pillow lab @ princeton

neural coding & computation group

Code

Generalized Linear Model (GLM)

GLMspiketraintutorial - tutorial code and slides from 2016 SFN short course, illustrating basics of Gaussian and Poisson GLMs for spike train data. [zip | readme]
neuroGLM - Poisson GLM for single-neuron trial-based data
[relevant pub: IM Park et al, Nat Neurosci 2014]
GLM dynamical behaviors - capturing repertoire of Izhikevich neuron
[relevant pub: Weber & Pillow, arxiv 2017]
GLMspiketools - multi-neuron Poisson GLM with spike-history and coupling
[relevant pub: Pillow et al, Nature 2008]

Receptive field estimation

fastASD - fast, scalable estimation for high-D receptive fields via automatic smoothness determination (ASD). [zip | readme]
[relevant pub: Aoi M & Pillow JW, bioRxiv 2017]
ALD - "automatic locality determination": receptive field estimation under localized priors
[relevant pub: M Park & Pillow, PLoS CB 2011]

Multi-filter LNP model

LNPfitting - maximum likelihood / maximally informative dimensions (MID) estimator for linear-nonlinear-Poisson (LNP) model [zip | readme].
[relevant pub: Williamson, Sahani & Pillow, PLoS Comp Biol 2015]
iSTAC - information-theoretic spike-triggered average & covariance for multi-filter LNP model
[relevant pub: Pillow & Simoncelli, J Vision 2006]

non-Poisson spiking models

flexibleModulatedPoisson - fitting of "flexible overdispersion model" for spike count data, which extends Goris et al 2014 model to account for various relationships between spike count mean and variance [zip | readme].
[relevant pub: Charles, Park, Weller, Horwitz, & Pillow, Neural Computation 2018]

Latent Dynamics / Model Comparison

StepRampMCMC - Model comparison for stepping and ramping spike train models
[relevant pub: Latimer et al, Science 2015]

Adaptive stimulus selection / Closed-loop experiments

adaptivePsychophysicsToolbox - adaptive stimulus selection for characterizing psychometric functions, incorporating multiple response options and lapse
[relevant pub: Bak & Pillow, bioRxiv 2018]
activelearningTCs - adaptive stimulus selection for neural tuning curves with Poisson noise
[relevant pub: Park & Pillow 2016]

Entropy estimation

CDMentropy - entropy estimation for binary spike trains using centered-Dirichlet mixture (CDM) priors
[relevant pub: Archer et al NIPS 2013]
PYMentropy - entropy estimation for discrete distributions with unknown support using Pitman-Yor Mixture (PYM) prior
[relevant pub: Archer et al, NIPS 2012]

Spike sorting

BinaryPursuitSpikeSorting - Binary Pursuit spike sorting for detecting synchronous and overlapping spikes
[relevant pub: Pillow et al, PLoS ONE 2013]

Other

Kalman filter for target tracking psychophysics - continuous psychophysics via target tracking
[relevant pub: Bonnen et al, Journal of Vision 2015]
Generalized Integrate-and-Fire model - ML fitting of spike-response model to spike train data via Fokker-Planck
[relevant pub: Pillow et al, J Neurosci 2005]

Please report any bugs to pillow@princeton.edu