Repositories list

• cellpose

  Public
  a generalist algorithm for cellular segmentation with human-in-the-loop capabilities

  segmentationcell-segmentationcell-biology

  segmentationcell-segmentationcell-biology

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •609609 forks•2.2k2.2k stars•6161 issues•3535 pull requests•Updated Apr 22, 2026Apr 22, 2026

• suite2p

  Public
  cell detection in calcium imaging recordings

  neurosciencedata-analysisimaging

  neurosciencedata-analysisimaging

  Python

  •

  GNU General Public License v3.0

  •271271 forks•445445 stars•3636 issues•1717 pull requests•Updated Apr 18, 2026Apr 18, 2026

• critical_init

  Public
  code for Pachitariu et al 2025

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 1, 2026Apr 1, 2026

• MouseLand.github.io

  Public
  website for Pachitariu-Stringer lab

  CSS

  •11 fork•00 stars•00 issues•00 pull requests•Updated Mar 19, 2026Mar 19, 2026

• Kilosort

  Public
  Fast spike sorting with drift correction

  neuroscienceelectrophysiologyspike-sorting

  neuroscienceelectrophysiologyspike-sorting

  Python

  •

  GNU General Public License v3.0

  •286286 forks•607607 stars•1212 issues•22 pull requests•Updated Mar 5, 2026Mar 5, 2026

• eye-vs-face

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 28, 2026Feb 28, 2026

• facemap

  Public
  Framework for predicting neural activity from mouse orofacial movements tracked using a pose estimation model. Package also includes singular value decompositio…

  pythonbehaviorgui+ 8

  pythonbehaviorguimoviedeep-learningneurosciencepytorchpose-estimationmatlab-guipupil+ 1

  Python

  •

  GNU General Public License v3.0

  •7474 forks•190190 stars•1313 issues•33 pull requests•Updated Jan 26, 2026Jan 26, 2026

• course-materials

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •33 forks•55 stars•00 issues•00 pull requests•Updated Aug 26, 2025Aug 26, 2025

• minimodel

  Public
  minimodels!

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •44 forks•33 stars•00 issues•00 pull requests•Updated Jul 31, 2025Jul 31, 2025

• zhong-et-al-2025

  Public
  code to make figures from Zhong et al, 2025

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •33 forks•77 stars•00 issues•00 pull requests•Updated Jul 6, 2025Jul 6, 2025

• neuropop

  Public
  analysis tools for large-scale neural recordings

  Python

  •

  GNU General Public License v3.0

  •22 forks•1717 stars•00 issues•00 pull requests•Updated Apr 4, 2025Apr 4, 2025

• rastermap

  Public
  a visualization method for neural data

  neuroscienceneuroscience-methodsunsupervised-clustering

  neuroscienceneuroscience-methodsunsupervised-clustering

  Python

  •

  GNU General Public License v3.0

  •5252 forks•245245 stars•1111 issues•00 pull requests•Updated Apr 4, 2025Apr 4, 2025

• cellpose-napari

  Public
  napari plugin for cellpose (see www.cellpose.org) - an anatomical segmentation tool

  segmentationnapari

  segmentationnapari

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •2626 forks•6363 stars•1111 issues•33 pull requests•Updated Oct 27, 2024Oct 27, 2024

• stringer-pachitariu-et-al-2018a

  Public
  Recordings of 10k neurons during spontaneous behaviors

  neuroscienceopenscience

  neuroscienceopenscience

  MATLAB

  •1616 forks•5454 stars•22 issues•22 pull requests•Updated Mar 22, 2024Mar 22, 2024

• pykilosort

  Public
  WIP: Python port of Kilosort2

  Python

  •

  GNU General Public License v2.0

  •2626 forks•5050 stars•2929 issues•33 pull requests•Updated Jul 8, 2023Jul 8, 2023

• stringer-et-al-2019

  Public
  paper figure code

  Python

  •

  GNU General Public License v3.0

  •1313 forks•2424 stars•11 issue•00 pull requests•Updated Jun 11, 2023Jun 11, 2023

• receptivefield-explorer

  Public
  GUI to compute and explore receptive fields, primarily from calcium imaging recordings

  Jupyter Notebook

  •11 fork•1313 stars•22 issues•00 pull requests•Updated Jun 26, 2021Jun 26, 2021

• facemap-napari

  Public
  napari plugin for facemap (www.github.com/mouseland/facemap) for processing behavioral data

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •11 fork•22 stars•00 issues•00 pull requests•Updated May 31, 2021May 31, 2021

• cellpose_web

  Public
  code for cellpose website

  JavaScript

  •

  GNU General Public License v3.0

  •22 forks•22 stars•00 issues•11 pull request•Updated Nov 24, 2020Nov 24, 2020

• steinmetz2019_NMA

  Public
  Jupyter Notebook

  •55 forks•44 stars•00 issues•00 pull requests•Updated Jul 21, 2020Jul 21, 2020

• EnsemblePursuit

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •11 fork•99 stars•00 issues•00 pull requests•Updated Jun 5, 2020Jun 5, 2020

• kesa-et-al-2019

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 6, 2019Nov 6, 2019

• stringer-pachitariu-et-al-2018b

  Public
  Responses of 10,000 neurons to 2,800 natural images

  neuroscienceopensciencevision-science

  neuroscienceopensciencevision-science

  MATLAB

  •2222 forks•7373 stars•33 issues•00 pull requests•Updated Sep 3, 2019Sep 3, 2019

• pachitariu-et-al-2018a

  Public
  Benchmarking spike deconvolution without ephys

  MATLAB

  •11 fork•66 stars•00 issues•00 pull requests•Updated May 3, 2018May 3, 2018