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    45 repositories

    • decision_dynamics_commitment

      Public
      Code and data accompanying: Luo*, Kim*, et al. (2025). Transitions in dynamical regime and neural mode underlie perceptual decision-making. PMID: 37904994
      MATLAB
      •
      Apache License 2.0
      •0•4•0•0•Updated Feb 16, 2026Feb 16, 2026

    • FHMDDM

      Public
      Factorial hidden Markov drift-diffusion model
      Julia
      •
      Apache License 2.0
      •0•4•0•0•Updated Feb 7, 2026Feb 7, 2026

    • fof_ads_interactions

      Public
      Python
      •0•0•0•0•Updated Dec 1, 2025Dec 1, 2025

    • findr

      Public
      FINDR: Flow-field Inference from Neural Data using deep Recurrent networks
      neurosciencelatent-variable-modelsneural-differential-equations
      Jupyter Notebook
      •
      Apache License 2.0
      •2•14•0•0•Updated Nov 26, 2025Nov 26, 2025

    • mouse_npx_holders

      Public
      3D files for chronic neuropixel holders modified by Jesse Kaminsky and Jorge Yanar from holders in Luo, Bondy et al. 2020.
      GNU General Public License v3.0
      •0•1•0•0•Updated Nov 4, 2025Nov 4, 2025

    • ClickDV

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Sep 22, 2025Sep 22, 2025

    • jbreda_animal_training

      Public
      Repository for the ingestion, cleaning and visualization of behavioral experiments
      Jupyter Notebook
      •0•2•39•0•Updated Sep 5, 2025Sep 5, 2025

    • chronic_neuropixels

      Public
      Repository of code, data and CAD files associated with Luo*, Bondy* et al (2020). "An approach for long-term, multi-probe Neuropixels recordings in unrestrained…
      MATLAB
      •
      Apache License 2.0
      •5•10•1•0•Updated Jul 1, 2025Jul 1, 2025

    • flexible_decision_making_rnn

      Public
      MATLAB
      •
      Apache License 2.0
      •0•0•0•0•Updated May 5, 2025May 5, 2025

    • flexible_decision_making_rats

      Public
      MATLAB
      •
      Apache License 2.0
      •0•2•1•0•Updated May 5, 2025May 5, 2025

    • PulseInputDDM.jl

      Public
      A Julia library for fitting DDMs to pulse-based evidence accumulations task data
      julialangneuroscience-methodsdrift-diffusion-model
      Julia
      •
      Apache License 2.0
      •2•5•3•2•Updated Apr 19, 2025Apr 19, 2025

    • tzl_spGLM

      Public
      Generalized linear model of the spike train of individual neurons recorded in the Poisson Clicks task
      Julia
      •0•0•0•0•Updated Dec 30, 2024Dec 30, 2024

    • JRCLUST

      Public
      JRCLUST
      MATLAB
      •
      Apache License 2.0
      •22•0•2•0•Updated Nov 21, 2024Nov 21, 2024

    • DePasquale-eLife-2024

      Public
      Data and analysis notebooks for DePasquale et. al eLife 2024
      Jupyter Notebook
      •
      Apache License 2.0
      •0•1•0•0•Updated Sep 16, 2024Sep 16, 2024

    • DataJoint2Julia.jl

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Sep 10, 2024Sep 10, 2024

    • bl_pipeline_python

      Public
      Python Data pipeline for BrodyLab
      Jupyter Notebook
      •3•0•0•0•Updated Jul 30, 2024Jul 30, 2024

    • MixtureAgentsModels

      Public
      Julia
      •
      MIT License
      •3•9•0•0•Updated Jul 4, 2024Jul 4, 2024

    • adrian_striatum_analysis

      Public
      code for wrangling and organizing striatum ephys recordings and associated GLM fits
      MATLAB
      •0•0•0•0•Updated Jun 22, 2024Jun 22, 2024

    • datajoint-tutorials

      Public
      Getting started materials for DataJoint - with Calcium Imaging, Electrophysiology, Machine Learning examples
      Jupyter Notebook
      •155•0•0•0•Updated May 17, 2024May 17, 2024

    • neu_437_public

      Public
      Public-facing repository for NEU 437 problem sets. Includes python notebooks (without answers) and associated data.
      Jupyter Notebook
      •0•0•0•0•Updated Apr 21, 2024Apr 21, 2024

    • accumulation-model

      Public
      Code for forward and backwards analytical solution to a drift diffusion advection model with pulse-based evidence
      MATLAB
      •1•0•0•0•Updated Apr 1, 2024Apr 1, 2024

    • neuroGLM

      Public
      Fitting and analysis of trial-based neural spike responses with Generalized Linear Model (GLM).
      MATLAB
      •
      MIT License
      •39•0•0•0•Updated Feb 15, 2024Feb 15, 2024

    • trialhistory_lapses_EA

      Public
      This repository contains code for generating figures for the manuscript "Trial-history biases in evidence accumulation can give rise to apparent lapses"
      MATLAB
      •
      Apache License 2.0
      •0•1•0•0•Updated Nov 20, 2023Nov 20, 2023

    • flexible_decision_making_training

      Public
      Training code for the rat flexible decision-making task
      MATLAB
      •
      Apache License 2.0
      •0•1•0•0•Updated Nov 17, 2023Nov 17, 2023

    • Kilosort2

      Public
      Fast spike sorting with drift correction for up to a thousand channels
      MATLAB
      •
      GNU General Public License v2.0
      •280•1•0•0•Updated Sep 6, 2023Sep 6, 2023

    • SGLXMetaToCoords

      Public
      Code to create geometry files for sorting from SpikeGLX metadata
      Python
      •6•0•0•0•Updated Jul 21, 2023Jul 21, 2023

    • emilyjandennis_PRA

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Apr 28, 2023Apr 28, 2023

    • boydmeredith_training_report

      Public
      GUI to monitor performance with training on PBups pipeline
      MATLAB
      •0•0•0•0•Updated Apr 25, 2023Apr 25, 2023

    • boydmeredith_bings_model_demo

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Feb 21, 2023Feb 21, 2023

    • boydmeredith_GitHubWorkflow_TipsAndTricks

      Public
      0•0•0•0•Updated Feb 7, 2023Feb 7, 2023