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https://github.com/gordonberman/MotionMapper

Software tool to work on videos (not poses).Uses image analysis and multivariate statistical methods to find stereotyped behaviors in flies, mice, and other species.

Proper citation: MotionMapper (RRID:SCR_021384) Copy   

•   Source: SciCrunch Registry

https://github.com/YttriLab/B-SOID

Software pipeline that pairs unsupervised pattern recognition with supervised classification to achieve fast predictions of behaviors that are not predefined by users.Unsupervised learning algorithm that discovers and classifies actions based on inherent statistics of data points provided.

Proper citation: Behavioral Segmentation of Open-field in DeepLabCut (RRID:SCR_021385) Copy   

•   Source: SciCrunch Registry

https://github.com/murthylab/sleap

Method for pose estimation that uses deep neural networks.Open source software tool as deep learning based framework for estimating positions of animal body parts.Supports multi animal pose estimation and tracking, and includes advanced labeling or training.SLEAP is next generation of LEAP and allows for tracking multiple animals.

Proper citation: Social LEAP (RRID:SCR_021382) Copy   

•   Source: SciCrunch Registry

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

Project related to involvement in larval zebrafish behavioral experiments.Provides integrated system for stimulation, tracking and closed loop behavioral experiments. Provides timed stimulus presentation, interfacing with external devices and simultaneous real time tracking of behavioral parameters such as position, orientation, tail and eye motion in both freely swimming and head restrained preparations.

Proper citation: Stytra project (RRID:SCR_021416) Copy   

•   Source: SciCrunch Registry

https://github.com/jonnew/Oat

Software tool as real time position tracker for behavioral research. Used for processing images, extracting object position information, and streaming data to disk and/or the network in real time.

Proper citation: Online Animal Tracker (RRID:SCR_021412) Copy   

•   Source: SciCrunch Registry

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

Portable behavioural set up that incorporates both gait analysis (using pedobarograph) and whisker movements (using high speed video camera and infrared light source).Automatically records both whisker and gait information and provides added statistical tools to analyse data. LocoWhisk system includes ARTv2 software for simultaneous measurement of locomotion behaviours and whisker movements.

Proper citation: LocoWhisk project (RRID:SCR_021430) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/facesync/, https://bio.tools/FaceSync

Project related to emotions and facial expressions. Includes open source guide to building affordable head mount for camera to maintain high temporal and spatial resolution of face throughout duration of experiment. Device is paired with FaceSync, Python toolbox which automatically synchronizes recorded facial expressions to videos and events such as social interactions.

Proper citation: FaceSync project (RRID:SCR_021393) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/head-fixed-setup-combined-behavior-electrophysiology-optogenetics/

Project related to temporally controlled rodent behavior. Provides system which utilizes optimal open source setup of hardware and software through behavioral setup for temporally controlled rodent behavior. Used for combined behavior, electrophysiology and optogenetics experiments. System allows for training of head fixed animals with calibrated sound stimuli, precisely timed fluid and air puff presentations as reinforcers.Combines microcontroller based behavior control with sound delivery system for acoustic stimuli, fast solenoid valves for reinforcement delivery and custom built sound attenuated chamber.

Proper citation: Head-Fixed Setup for Combined Behavior, Electrophysiology, and Optogenetics project (RRID:SCR_021427) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/kinemouse-wheel/

Project is related to Columbia University designed KineMouse Wheel, light weight running wheel for head fixed locomotion that allows for 3D positioning of mice with single camera. System uses single camera and DeepLabCut (or similar) software.

Proper citation: KineMouse Wheel project (RRID:SCR_021425) Copy   

•   Source: SciCrunch Registry

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

Project related to capturing detailed behavior in freely moving mice. System combines lightweight head mounted camera and head movement sensors to detect behaviors in mice. Used to monitor behaviors including eye position, whisking, and ear movements in unrestrained animals.Can be mounted in combination with neural implants for recording brain activity.Provides software Python package with functions for extracting and analyzing data recorded using camera.

Proper citation: Mousecam project (RRID:SCR_021422) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/cap-touch-sensor/

Project related to accurately counting and monitoring the behavior of organisms.Provides open source capacitive touch sensing system.Capacitive sensors are positioned to readily detect direct physical touches from rodent under investigation. Device,designed around capacitive touch sensor MPR121,accurately counts and monitors behavior of organisms.

Proper citation: Capactive Touch Sensor project (RRID:SCR_021486) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/2abt/

Project related to training mice on task that requires continued updating of action/outcome relationships. Behavioral project includes task protocol and corresponding build instructions.Open source behavioral box used to train mice on task that requires continued updating of action/outcome relationships. Permits investigation of motivated behavior that requires flexible relationships between sensory stimuli and motor action. Project provided by Harvard Medical School scientists.

Proper citation: Two Armed Bandit Task project (RRID:SCR_021483) Copy   

•   Source: SciCrunch Registry

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

Project related to fluorescent imaging. Provides single photon fluorescent imaging microscope systems. System includes modular in vivo all optical neurophysiology rigs with transparent hardware, and acquisition and analysis software.Provide designs for 3D printed, lightweight, wireless capable microscope and motorized commutator, designed for multi month monitoring neural activity of zebra finches while they sing their courtship songs. Adapted for rodents and birds such as canaries.

Proper citation: FinchScope project (RRID:SCR_021484) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/ucla-miniscope/

Project related to fluorescence imaging to record neural activity in awake, freely behaving mice.Provided system is developed by UCLA scientists. Miniscope system includes Miniscope with single, flexible coaxial cable to carry power, control signals, and imaging data to open source Data Acquisition hardware and software. Open source miniature fluorescence microscope uses wide-field fluorescence imaging to record neural activity in awake, freely behaving mice.

Proper citation: UCLA Miniscope project (RRID:SCR_021480) Copy   

•   Source: SciCrunch Registry

https://github.com/cMadan/stl-toolbox

Software toolbox for visualizing and quantifying movement from pre-recorded videos.Used for summarizing animal movement data as single image ( spectral time lapse algorithm) as well as automate analysis of animal movement data.

Proper citation: Quantifying Animal Movement from Pre-recorded Videos (RRID:SCR_021515) Copy   

•   Source: SciCrunch Registry

https://github.com/ikodvanj/ratPASTA/

Software package for processing and visualising data from startle experiments in rodents or experiments measuring grip strength in rodents.

Proper citation: Platform for Acoustic STArtle (RRID:SCR_021516) Copy   

•   Source: SciCrunch Registry

https://github.com/MouseLand/facemap

Software toolbox for unsupervised video analysis of rodent behavior.Used for videographic processing of head fixed rodent behavior.

Proper citation: FaceMap (RRID:SCR_021513) Copy   

•   Source: SciCrunch Registry

https://github.com/kscottz/SkinnerBox

Software tool for data logging and analysis.

Proper citation: Skinner Box (RRID:SCR_021514) Copy   

•   Source: SciCrunch Registry

https://github.com/bonsai-rx/bonsai

Software tool as event based framework for processing and controlling data streams. Open source software tool as visual language for reactive programming.Used for composing reactive and asynchronous data streams coming from video cameras, microphones, electrophysiology systems or data acquisition boards.

Proper citation: Bonsai (RRID:SCR_021512) Copy   

•   Source: SciCrunch Registry

https://github.com/cortex-lab/Rigbox

Open source software MATLAB toolbox for running behavioral neuroscience experiments and managing data.Used for probing neurons and behavior. Used for managing behavioral neuroscience experiments and acquiring experiment related data.

Proper citation: Rigbox (RRID:SCR_021517) Copy   

•   Source: SciCrunch Registry