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https://github.com/ratcave/ratcave

Software 3D graphics python package for cognitive psychology experiments. Open source, cross platform Python library that adds 3D stimulus support to all OpenGL-based 2D Python stimulus libraries. These libraries include VisionEgg, Psychopy, Pyglet, and PyGam.

Proper citation: Ratcave (RRID:SCR_021599) Copy   

•   Source: SciCrunch Registry

https://github.com/mne-tools/mne-cpp

Software tool for real time processing of electrophysiological data.

Proper citation: MNE Scan (RRID:SCR_021530) Copy   

•   Source: SciCrunch Registry

https://github.com/KravitzLab/fed/wiki

Flexible open-source device for measuring feeding behavior. FED measures food intake in mice. It is battery powered and designed to be used in rodent colony caging.Home cage-compatible feeding system that measures food intake with high accuracy and temporal resolution. FED offers alternative to commercial feeders, with convenience of use in tradition colony rack caging.

Proper citation: Feeding Experimentation Device project (RRID:SCR_015942) Copy   

•   Source: SciCrunch Registry

https://github.com/sanworks

Software for a measurement and control system for behavior research, most often used to implement operant (Go/NoGo, 2AFC) tasks. This software controls a hierarchy of hardware modules, each powered by an Arduino-programmable microcontroller.

Proper citation: Bpod (RRID:SCR_015943) 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/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/ThomasAkam/active_commutator

Open source active commutator for Open Ephys / Intan electrophysiology systems. Motorized device used in neuroscience research, particularly in studies involving freely moving animals, to manage wires or fibers connecting headstage or other device to external equipment. Addresses common issue of tether tangling during experiments with freely moving subjects. Relies on Hall-Effect sensor detecting rotation of cable, this information is continuously fed to Adafruit microcontroller that operates servo motor to counter-rotate cable as needed, preventing twisting and ensuring clear, uninterrupted data collection. System can also be paused, restarted, and its neutral position recalibrated with simple button presses, allowing for flexible operation.

Proper citation: Active Commutator (RRID:SCR_027098) 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/DepartmentofNeurophysiology/Matlab-Whisker-Tracker

Shared database of videos featuring juvenile and adult male rats and adult male mice exploring stationary objects.This dataset includes wide variety of experimental conditions including genetic, pharmacological, and sensory deprivation interventions to explore how active sensing behavior is modulated by different factors. Database of high speed videos of whisking behavior in freely moving rodents.Open source high speed infrared videography database to study principles of active sensing in freely navigating rodents.

Proper citation: Open Source Whisking Video Database (RRID:SCR_021407) 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://github.com/fdechaumont/lmt-analysis

Software package for Live Mouse Tracker analysis. lmt-analysis provides all analysis tools needed to extract information from tracking performed by live mouse tracker.

Proper citation: Live Mouse Tracker analysis (RRID:SCR_021505) 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