters 1, 2, 3
Wilson, Chapter 5 (numerical methods)



Differential equations and neural dynamics: Discussion


Simulink tutorial (optional)


Journal club:



Robinson (primary paper)

Fuchs, Scudder and Kaneko (physiological counterpart to Robinson paper)


Class Discussion


Supplementary material:

Villus material part 1

Villus material part 2

Villus material part 3

simulink model (works on Matlab 5)


Fourier Analysis, Filters and Convolution

Press et al., Numerical Recipes, pages 496-508 (2nd edition, this is beginning of Ch. 12); Ch. 13
Koch, Biophysics of Computation, Appendix B
Wandell, Foundations of Vision, Appendix A (a mix of linear algebra and linear systems stuff).


Fourier Analysis, Filters and Convolution: Discussion

Fourier analysis tutorial

linear systems primer from Eero Simoncelli (note this is not the same as the linear algebra one above - has a lot of Fourier stuff in it).

linear systems primer from David Heeger

Partha Mitra’s open source Matlab code for spectral analysis, with links to online tutorials: http://chronux.org/home/

spectral analysis notes from Kleinfeld


Journal club:


methods paper (read first): Betzig

discussion paper: Dani

supplementary: Xu


Class Discussion




Introduction to the Theory of Stochastic Processes

Howard Berg, Random Walks in Biology, Appendix A
Koch, Chapter 15
Duda, Hart and Stork, Pattern Classification (2nd edition), Appendix 4

probability basics tutorial


Introduction to the Theory of Stochastic Processes: Discussion

Stochastic Processes Tutorial

accessory files (note: make sure they are all on Matlab's path)

Moment generating functions tuturial (you need both files in folder)

Kemeny and Snell, Finite Markov Chains




Journal club:


Shadlen et al (primary paper for discussion)

de la Rocha et al. (supplement re how correlated activity is shaped)


Class Discussion



3/3 PCA and Dimensional Reduction

PCA tutorial

Shlens PCA review

rgc spike data

single photon response data

3/5 PCA and Dimensional Reduction: Discussion

Journal club:




Rust et al (primary discussion paper)

Yang Dan complex cell paper

Simoncelli chapter (good intro to PCA and friends)

Golomb LGN paper

Horwitz V1 paper


Class Discussion


Instructors and contact info:

Adrienne Fairhall fairhall@uw.edu
Fred Rieke rieke@uw.edu
Wyeth Bair wyeth.bair@gmail.com
Yoni Browning yonib@uw.edu


Course project:

suggested projects

Computers, etc:

Computers with MATLAB are available in the PBIO computer room and the NeuBeh office.

Contact one of us if you are having problems finding a machine you can use.

Useful links:

site for Theoretical Neuroscience, Dayan and Abbott (see Exercises)

Villus web site

Mathematical details of Fourier analysis from Wolfram Research

Fourier transform primer (vision centered)