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    29 repositories

    • 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 Jan 22, 2026Jan 22, 2026

    • mesmerize-core

      Public
      High level pandas-based API for batch analysis of Calcium Imaging data using CaImAn
      Python
      •
      Other
      •19•0•0•0•Updated Jan 9, 2026Jan 9, 2026

    • Ethan_misc

      Public
      Ethan's miscellaneous Matlab utilities
      MATLAB
      •0•0•0•0•Updated Dec 24, 2025Dec 24, 2025

    • wisser_blackwood_fig8_2p_analysis

      Public
      2P and behavioral analysis code for Figure 8 of Wisser, Blackwood et al., 2025
      GNU General Public License v2.0
      •0•0•0•0•Updated Sep 14, 2025Sep 14, 2025

    • remote_ikernel

      Public
      All your Jupyter kernels, on all your machines, in one place.
      Python
      •
      BSD 2-Clause "Simplified" License
      •15•0•0•0•Updated Aug 12, 2025Aug 12, 2025

    • Diego_code

      Public
      MIT License
      •0•0•0•0•Updated Aug 8, 2025Aug 8, 2025

    • mesmerize-viz

      Public
      Widgets for calcium imaging analysis visualization in notebooks
      Python
      •
      GNU General Public License v3.0
      •7•0•0•0•Updated Jul 17, 2025Jul 17, 2025

    • Jennifer_code

      Public
      MATLAB
      •0•0•0•0•Updated Sep 4, 2024Sep 4, 2024

    • WaveAnalysis

      Public
      matlab routines used to analyze spatiotemporal waves in neurophysiological recordinds
      MATLAB
      •0•0•0•0•Updated Feb 9, 2024Feb 9, 2024

    • PBupsModel.jl

      Public
      Julia
      •
      Other
      •9•0•0•0•Updated Feb 1, 2024Feb 1, 2024

    • GeneralUtils.jl

      Public
      Julia
      •
      Other
      •2•0•0•0•Updated Jan 26, 2024Jan 26, 2024

    • SPI_Mouse_Control

      Public
      Code for communicating with ADNS3080 chip on MX18 mouse using Teensy 3.1
      C++
      •3•0•0•0•Updated Aug 31, 2023Aug 31, 2023

    • stereoEEG

      Public
      Repository to house code for a collaborative project analyzing stereoEEG data during anesthesia induction and sleep
      MATLAB
      •1•0•0•0•Updated Apr 18, 2023Apr 18, 2023

    • mouseVR

      Public
      Harvey Lab miniaturized mouse VR rig for virtual navigation and decision-making tasks
      MATLAB
      •
      MIT License
      •16•0•0•0•Updated Mar 10, 2023Mar 10, 2023

    • ssm

      Public
      Bayesian learning and inference for state space models
      Jupyter Notebook
      •
      MIT License
      •225•0•0•0•Updated Jan 31, 2023Jan 31, 2023

    • local-linear-segmentation

      Public
      This repository contains the main scripts for local linear segmentation and subsequent analysis of the resulting model space
      Jupyter Notebook
      •8•0•0•0•Updated Jan 12, 2023Jan 12, 2023

    • LOOPER

      Public
      Maintained version of LOOPER
      MATLAB
      •
      MIT License
      •0•0•0•1•Updated Sep 27, 2022Sep 27, 2022

    • spec-state-trans

      Public
      Investigating spectral state transitions in anesthetized rodent LFP.
      MATLAB
      •0•0•0•0•Updated May 19, 2022May 19, 2022

    • NonNegativeMatrixFactorization

      Public
      MATLAB
      •0•1•0•0•Updated Sep 25, 2021Sep 25, 2021

    • Adeeti_code

      Public
      All of Adeeti's code for her projects
      MATLAB
      •0•0•0•0•Updated Aug 25, 2020Aug 25, 2020

    • ClearMap2

      Public
      ClearMap 2.0 with WobblyStitcher, TubeMap and CellMap
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •59•0•0•0•Updated Aug 6, 2020Aug 6, 2020

    • LOOPER-paper

      Public
      Code for LOOPER publication
      MATLAB
      •
      MIT License
      •0•0•0•0•Updated Jul 14, 2020Jul 14, 2020

    • SpectralAnalysis

      Public
      spectral analysis tools due to Drew Hudson
      MATLAB
      •0•0•0•0•Updated Apr 18, 2020Apr 18, 2020

    • Navigation

      Public
      Python
      •0•0•0•0•Updated Apr 15, 2020Apr 15, 2020

    • connor_random

      Public
      Random code from the one, the only ME!
      MATLAB
      •
      MIT License
      •0•0•0•0•Updated Apr 7, 2020Apr 7, 2020

    • ARfit

      Public
      autoregressive modeling using the ARfit package
      MATLAB
      •0•0•0•0•Updated Apr 7, 2020Apr 7, 2020

    • Stats

      Public
      Useful Statistical Tests and Circular Statistics due to Drew Hudson
      MATLAB
      •0•0•0•0•Updated Apr 7, 2020Apr 7, 2020

    • group_code

      Public
      MATLAB
      •0•0•0•0•Updated Apr 7, 2020Apr 7, 2020

    • NeuroPattToolbox-1

      Public
      MATLAB toolbox to automatically detect, analyze and visualize spatiotemporal patterns in neural population activity, developed by Dr. Pulin Gong's group at University of Sydney
      MATLAB
      •
      GNU General Public License v3.0
      •16•0•0•0•Updated Jan 15, 2019Jan 15, 2019