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https://github.com/UmSenhorQualquer/d-track/blob/master/docs/source/index.rst

Software package to track object in 3D based on 3D schematics of scene.Semi automatic 3D video tracking technique to analyse movements and routines of aquatic animals with application to captive dolphins.

Proper citation: D-Track (RRID:SCR_021394) Copy   

•   Source: SciCrunch Registry

https://github.com/wehr-lab/autopilot

Software tool as open source Python framework for behavioral neuroscience that distributes experiments over networked swarms of Raspberry Pis. Toolkit of flexible modules to design experiments without rigid programming and API limitations.

Proper citation: AutoPilot (RRID:SCR_021518) Copy   

•   Source: SciCrunch Registry

https://github.com/jgraving/DeepPoseKit

Software toolkit with high level API for 2D pose estimation of user defined keypoints using deep learning.Written in Python and built using Tensorflow and Keras.Method for pose estimation developed by behavioral scientists at the Max Planck Institute of Animal Behavior.

Proper citation: DeepPoseKit (RRID:SCR_021405) Copy   

•   Source: SciCrunch Registry

https://github.com/DrCoffey/DeepSqueak

Software MATLAB package for high throughput ultrasonic vocalizations detection, classification, and analysis.

Proper citation: DeepSqueak (RRID:SCR_021524) Copy   

•   Source: SciCrunch Registry

https://github.com/alexcwsmith/PiRATeMC

Software data management pipeline for camera synchronization and combined data directories.

Proper citation: Pi-based Remote Acquisition Technology for Motion Capture (RRID:SCR_022327) Copy   

•   Source: SciCrunch Registry

https://github.com/lapphe/raspberry_rat

Software Python platform for recording, converting, and uploading videos to cloud and for performing scheduled video recordings. Repository also includes wiki section with comprehensive guide to setting up Raspberry Pis for this purpose. Raspberry Pis are often cheaper than camcorder and can produce HD video. They are also equipped with infrared camera, making them ideal for recordings of animals that are active in low light conditions.

Proper citation: Rasberry rat (RRID:SCR_023467) Copy   

•   Source: SciCrunch Registry

https://github.com/lambdaloop/anipose

Software package for 3D pose estimation. Uses DeepLabCut for 2D tracking and uses triangulation methods to project pose estimations into three dimensions.Toolkit for robust markerless 3D pose estimation.

Proper citation: Anipose (RRID:SCR_023041) Copy   

•   Source: SciCrunch Registry

https://github.com/helioalexandre/MouBeAT

Software package to analyze different behavioral tests in rodents semi-automatically. These tests include Open Field (OF), Elevated Plus Maze (EPM), Y-maze (YM) test and Morris Water Maze (MWM).

Proper citation: Mouse Behavioral Analysis Toolbox (RRID:SCR_023291) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=Rtrack

Software R package for analysis of paths from spatial tracking experiments such as Morris water maze and calculation of goal finding strategies. Used for in depth analysis of tracking coordinates from video.

Proper citation: Rtrack (RRID:SCR_023025) Copy   

•   Source: SciCrunch Registry

https://github.com/kemerelab/ghostipy

Software signal processing and spectral analysis toolbox designed for local field potential recordings.

Proper citation: ghostipy (RRID:SCR_026231) Copy   

•   Source: SciCrunch Registry

https://github.com/Sakata-Lab/SaLSa

Software MATLAB package for analyzing and categorizing behaviors using pose estimation data. Integrates semi-automatic labeling with machine learning, specifically Long Short-Term Memory neural networks, to classify behavioral "syllables” (distinct, repeatable behaviors). Combinatory approach of semi-automatic labeling and long short-term memory to classify behavioral syllables.

Proper citation: SaLSa (RRID:SCR_026182) Copy   

•   Source: SciCrunch Registry

https://github.com/NC4Lab/NC4gate

Code for testing and operating NC4gate modules of modular gate system for autonomous control of rodent behavior. Fully customizable gate system that can be used in behavioral experiments involving rodent mazes (T-maze, Y-maze, radial arm, etc.).

Proper citation: NC4gate (RRID:SCR_026445) Copy   

•   Source: SciCrunch Registry

https://github.com/tomcatsmith19/ArucoDetection

Automated rodent behavioral scoring system, complete with 3D design files and code/software. System monitors behavioral engagement using open-source software. 3D design files and necessary software has been made available, as well as code that can be used for data analysis.

Proper citation: ArUco (RRID:SCR_026572) Copy   

•   Source: SciCrunch Registry

https://github.com/tne-lab/py-behav-box-v2

Open source software interface and framework for controlling behavioral experiments in neuroscience and psychology. Python-based framework for designing and controlling behavioral experiments in animals. Used to develop, perform, and control behavioral tasks.

Proper citation: PyBehave (RRID:SCR_025406) Copy   

•   Source: SciCrunch Registry

https://github.com/mtu-most/linear-actuator

Code and model files for open source linear actuator. Part of Pearce Lab Syringe Pump system.

Proper citation: linear actuator (RRID:SCR_021613) Copy   

•   Source: SciCrunch Registry

https://github.com/KravitzLab/ROBucket

Software tool as ROBucket source code.

Proper citation: Rodent Operant Bucket (RRID:SCR_021610) Copy   

•   Source: SciCrunch Registry

https://github.com/jf-lab/chendoscope

Software tool as part of CHEndoscope. Acquisition software that interfaces with CHEndoscope Ximea USB camera. This code is compatible with Linux and Windows systems.

Proper citation: chendoscope (RRID:SCR_021616) Copy   

•   Source: SciCrunch Registry

https://github.com/jamieboyd/AutoHeadFix

Software Python code for automated control of behavioural apparatus and imaging for mice in home cage environment.Part of Homecage Task Training and Mesoscale Imaging system.

Proper citation: AutoHeadFix (RRID:SCR_021617) Copy   

•   Source: SciCrunch Registry

https://github.com/bsbrl/craniobot

Software tool as part of Craniobot system.Generates, sends, and receives commands to communicate with the Craniobot.

Proper citation: craniobot (RRID:SCR_021609) Copy   

•   Source: SciCrunch Registry

https://murphylab.med.ubc.ca/automated-homecages/

Software tool as part of Automated Home Cage Functional Imaging system.

Proper citation: Automated Home-Cage Functional Imaging (RRID:SCR_021607) Copy   

•   Source: SciCrunch Registry