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alphatracker2

bonpsi

Repository for storing scripts using OpenEphys Bonsai video capture tool across multiple boxes.

bruker_control

Repository for code running the lab's multi-photon imaging experiments at the Bruker Ultima Investigator scope. Unites Arduino, Prairie View, and GenTL machine cameras in Python.

bruker_pipeline

Python implementation of data processing pipeline for data from the Bruker Ultima microscope in conjunction with bruker_control.

cropping

Crop video for SLEAP

elife_2023

Code and source data supporting the results of the manuscript, Kimchi et al. 2023. https://doi.org/10.7554/eLife.89093.1

headfix_behavior_data_dev

Headfixed behavior repository for analyzing DAQ data.

hmmglm

The code for the Hidden Markov Model Generalized Linear Model used to model discrete complex behavior profiles of mice using neural activity

ln2f

Metadata generation for animals, experiments, equipment, and reagents.

mousefacialexpressionanalysis

Extracting emotions from facial expressions in mice

realtime_alphaclass

Realtime Behavior Classification through AlphaClass, Raspberry Pi, for Optogenetics

sleap

A deep learning framework for multi-animal pose tracking.

sleap_benchmarking

Benchmarking Dr. Talmo Pereira's SLEAP in the Tye Lab

sleapyfaces

sleapyfaces-wheel

sleapyfacesexample

specialk

Team Specialk metadata/data manipulation repo

suite2p

cell detection in calcium imaging recordings

two-photon

Common scripts, libraries, and utilities for 2p experiments