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https://github.com/Optophys-Lab/FreiBox

Versatile open source behavioral system for investigating neuronal correlates of behavioral flexibility via 1-Photon Imaging in freely moving mice. Behavioral testing platform consists of FreiBox, novel low-cost Arduino behavioral setup, controlled by custom Python interface and integrates new licking sensor (strain gauge lickometer) for controlling spatial licking behavioral tasks.

Proper citation: Freibox (RRID:SCR_023918) Copy   

•   Source: SciCrunch Registry

https://github.com/nickpetersen93/LIQ_HD

Arduino code, 3D print design files, and tutorial video on how to build LIQ HD system. Open source tool for recording undisturbed two-bottle drinking behavior in home cage environment. All designs and software are open source to allow other researchers to build on the system and adapt LIQ HD to their animal home cages.

Proper citation: Lick Instance Quantifier Home cage Device (RRID:SCR_023802) Copy   

•   Source: SciCrunch Registry

https://github.com/singerlabgt/BrainWAVE

Code to program and run flicker stimulation on BrainWAVE stimulator device. This brain oscillation stimulating software can be adapted across subjects and integrated into variety of experimental designs like electrophysiology, neuroimaging, EEG, MRI. Flexible method for noninvasive stimulation of brain rhythms across species. Used to measure effects of rhythmic brain activity on behavior.

Proper citation: BrainWAVE (RRID:SCR_024396) Copy   

•   Source: SciCrunch Registry

https://github.com/VioletteChiara/AnimalTA

Software video tracking tool for tracking and analysing animal movement in different environments.

Proper citation: AnimalTA (RRID:SCR_023784) Copy   

•   Source: SciCrunch Registry

https://github.com/zelanolab/hfoapp

Software for detecting and identifying high frequency oscillations observed in EEG recordings. MATLAB based graphical user interface for High Frequency Oscillation marking.

Proper citation: HFOApp (RRID:SCR_024864) 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/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/lvrgb777/STPoseNet

Source code for pose recognition model for laboratory mice based on yolov8. Real-time spatiotemporal network model for robust mouse pose estimation.

Proper citation: STPoseNet (RRID:SCR_026834) Copy   

•   Source: SciCrunch Registry

https://github.com/ntorquet/lmt_toolkit_analysis

Open source web application created to analyze Live Mouse Tracker data easily and intuitively. Used to check reliability and to make some analysis of data from Live Mouse Tracker experiments. LMT stores data in SQLite files that requires some computer skills, but LMT-toolkit makes it easy to compute and extract behavioral profiles for each animal tested following step-by-step process.

Proper citation: Live Mouse Tracker Toolkit Analysis (RRID:SCR_024592) Copy   

•   Source: SciCrunch Registry

https://mousebytes.ca/home

Open access database for all cognitive data collected from touchscreen related tasks. Performs data comparison and interactive data visualization for any data uploaded onto the site. There are also guidelines and video tutorials available.

Proper citation: Mousebytes (RRID:SCR_017904) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/spikeforest/

Project related to neural data analysis. Provides open-source and reproducible software suite that benchmarks performance of automated spike sorting algorithms across extensive, curated database of ground truth electrophysiological recordings, displaying results interactively on continuously updating website.

Proper citation: Spike Forest project (RRID:SCR_021472) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/pypreclin/

Project related to preprocessing of images. Provieds software Python tool to processes raw macaque fMRI images using algorithms embedded in automatic pipeline.

Proper citation: Pypreclin project (RRID:SCR_021473) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/mne-scan/

Project related to real time acquisition and processing of electrophysiological data.Provides software tool for acquisition and processing of electrophysiological data.

Proper citation: MNE Scan project (RRID:SCR_021470) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/3dtracker/, http://www.3dtracker.org/

Project related to markerless computerized behavioral analysis for laboratory animals.Provides open source 3D video based behavioral analysis system for neuroscience. System includes open source software tool for 3D-video based markerless computerized behavioral analysis.

Proper citation: 3DTracker project (RRID:SCR_021440) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/lincom/

Project related to animal behavior in complex mazes.Provides software MATLAB package for linearization of place fields in complex mazes.

Proper citation: LinCoM project (RRID:SCR_021438) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/ethowatcher/

Project related to video tracking, detailed ethography, and extraction of kinematic variables from digital video files of laboratory animals.Provides computational tool developed at Federal University of Santa Catarina.

Proper citation: EthoWatcher project (RRID:SCR_021435) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/automated-rodent-tracker-art/

Project related to development of automated rodent tracking position and movement. Provides software tool to automatically track rodent.Used to track head movements, body movements and also aspects of body size.Identifies certain behaviours from video footage, such as rotations, moving forwards, interacting with objects and staying still.

Proper citation: Automated Rodent Tracker project (RRID:SCR_021432) Copy   

•   Source: SciCrunch Registry