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https://github.com/helioalexandre/MouBeAT

Software package to analyze different behavioral tests in rodents semi-automatically. These tests include Open Field (OF), Elevated Plus Maze (EPM), Y-maze (YM) test and Morris Water Maze (MWM).

Proper citation: Mouse Behavioral Analysis Toolbox (RRID:SCR_023291) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=Rtrack

Software R package for analysis of paths from spatial tracking experiments such as Morris water maze and calculation of goal finding strategies. Used for in depth analysis of tracking coordinates from video.

Proper citation: Rtrack (RRID:SCR_023025) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/pi-usb-cam/

Project related to video recording.Provides system for high throughput video capture. Pi USB Cam system includes low cost Raspberry Pi microcomputer, DIY electronics peripherals, freely available open-source firmware, and custom 3D-printed casings.

Proper citation: Pi USB Cam project (RRID:SCR_022834) Copy   

•   Source: SciCrunch Registry

https://github.com/Whitlock-Group/HERBS

Open source, extendable, intuitive and interactive software platform for image visualisation and image registration. Python based GUI for histological E-data registration in brain space.

Proper citation: Histological E data Registration in rodent Brain Spaces (RRID:SCR_022776) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/3d-printed-superfusion-chamber/

Project consists of suite of 3D-printed tools including superfusion chamber with independent brain presser and animal stand. Modular device that facilitates transfer of pharmacological agents and brain access for electrodes and/or lenses for imaging. Provides stable conditions for electrophysiological and neuroimaging recordings. Device can be print either in-house or through 3d-printing service.

Proper citation: 3D Printed Superfusion Chamber (RRID:SCR_022901) Copy   

•   Source: SciCrunch Registry

https://github.com/spoonsso/dannce

Convolutional neural network that calculates 3D positions of user-defined anatomical landmarks on behaving animals from videos taken at multiple angles. Works on recorded video data from multiple cameras. Used for 3D markerless pose estimation and tracking.

Proper citation: DANNCE (RRID:SCR_023061) Copy   

•   Source: SciCrunch Registry

https://github.com/neurobio-hiroshima/WRAQ

Open source microcontroller based system for wheel running activity in mice.Used to track circadian rhythms of rodents using microcontroller, powered by lithium polymer battery, and surveys exercise activity for up to 30 days. Data can be stored on microSD card or using online server using WiFi connection. Python software provides system interface with ActogramJ to analyze chronobiological aspects of data.Repository includes guide for installing integrated developmental environment and dependent libraries for building and setting up WRAQ systems - WRAQ and WRAQ-Wifi. WRAQ and WRAQ-WiFi are based on Adafruit Adalogger and DFRobot FireBeetle ESP32 connected to 4- and 8-bit binary counters receiving signal from reed switch attached to 5-inch flying saucer respectively.

Proper citation: Wheel Running Activity acQuisition (RRID:SCR_023353) Copy   

•   Source: SciCrunch Registry

https://github.com/CaT-zTools/CaT-z_Software

Software tool for 3D tracking and automatic classification of rodent behavior. Used for acquisition, annotation, and automatic behavioral profile characterization of laboratory rodents' RGB-D videos. Utilizes video segmentation, tracking of body parts, and automated classification of behaviors through machine learning and computer vision methods. Setup uses low costing RGB-D cameras for tracking behaviors in various environments. Software includes GUI interfaces for video acquisition, annotation, and processing of behavioral data. Software is capable of automated behavior detection with only 30 minutes of annotated video.

Proper citation: CaT-z (RRID:SCR_023399) Copy   

•   Source: SciCrunch Registry

https://github.com/KumarLabJax/JABS-behavior-classifier

Video based phenotyping platform for laboratory mouse. Provides complete details of software and hardware, including 3D designs used for data collection. Data acquisition system consists of video collection hardware and software, behavior labeling and active learning app, and online database for sharing classifiers. Hardware and software solution collects high quality data for behavior analysis.

Proper citation: JAX Animal Behavior System (RRID:SCR_023721) Copy   

•   Source: SciCrunch Registry

https://github.com/mtu-most/linear-actuator

Code and model files for open source linear actuator. Part of Pearce Lab Syringe Pump system.

Proper citation: linear actuator (RRID:SCR_021613) Copy   

•   Source: SciCrunch Registry

https://github.com/KravitzLab/ROBucket

Software tool as ROBucket source code.

Proper citation: Rodent Operant Bucket (RRID:SCR_021610) Copy   

•   Source: SciCrunch Registry

https://github.com/jf-lab/chendoscope

Software tool as part of CHEndoscope. Acquisition software that interfaces with CHEndoscope Ximea USB camera. This code is compatible with Linux and Windows systems.

Proper citation: chendoscope (RRID:SCR_021616) Copy   

•   Source: SciCrunch Registry

https://github.com/jamieboyd/AutoHeadFix

Software Python code for automated control of behavioural apparatus and imaging for mice in home cage environment.Part of Homecage Task Training and Mesoscale Imaging system.

Proper citation: AutoHeadFix (RRID:SCR_021617) 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://murphylab.med.ubc.ca/automated-homecages/

Software tool as part of Automated Home Cage Functional Imaging system.

Proper citation: Automated Home-Cage Functional Imaging (RRID:SCR_021607) Copy   

•   Source: SciCrunch Registry

https://github.com/dublon/scintillate

Open source graphical viewer for time series calcium imaging evaluation and pre-processing.

Proper citation: Scintillate (RRID:SCR_021531) Copy   

•   Source: SciCrunch Registry

https://github.com/ribeiro-lab/flyPAD-fpga

FPGA code for running main board of flyPAD. Code written in VHDL using Quartus 2 web edition software.

Proper citation: flyPAD (RRID:SCR_021522) Copy   

•   Source: SciCrunch Registry

https://github.com/KaetzelLab

Operant Box code

Proper citation: pyOS-5 (RRID:SCR_022336) Copy   

•   Source: SciCrunch Registry

https://github.com/DeNardoLab/BehaviorDEPOT

Software tool for automated behavioral detection based on markerless pose tracking. Behavioral analysis tool to first compile and clean point-tracking output from DeepLabCut, and then classify behavioral epochs using custom behavior classifiers. Used to detect frame by frame behavior from video time series and can analyze results of common experimental assays, including fear conditioning, decision-making in T-maze, open field, elevated plus maze, and novel object exploration. Calculates kinematic and postural statistics from keypoint tracking data from pose estimation software outputs.

Proper citation: BehaviorDEPOT (RRID:SCR_023602) Copy   

•   Source: SciCrunch Registry

https://github.com/Optophys-Lab/FreiBox/tree/main/Commutator_FreiBox2022

Affordable commutator that is equipped with novel sensing system that improves online tracking of cable rotations without impairing the 1-photon calcium imaging via Miniscope. Commutator to allow freely moving behaviors while recording neural activity from platforms such as Miniscope V4 and OpenEphys. Used to perform calcium imaging.

Proper citation: commutator (RRID:SCR_023919) Copy   

•   Source: SciCrunch Registry