Repositories list

• mesmerize-core

  Public
  High level pandas-based API for batch analysis of Calcium Imaging data using CaImAn

  Python

  •

  Other

  •1919 forks•00 stars•00 issues•00 pull requests•Updated Apr 18, 2026Apr 18, 2026

• cmcode

  Public
  2P calcium image source extraction and session alignment using CaImAn and mesmerize-core

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 14, 2026Apr 14, 2026

• suite2p

  Public
  cell detection in calcium imaging recordings

  Python

  •

  GNU General Public License v3.0

  •270270 forks•00 stars•00 issues•00 pull requests•Updated Apr 14, 2026Apr 14, 2026

• CaImAn

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

  Python

  •

  GNU General Public License v2.0

  •397397 forks•00 stars•00 issues•00 pull requests•Updated Apr 6, 2026Apr 6, 2026

• wisser_blackwood_fig8_2p_analysis

  Public
  2P and behavioral analysis code for Figure 8 of Wisser, Blackwood et al., 2025

  Python

  •

  GNU General Public License v2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 30, 2026Mar 30, 2026

• lolcat

  Public
  Code for "Transcriptomic cell type structures in vivo neuronal activity across multiple time scales"

  Jupyter Notebook

  •11 fork•00 stars•00 issues•00 pull requests•Updated Mar 3, 2026Mar 3, 2026

• Ethan_misc

  Public
  Ethan's miscellaneous Matlab utilities

  MATLAB

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 24, 2025Dec 24, 2025

• remote_ikernel

  Public
  All your Jupyter kernels, on all your machines, in one place.

  Python

  •

  BSD 2-Clause "Simplified" License

  •1515 forks•00 stars•00 issues•00 pull requests•Updated Aug 12, 2025Aug 12, 2025

• Diego_code

  Public
  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 8, 2025Aug 8, 2025

• mesmerize-viz

  Public
  Widgets for calcium imaging analysis visualization in notebooks

  Python

  •

  GNU General Public License v3.0

  •77 forks•00 stars•00 issues•00 pull requests•Updated Jul 17, 2025Jul 17, 2025

• Jennifer_code

  Public
  MATLAB

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 4, 2024Sep 4, 2024

• WaveAnalysis

  Public
  matlab routines used to analyze spatiotemporal waves in neurophysiological recordinds

  MATLAB

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 9, 2024Feb 9, 2024

• PBupsModel.jl

  Public
  Julia

  •

  Other

  •99 forks•00 stars•00 issues•00 pull requests•Updated Feb 1, 2024Feb 1, 2024

• GeneralUtils.jl

  Public
  Julia

  •

  Other

  •22 forks•00 stars•00 issues•00 pull requests•Updated Jan 26, 2024Jan 26, 2024

• SPI_Mouse_Control

  Public
  Code for communicating with ADNS3080 chip on MX18 mouse using Teensy 3.1

  C++

  •33 forks•00 stars•00 issues•00 pull requests•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

  •11 fork•00 stars•00 issues•00 pull requests•Updated Apr 18, 2023Apr 18, 2023

• mouseVR

  Public
  Harvey Lab miniaturized mouse VR rig for virtual navigation and decision-making tasks

  MATLAB

  •

  MIT License

  •1616 forks•00 stars•00 issues•00 pull requests•Updated Mar 10, 2023Mar 10, 2023

• ssm

  Public
  Bayesian learning and inference for state space models

  Jupyter Notebook

  •

  MIT License

  •229229 forks•00 stars•00 issues•00 pull requests•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

  •88 forks•00 stars•00 issues•00 pull requests•Updated Jan 12, 2023Jan 12, 2023

• LOOPER

  Public
  Maintained version of LOOPER

  MATLAB

  •

  MIT License

  •00 forks•00 stars•00 issues•11 pull request•Updated Sep 27, 2022Sep 27, 2022

• spec-state-trans

  Public
  Investigating spectral state transitions in anesthetized rodent LFP.

  MATLAB

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 19, 2022May 19, 2022

• NonNegativeMatrixFactorization

  Public
  MATLAB

  •00 forks•11 star•00 issues•00 pull requests•Updated Sep 25, 2021Sep 25, 2021

• Adeeti_code

  Public
  All of Adeeti's code for her projects

  MATLAB

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 25, 2020Aug 25, 2020

• ClearMap2

  Public
  ClearMap 2.0 with WobblyStitcher, TubeMap and CellMap

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •6060 forks•00 stars•00 issues•00 pull requests•Updated Aug 6, 2020Aug 6, 2020

• LOOPER-paper

  Public
  Code for LOOPER publication

  MATLAB

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 14, 2020Jul 14, 2020

• SpectralAnalysis

  Public
  spectral analysis tools due to Drew Hudson

  MATLAB

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 18, 2020Apr 18, 2020

• Navigation

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 15, 2020Apr 15, 2020

• connor_random

  Public
  Random code from the one, the only ME!

  MATLAB

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 7, 2020Apr 7, 2020

• ARfit

  Public
  autoregressive modeling using the ARfit package

  MATLAB

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 7, 2020Apr 7, 2020

• Stats

  Public
  Useful Statistical Tests and Circular Statistics due to Drew Hudson

  MATLAB

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 7, 2020Apr 7, 2020