MouseLand/course-materials

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MouseLand/course-materials

MouseLand

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cellpose

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

Jupyter Notebook

Kilosort

Fast spike sorting with drift correction for up to a thousand channels

suite2p

cell detection in calcium imaging recordings

Jupyter Notebook

rastermap

a visualization method for neural data

facemap

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.

stringer-pachitariu-et-al-2018b

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

pykilosort

WIP: Python port of Kilosort2

stringer-pachitariu-et-al-2018a

Recordings of 10k neurons during spontaneous behaviors

cellpose-napari

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

stringer-et-al-2019

paper figure code

receptivefield-explorer

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

Jupyter Notebook

neuropop

analysis tools for large-scale neural recordings

EnsemblePursuit

Jupyter Notebook

pachitariu-et-al-2018a

Benchmarking spike deconvolution without ephys

steinmetz2019_NMA

Jupyter Notebook

cellpose_web

code for cellpose website

facemap-napari

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