Repositories list

• Kilosort

  Public
  Fast spike sorting with drift correction

  neuroscienceelectrophysiologyspike-sorting

  Python

  •

  GNU General Public License v3.0

  •252•497•16•4•Updated Jan 3, 2025Jan 3, 2025

• suite2p

  Public
  cell detection in calcium imaging recordings

  neurosciencedata-analysisimaging

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •243•367•104•7•Updated Jan 2, 2025Jan 2, 2025

• facemap

  Public
  Framework for predicting neural activity from mouse orofacial movements tracked using a pose estimation model. Package also includes singular value decomposition (SVD) of behavioral videos.

  behaviorguimovie+ 8neurosciencepose-estimationmatlab-guipupilrodentspythondeep-learning+ 1

  Python

  •

  GNU General Public License v3.0

  •62•161•11•1•Updated Dec 5, 2024Dec 5, 2024

• cellpose

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

  segmentationcell-segmentationcell-biology

  Jupyter Notebook

  •

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

  •415•1.4k•57•16•Updated Nov 21, 2024Nov 21, 2024

• MouseLand.github.io

  Public
  website for Pachitariu-Stringer lab

  CSS

  •0•0•0•0•Updated Nov 14, 2024Nov 14, 2024

• cellpose-napari

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

  segmentationnapari

  Python

  •

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

  •22•48•8•2•Updated Oct 27, 2024Oct 27, 2024

• rastermap

  Public
  a visualization method for neural data

  neuroscienceneuroscience-methodsunsupervised-clustering

  Python

  •

  GNU General Public License v3.0

  •48•200•5•0•Updated Oct 19, 2024Oct 19, 2024

• course-materials

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •1•3•0•0•Updated Aug 27, 2024Aug 27, 2024

• stringer-pachitariu-et-al-2018a

  Public
  Recordings of 10k neurons during spontaneous behaviors

  neuroscienceopenscience

  MATLAB

  •15•50•2•2•Updated Mar 22, 2024Mar 22, 2024

• neuropop

  Public
  analysis tools for large-scale neural recordings

  Python

  •

  GNU General Public License v3.0

  •2•12•0•0•Updated Nov 16, 2023Nov 16, 2023

• pykilosort

  Public
  WIP: Python port of Kilosort2

  Python

  •

  GNU General Public License v2.0

  •28•50•28•3•Updated Jul 8, 2023Jul 8, 2023

• stringer-et-al-2019

  Public
  paper figure code

  Python

  •

  GNU General Public License v3.0

  •14•25•1•0•Updated Jun 11, 2023Jun 11, 2023

• receptivefield-explorer

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

  Jupyter Notebook

  •1•12•2•0•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

  •1•2•0•0•Updated May 31, 2021May 31, 2021

• cellpose_web

  Public
  code for cellpose website

  JavaScript

  •

  GNU General Public License v3.0

  •2•2•0•1•Updated Nov 24, 2020Nov 24, 2020

• steinmetz2019_NMA

  Public
  Jupyter Notebook

  •5•4•0•0•Updated Jul 21, 2020Jul 21, 2020

• EnsemblePursuit

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •1•9•0•0•Updated Jun 5, 2020Jun 5, 2020

• kesa-et-al-2019

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Nov 6, 2019Nov 6, 2019

• stringer-pachitariu-et-al-2018b

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

  neuroscienceopensciencevision-science

  MATLAB

  •21•68•3•0•Updated Sep 3, 2019Sep 3, 2019

• pachitariu-et-al-2018a

  Public
  Benchmarking spike deconvolution without ephys

  MATLAB

  •1•5•0•0•Updated May 3, 2018May 3, 2018