Repositories list

• pearsonlab.github.io

  Public
  Lab webpage

  TeX

  •16•17•0•1•Updated Oct 31, 2025Oct 31, 2025

• efficientcodingcolor

  Public
  Color project (David St-Amand)

  Jupyter Notebook

  •

  MIT License

  •4•0•0•0•Updated Oct 27, 2025Oct 27, 2025

• efficientcoding

  Public
  Python

  •

  MIT License

  •4•3•0•0•Updated May 9, 2024May 9, 2024

• autoencoded-vocal-analysis

  Public
  Modeling animal vocalizations with variational autoencoders

  Python

  •

  MIT License

  •7•24•0•0•Updated Mar 2, 2024Mar 2, 2024

• Bubblewrap

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •4•6•0•3•Updated Aug 8, 2023Aug 8, 2023

• proSVD

  Public
  Python

  •

  GNU General Public License v3.0

  •1•2•0•0•Updated Aug 8, 2023Aug 8, 2023

• syrinx

  Public
  Code for modeling song generation in the avian vocal periphery

  Jupyter Notebook

  •

  MIT License

  •1•0•0•0•Updated Aug 4, 2023Aug 4, 2023

• POISE-VAE-JAX

  Public
  Experimental implementation of POISE-VAE in JAX

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Jan 18, 2023Jan 18, 2023

• VAE-GAM-

  Public
  Code for VAE-GAM fMRI model

  Python

  •0•0•0•0•Updated Mar 28, 2022Mar 28, 2022

• anti-bayes

  Public
  Modeling of non-Bayesian psychometric behavior in a jump detection task

  Stan

  •0•0•0•0•Updated Jan 2, 2022Jan 2, 2022

• finch-vae

  Public
  Joint-encoding VAE for zebra finch song and neural data

  Python

  •

  MIT License

  •0•2•0•0•Updated Oct 20, 2021Oct 20, 2021

• legal

  Public
  Analysis models for Duke Legal Decision Making Survey

  rsurveybayesian+ 1stan

  R

  •5•2•0•0•Updated Aug 24, 2021Aug 24, 2021

• pupil

  Public
  Matlab and Python code for pupillometry studies.

  Python

  •4•14•0•0•Updated May 27, 2021May 27, 2021

• CaImAn

  Public
  Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.

  Python

  •

  GNU General Public License v2.0

  •394•0•0•0•Updated Oct 14, 2020Oct 14, 2020

• BinaryStim

  Public
  Repo for code and figures associated with the paper 'Online Neural Connectivity Estimation with Noisy Group Testing'

  Python

  •1•3•0•0•Updated Oct 12, 2020Oct 12, 2020

• stoblodetnet

  Public
  Julia

  •0•0•0•1•Updated Aug 18, 2020Aug 18, 2020

• tf_gbds

  Public
  TensorFlow implementation of goal-based dynamical system model

  Python

  •

  MIT License

  •1•0•0•0•Updated Mar 4, 2020Mar 4, 2020

• sfn-2019

  Public
  John's talk at the 2019 Society for Neuroscience meeting

  CSS

  •0•0•0•0•Updated Oct 23, 2019Oct 23, 2019

• penaltyshot_task

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Sep 19, 2019Sep 19, 2019

• SpikingNeuralNets.jl

  Public
  A Julia library for simulating arbitray populations of spiking neurons.

  Julia

  •

  MIT License

  •0•0•0•0•Updated Aug 6, 2019Aug 6, 2019

• modeling-differential-games

  Public
  John's talk: "Modeling real behavior in two-person differential games"

  JavaScript

  •0•0•0•0•Updated Apr 16, 2019Apr 16, 2019

• dibs-zebrafish-incubator

  Public
  CSS

  •0•0•0•0•Updated Oct 25, 2018Oct 25, 2018

• artificial-agents-social-decisions

  Public
  John's talk at Duke's Basic Science Day 2018

  CSS

  •0•0•0•0•Updated Oct 18, 2018Oct 18, 2018

• imagemp

  Public
  Concurrent image acquisition and processing (producer-consumers model), with maximized efficiency and minimized chance of missing a frame

  Python

  •

  MIT License

  •1•0•0•0•Updated Sep 23, 2018Sep 23, 2018

• concrete

  Public
  continuous relaxation of HMM

  Python

  •0•0•0•0•Updated Sep 10, 2018Sep 10, 2018

• stitch

  Public
  Server for piping zebrafish images through CaImAn

  Python

  •0•0•0•0•Updated Apr 27, 2018Apr 27, 2018

• beyond-tuning-curve

  Public
  John's talk "Systems neuroscience beyond the tuning curve"

  CSS

  •0•0•0•0•Updated Feb 15, 2018Feb 15, 2018

• gbds

  Public
  Goal-Based Dynamical System for behavioral data analysis

  Python

  •1•3•0•0•Updated Sep 26, 2017Sep 26, 2017

• edf_data_processing

  Public
  Python scripts for initial data processing of edf files on back-end server

  Python

  •0•0•0•0•Updated Sep 4, 2017Sep 4, 2017

• spiketopics

  Public
  Topic modeling for neural populations

  Jupyter Notebook

  •2•2•0•0•Updated Aug 21, 2017Aug 21, 2017