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https://edspace.american.edu/openbehavior/project/wave-surfer/

Project related to neurophysiology data acquisition and analysis.Included open source software application for neurophysiology data acquisition and analysis is provided by Howard Hughes Medical Institute Janelia Research Campus scientists. Program is based in MatLab, and evolved from earlier open source software package called Ephus.

Proper citation: Wave Surfer project (RRID:SCR_021476) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/self-grooming-mice/

Portal provides protocol that implements JAABA, open source machine learning based behavior detection system; motr, open-source mouse trajectory tracking software; and bonsai, open source system capable of streaming and recording video. Together they use these tools to process videos of mice performing grooming behaviors in variety of behavioral setups.

Proper citation: Automated Classification of Self-grooming in Mice project (RRID:SCR_021597) Copy   

•   Source: SciCrunch Registry

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

Project related to calcium imaging.Provides software library, CaImAn, for one and two-photon Calcium Imaging data Analysis.

Proper citation: Calcium Imaging data Analysis project (RRID:SCR_021477) Copy   

•   Source: SciCrunch Registry

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

Project related to creating and controlling visual environments.Provided open source software package for creating and controlling visual environments was developed by University College London scientists.

Proper citation: BonVision project (RRID:SCR_021491) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/open-source-whisking-video-database/

Portal provides 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 portal (RRID:SCR_021404) 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/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/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/aspence/tmilltracker

Open source computer vision controlled treadmill system for small running animals such as insects and mice. Treadmill is controlled by Python software, allowing for flexible control of video tracking parameters, behavioral triggers, distance ran, and feedback. Used for studying locomotor behavior.

Proper citation: tmilltracker (RRID:SCR_023511) Copy   

•   Source: SciCrunch Registry

https://www.sciencedirect.com/science/article/pii/S2352289523000061

Open source automated platform for assessing working memory and prefrontal circuit function. Designed for automated, high-throughput assessments of working memory and simultaneous two-photon imaging in chronic stress studies. Physiology compatible behavioral platform designed specifically for studying circuit mechanisms underlying working memory and related cognitive functions in chronic stress states.

Proper citation: Automated 2 Photon Imaging Compatible Platform for Assessing Working Memory (RRID:SCR_023463) Copy   

•   Source: SciCrunch Registry

https://www.instructables.com/3D-Printed-Syringe-Pump-Rack/

System includes 3D Printed Syringe Pump Rack composed by 5 Syringe Pumps to have 2 continuous flow systems and one remaining pump. Syringe Pump is used to gradually administer small amounts of fluid to patient or for use in chemical and biomedical research. Main features include Open hardware/software, Extremely compact size ( 7cm movement range ), High precision lead screw and nut, Simple to use (command line interface), Simple to replicate, Minimal clean Design.

Proper citation: 3D Printed Multi Pump System (RRID:SCR_023575) Copy   

•   Source: SciCrunch Registry

https://github.com/JosePardoVazquez/RatHeadphones

Repository for highly controlled sound presentation in freely moving rats. Provides all necessary information for building, adjusting, and using Ratphones to reliably present auditory stimulation to freely moving rats. Used for 3D printing of headphones designed for auditory psychophysics in behaving rats.

Proper citation: RatHeadphones (RRID:SCR_023667) Copy   

•   Source: SciCrunch Registry

https://github.com/J-east/JevonsCameraViewer

Software tool as part of system designed to be easy to build and setup for real time eye tracking.Open source software provides accurate eye tracking. Can identify shapes such as circles, lines, and triangles.You can rotate and mirror images and also use variety of filters.Capable of processing video in real-time for optical flow. App for viewing multiple video streams from USB cameras.

Proper citation: Low Cost Open Source Eye Tracking (RRID:SCR_021497) Copy   

•   Source: SciCrunch Registry

https://github.com/chand-lab/openEyeTrack

Open source software tool used as part of multithreaded eye tracker.Video based eye tracker.

Proper citation: openEyeTrack (RRID:SCR_021401) Copy   

•   Source: SciCrunch Registry

https://github.com/ninscope

Sofware tool for use with NINscope.

Proper citation: NINscope software (RRID:SCR_021583) Copy   

•   Source: SciCrunch Registry

https://github.com/openmv

Software tool as part of OpenMV system.

Proper citation: OpenMV (RRID:SCR_021615) Copy   

•   Source: SciCrunch Registry