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

Project related to high speed tracking of animals.Provides software tool for tracking organisms.Can handle one or several animals in one or several environments.Used for fish, insects, rodents, etc.

Proper citation: ToxTrac project (RRID:SCR_021424) Copy   

•   Source: SciCrunch Registry

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

Portal provides tools for investigating visuomotor integration specific to high speed kinematic tracking in small model organisms in closed loop experiments. University of Toronto scientists developed suite of Bonsai modules for specifically tracking and analyzing zebrafish movements and integrating these data with closed-loop experiments. BonZeb modules can also be used in an open-loop fashion for collecting, analyzing, and integrating data from multiple sources in real time, or from offline sources for batch processing of pre-recorded data.

Proper citation: BonZeb project (RRID:SCR_021388) 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/NeLy-EPFL/DeepFly3D

Software tool as PyTorch and PyQT5 implementation of 2D-3D tethered Drosophila pose estimation. Image annotation tool used for pose estimation and appendage tracking. Provides interface for pose estimation and to permit further correction of 2D pose estimates, which are automatically converted to 3D pose.

Proper citation: DeepFly3D (RRID:SCR_021402) 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://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/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/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/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/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/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/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://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