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https://edspace.american.edu/openbehavior/project/tonebox-system-automated-auditory-operant-conditioning/

Project related to auditory behavioral task data collection.Provided high throughput operant conditioning in mouse homecage system was developed by University of Maryland,College Park, scientists.Automated system for training up to hundreds of mice in auditory behavioral task features custom Matlab GUI running on desktop which connects to Raspberry Pi to administer auditory stimuli from USB soundcard and collects auditory data as well as licking data from water spout with commercially available capacitive sensors. Parts list and build instructions are readily available from paper and associated GitHub repository.

Proper citation: ToneBox (RRID:SCR_021548) Copy   

•   Source: SciCrunch Registry

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/yorambenshaul/optimouse

Software tool for analysis of mouse position data.Open source software to analyze positions of individual mice, specifically their nose positions, in behavioral arena with the goal of minimizing error.

Proper citation: Optimouse (RRID:SCR_021527) 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/portugueslab/stytra

Open source software Python package to control stimulation and track behaviour.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 (RRID:SCR_021500) Copy   

•   Source: SciCrunch Registry

https://github.com/openworm/tracker-commons

Software tool as repository of documentation, software, and discussions to share worm tracking data and analysis routines.Open access repository for storing, accessing, and filtering data; interchange format for notating single or multi worm behavior; and file formats written in Python for feature extraction, review, and analysis.

Proper citation: Worm Behavior Platform (RRID:SCR_021501) Copy   

•   Source: SciCrunch Registry

https://github.com/olivierfriard/BORIS

Open source event logging software for video/audio coding and live observations.Multiplatform standalone program that allows user specific coding environment for computer based review of previously recorded videos or live observations.

Proper citation: Behavioral Observation Research Interactive Software (RRID:SCR_021509) Copy   

•   Source: SciCrunch Registry

https://github.com/chenxinfeng4/ArControl

Software tool as Arduino UNO/Mega based, visual programming and real-time behavioral platform for neuroscience. It can run Go/No-Go, 2AFPC and Optogenetic stimulation tasks. Stand alone and intuitive Gaphical User Interface application.Part of ArControl system.

Proper citation: ArControl (RRID:SCR_021605) Copy   

•   Source: SciCrunch Registry

https://github.com/bonvision

Open source software package for creating and controlling visual environments.Software package for Bonsai which allows for control of 2D and 3D environments.

Proper citation: BonVision (RRID:SCR_021534) Copy   

•   Source: SciCrunch Registry

https://github.com/cosanlab/facesync

Open source software Python toolbox which automatically synchronizes recorded facial expressions to videos and events such as social interactions.Framework for recording facial expressions with head mounted cameras.

Proper citation: FaceSync (RRID:SCR_021396) Copy   

•   Source: SciCrunch Registry

https://github.com/UmSenhorQualquer/d-track/blob/master/docs/source/index.rst

Software package to track object in 3D based on 3D schematics of scene.Semi automatic 3D video tracking technique to analyse movements and routines of aquatic animals with application to captive dolphins.

Proper citation: D-Track (RRID:SCR_021394) Copy   

•   Source: SciCrunch Registry

https://github.com/wehr-lab/autopilot

Software tool as open source Python framework for behavioral neuroscience that distributes experiments over networked swarms of Raspberry Pis. Toolkit of flexible modules to design experiments without rigid programming and API limitations.

Proper citation: AutoPilot (RRID:SCR_021518) Copy   

•   Source: SciCrunch Registry

https://github.com/jgraving/DeepPoseKit

Software toolkit with high level API for 2D pose estimation of user defined keypoints using deep learning.Written in Python and built using Tensorflow and Keras.Method for pose estimation developed by behavioral scientists at the Max Planck Institute of Animal Behavior.

Proper citation: DeepPoseKit (RRID:SCR_021405) Copy   

•   Source: SciCrunch Registry

https://github.com/DrCoffey/DeepSqueak

Software MATLAB package for high throughput ultrasonic vocalizations detection, classification, and analysis.

Proper citation: DeepSqueak (RRID:SCR_021524) Copy   

•   Source: SciCrunch Registry

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

Project related to individual mice positions analysis, specifically their nose positions. Includes software tool for analysis of mouse position data designed by Hebrew University scientists. Provides open source software to analyze positions of individual mice, specifically their nose positions, in behavioral arena with the goal of minimizing error.

Proper citation: Optimouse project (RRID:SCR_021463) Copy   

•   Source: SciCrunch Registry

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

Portal provides software tool for analysis and quantification of both single and socially interacting zebrafish. Software data extraction and analysis tool built in open source R language for tracking zebrafish behavior.

Proper citation: Argus (RRID:SCR_021585) Copy   

•   Source: SciCrunch Registry

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

Portal provides MouseMove software system used to analyze Open Field behavior of mice after experimental stroke to show reduced locomotor activity and to quantify laterality deficits. System is used in combination with open source program ImageJ and MTrack2 plugin to analyze pre recorded Open Field test video. System has two downloadable components, ImageJ macro and separate program with custom built MouseMove GUI. ImageJ is used to subtract background video from experiment and create image of animals total trajectory. MouseMove GUI then completes detailed analysis of movement patterns, measuring fractional time spent stationary, distance traveled, speed mean and various details of laterality.

Proper citation: MouseMove project (RRID:SCR_021581) Copy   

•   Source: SciCrunch Registry

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

Project related to mouse tracking and analysis of mouse movements during computerized lab experiments. Provides open source software plugin to record and analyze mouse movements.

Proper citation: Mousetrap project (RRID:SCR_021456) Copy   

•   Source: SciCrunch Registry

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

Project related to saving precise times of behavioral events.Provides software tool to read MedPC data into Python and Matlab.

Proper citation: MedParse project (RRID:SCR_021455) Copy   

•   Source: SciCrunch Registry