Quantitative methods in neuroscience

Neuro 545/PBIO 545

Tu/Th 12:30-1:50, T531 HSB

Date Topic and Handouts

Reading and Discussion topics

1/5

Linear Algebra

some logistics

linear algebra primer from Eero Simoncelli

Dean Pospisil's primer

Linear transformations on Wikipedia

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

1/7

Linear Algebra part 2

link to videos

Discussion

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)

1/12

Journal club

 

 

 

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)

1/14

Class Discussion and module wrapup

 


1/19

Fourier Analysis, Filters and Convolution

link to videos

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).

graphical convolution tutorial

1/21

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

1/26

Journal club:

 

 

methods paper (read first): Betzig

discussion paper: Dani

supplementary: Xu

 

1/28

Class Discussion and module wrapup

 

 

2/2

Differential equations and neural dynamics

notes on integrating linear differential equations

link to videos

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

2/4

Differential equations and neural dynamics: Discussion

tutorial

Simulink tutorial (optional)

2/9

Journal club:

 

Robinson (primary paper)

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

2/11

Class Discussion and module wrapup

 

Supplementary material:

Villus material part 1

Villus material part 2

Villus material part 3

simulink model (works on Matlab 5)

2/16

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

2/18

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

kemeny_snell_ch1

kemeny_snell_ch2

2/23

Journal club:

 

Shadlen et al (primary paper for discussion)

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

2/24

Class Discussion and module wrapup

 

 

3/1 PCA and Dimensional Reduction

PCA tutorial

Shlens PCA review

rgc spike data

single photon response data

3/3 PCA and Dimensional Reduction: Discussion
3/8

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

3/10

Class Discussion and module wrapup

 

Instructors and contact info:

Adrienne Fairhall fairhall@uw.edu
Fred Rieke rieke@uw.edu
Wyeth Bair wyeth.bair@gmail.com
Dean Pospisil deanp3@uw.edu
 

 

Course project:

suggested projects

Computers, etc:

Computers with MATLAB are available in the PBIO computer room and the Neuroscience 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)