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    • alyx

      Public
      Database for experimental neuroscience laboratories
      Python
      1248675Updated Aug 1, 2025Aug 1, 2025
    • allenCCF

      Public
      Tools to work with Allen Inst CCF data in matlab
      MATLAB
      77138282Updated Jul 15, 2025Jul 15, 2025
    • phylib

      Public
      Lightweight electrophysiological data analysis library
      Python
      281483Updated Jul 8, 2025Jul 8, 2025
    • datostim

      Public
      C
      0000Updated Jun 17, 2025Jun 17, 2025
    • PinkRigs

      Public
      Shared code for processing data on the pink rigs
      Python
      1580Updated Apr 7, 2025Apr 7, 2025
    • Information about Neuropixels electrode arrays
      MATLAB
      1592460Updated Dec 15, 2024Dec 15, 2024
    • A script to post weekend water to Alyx and email users
      MATLAB
      0000Updated Nov 28, 2024Nov 28, 2024
    • phy

      Public
      phy: interactive visualization and manual spike sorting of large-scale ephys data
      Python
      1723672313Updated Aug 2, 2024Aug 2, 2024
    • psychofit

      Public
      A module for fitting 2AFC psychometric data
      Jupyter Notebook
      6601Updated Jul 2, 2024Jul 2, 2024
    • Rigbox

      Public
      A MATLAB toolbox for running behavioral neuroscience experiments and managing data
      HTML
      1733986Updated May 28, 2024May 28, 2024
    • LabCI

      Public
      Automation server for MATLAB & Python continuous integration, written in Node.js
      JavaScript
      14199Updated Mar 26, 2024Mar 26, 2024
    • KiloSort

      Public
      GPU code for spike sorting
      MATLAB
      1001861341Updated Feb 19, 2024Feb 19, 2024
    • spikes

      Public
      cortex lab code for electrophysiology
      MATLAB
      848394Updated Feb 5, 2024Feb 5, 2024
    • Suite2P

      Public
      Tools for processing 2P recordings
      MATLAB
      67127421Updated Oct 9, 2023Oct 9, 2023
    • Functions to assess quality of spike sorting results
      MATLAB
      233420Updated Sep 6, 2023Sep 6, 2023
    • signals

      Public
      Intuitive behavioral neuroscience experiment design in MATLAB
      C
      10301Updated Aug 31, 2023Aug 31, 2023
    • Some MATLAB functions for easier interfacing with an Alyx database
      MATLAB
      33221Updated Aug 31, 2023Aug 31, 2023
    • MATLAB software for analysis of single-cell RNA sequencing data, including probabilistic clustering, latent factor modeling, nbtSNE, visualization tools
      MATLAB
      4600Updated Aug 2, 2023Aug 2, 2023
    • PoppyRig

      Public
      Code for poppy rig
      MATLAB
      0000Updated Aug 24, 2022Aug 24, 2022
    • experiment definition files (primarily Signals)
      MATLAB
      0010Updated Jul 29, 2022Jul 29, 2022
    • Lilrig

      Public
      code specific to Lilrig
      MATLAB
      0000Updated Jun 15, 2022Jun 15, 2022
    • MATLAB
      3420Updated Jan 3, 2021Jan 3, 2021
    • npytools

      Public
      [WIP] Command-line utilities to deal with NPY array files
      Python
      1800Updated Jun 22, 2020Jun 22, 2020
    • Experimental code to read/write NumPy .NPY files in MATLAB
      Jupyter Notebook
      220300Updated Jun 19, 2020Jun 19, 2020
    • [WIP] Python port of Kilosort 2
      Python
      26100Updated Mar 6, 2020Mar 6, 2020
    • widefield

      Public
      Image processing and tools for widefield imaging
      MATLAB
      51880Updated Dec 7, 2019Dec 7, 2019
    • mmmGUI

      Public
      "mouse movie manager" and GUI
      MATLAB
      2040Updated Nov 28, 2019Nov 28, 2019
    • Converts ALF format to be read in neuroscope
      Python
      0100Updated Nov 8, 2019Nov 8, 2019
    • ALF

      Public
      0100Updated Nov 8, 2019Nov 8, 2019
    • mpep

      Public
      mPEP runs experiments where stimuli and timings can be decided in advance (i.e. not in the context of behavior)
      MATLAB
      0000Updated Oct 8, 2019Oct 8, 2019