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2014_pnas

This is the analysis code from de Gee JW, Knapen T & Donner TH. 2014. Decision-related pupil dilation reflects upcoming choice and individual bias. Proceedings of the National Academy of Sciences USA, 111(5), E618-E625.

2017_elife

This is the analysis code from de Gee JW, Colizoli O, Kloosterman NA, Knapen T, Nieuwenhuis S & Donner TH. 2017. Dynamic modulation of decision biases by brainstem arousal systems. eLife.

2018_meg_yesno

2020_elife_pupil_bias

2021_cereb_cortex_prediction_error

Data and code

accumodel

Estimating accumulation models

accumodels

various accumulation model tools

esmp2013_simulation

Simulations that we worked out for our talk at the European Mathematical Psychology Seminar in 2013.

exptools

Port of experimental tools of Knapen lab to Python package

eyescript

Stimulus presentation for EyeLink eyetrackers

hddm

HDDM is a python module that implements Hierarchical Bayesian parameter estimation of Drift Diffusion Models (via PyMC).

hddm_tools

hierarchical DDM fitting tools

human_experiments

human psychophysics experiments

intro2python

3-days intro to Python course

ipython-notebook-tutorials

These are IPython Notebook tutorials

jwdegee.github.io

personal website

kabuki

kabuki is a python toolbox that allows easy creation of hierarchical bayesian models for the cognitive sciences.

kilosort2

Fast spike sorting with drift correction for up to a thousand channels

mcginley-lab.github.io

McGinley lab info

nptdms

NumPy based Python module for reading TDMS files produced by LabView

py_covid19

covid19 plots

pysurfer

Cortical neuroimaging visualization in Python

python-psignifit

Python clone of psignifit providing basic functionality

suite2p

cell detection in calcium imaging recordings

uva_experiments

Experiments University of Amsterdam