MouseLand

All

23 repositories

Kilosort
Public
Fast spike sorting with drift correction
neuroscience electrophysiology spike-sorting
Python
•
GNU General Public License v3.0
•271•547•20•2•Updated Aug 8, 2025Aug 8, 2025
cellpose
Public
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
segmentation cell-segmentation cell-biology
Python
•
BSD 3-Clause "New" or "Revised" License
•513•1.8k•49•16•Updated Aug 6, 2025Aug 6, 2025
minimodel
Public
minimodels!
Jupyter Notebook
•
GNU General Public License v3.0
•2•3•0•0•Updated Jul 31, 2025Jul 31, 2025
MouseLand.github.io
Public
website for Pachitariu-Stringer lab
CSS
•0•0•0•0•Updated Jul 29, 2025Jul 29, 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.
behavior gui movie neuroscience pose-estimation matlab-gui pupil rodents python deep-learning
Python
•
GNU General Public License v3.0
•67•174•14•1•Updated Jul 24, 2025Jul 24, 2025
course-materials
Public
Jupyter Notebook
•
GNU General Public License v3.0
•2•3•0•0•Updated Jul 15, 2025Jul 15, 2025
zhong-et-al-2025
Public
code to make figures from Zhong et al, 2025
Jupyter Notebook
•
GNU General Public License v3.0
•2•7•0•0•Updated Jul 6, 2025Jul 6, 2025
suite2p
Public
cell detection in calcium imaging recordings
neuroscience data-analysis imaging
Jupyter Notebook
•
GNU General Public License v3.0
•258•396•124•13•Updated Jun 11, 2025Jun 11, 2025
neuropop
Public
analysis tools for large-scale neural recordings
Python
•
GNU General Public License v3.0
•2•15•0•0•Updated Apr 4, 2025Apr 4, 2025
rastermap
Public
a visualization method for neural data
neuroscience neuroscience-methods unsupervised-clustering
Python
•
GNU General Public License v3.0
•51•235•10•0•Updated Apr 4, 2025Apr 4, 2025
critical_init
Public
code for Pachitariu et al 2025
Jupyter Notebook
•
GNU General Public License v3.0
•0•0•0•0•Updated Feb 28, 2025Feb 28, 2025
cellpose-napari
Public
napari plugin for cellpose (see www.cellpose.org) - an anatomical segmentation tool
segmentation napari
Python
•
BSD 3-Clause "New" or "Revised" License
•24•55•10•2•Updated Oct 27, 2024Oct 27, 2024
stringer-pachitariu-et-al-2018a
Public
Recordings of 10k neurons during spontaneous behaviors
neuroscience openscience
MATLAB
•16•52•2•2•Updated Mar 22, 2024Mar 22, 2024
pykilosort
Public
WIP: Python port of Kilosort2
Python
•
GNU General Public License v2.0
•26•50•29•3•Updated Jul 8, 2023Jul 8, 2023
stringer-et-al-2019
Public
paper figure code
Python
•
GNU General Public License v3.0
•14•24•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•13•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
neuroscience openscience vision-science
MATLAB
•21•70•3•0•Updated Sep 3, 2019Sep 3, 2019
pachitariu-et-al-2018a
Public
Benchmarking spike deconvolution without ephys
MATLAB
•1•6•0•0•Updated May 3, 2018May 3, 2018