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b-soid

Behavioral segmentation of open field in DeepLabCut, or B-SOID ("B-side"), is an unsupervised learning algorithm written in MATLAB that serves to discover behaviors that are not pre-defined by users.

cortexwidelowdimensionalspatiotemporaldynamics

Example Data and Figure Generation Code

deeplabcut

Markerless pose estimation of user-defined features with deep learning for all animals, including humans

fpcnmf

Flexible Penalized Convolutional Non-negative Matrix Factorization (fpCNMF) for large-scale neural imaging data

genutils

A collection of general utilities to be used with other repos. Still being updated

gramm

Gramm is a complete data visualization toolbox for Matlab. It provides an easy to use and high-level interface to produce publication-quality plots of complex data with varied statistical visualizations. Gramm is inspired by R's ggplot2 library.

motionmapper

Sample implementation of the MotionMapper behavioral analysis algorithms

multiplexedsubspaces

Code associated with Multiplexed Subspaces Route Neural Activity Across Brain-wide Networks. Contact [email protected] with any questions.

simplemousetracker

Simple gui to allow a user to track a mouse (or dark object) in an image. Designed for three chamber social assay but reasonably flexible to any environment that is lighter than the mouse.

umap

Uniform Manifold Approximation and Projection

umap-matlab-wrapper

A simple MATLAB wrapper for umap

widefield_imaging_control