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https://github.com/sanworks

Software for a measurement and control system for behavior research, most often used to implement operant (Go/NoGo, 2AFC) tasks. This software controls a hierarchy of hardware modules, each powered by an Arduino-programmable microcontroller.

Proper citation: Bpod (RRID:SCR_015943) 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://github.com/sanworks/PulsePal

Software tool as part of Pulse Pal system which allows users to create and trigger software defined trains of voltage pulses with high temporal precision.

Proper citation: Pulse Pal (RRID:SCR_021611) Copy   

•   Source: SciCrunch Registry

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

Company to design and sell powerful neuroscience hardware that interfaces with open source software platform supported by large community of scientists and developers. Support efforts of open source community in commercially sustainable way.

Proper citation: SpikeGadgets (RRID:SCR_021623) Copy   

•   Source: SciCrunch Registry

https://github.com/strawlab/freemovr_engine

Software tool as virtual reality engine built on ROS and OpenSceneGraph.Perspective correct Virtual Reality for freely moving animals engine. Used for multicomputer realtime tracking and display with goal of being useful for scientific studies of vision and behavior.Part of FreemoVR system.

Proper citation: FreemoVR (RRID:SCR_021601) Copy   

•   Source: SciCrunch Registry

https://github.com/FlySorterLLC

Software tool to automate various fly handling tasks.Control software for Drosophila handling robot MAPLE.

Proper citation: Modular Automated Platform for Large Scale Experiments (RRID:SCR_021600) Copy   

•   Source: SciCrunch Registry

https://github.com/amchagas/poke_device_arduino

Software tool as script to test if IR led, IR photodiode, arduino and 3D printed nose poke device work properly. Part of Nose Poke Device system.

Proper citation: poke device arduino (RRID:SCR_021608) Copy   

•   Source: SciCrunch Registry

https://github.com/delcasso/hope

Softwre tool as part of Hybrid-drive combining Optogenetics, Pharmacology, and Electrophysiology project for brain implant.

Proper citation: Hybrid-drive combining Optogenetics, Pharmacology, and Electrophysiology (RRID:SCR_021606) Copy   

•   Source: SciCrunch Registry

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

Software Pyton scripts to run computerised task of Reaction Time. Scripts, together with their instructions and scoresheets.Used for assessment of RTs that is freely available, compatible with all operating systems, without license and activation costs, and based on open source software platform.

Proper citation: OORTT (RRID:SCR_022331) 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://www.eneuro.org/content/9/5/ENEURO.0099-22.2022

Open source modular apparatus to produce guide cannulas exploiting 3D printing technology. Step by step procedure to realize hippocampal guide cannulas. 3D-printed guide cannula implant, as well as rotary tool based cutting station for fabrication of cannulae. Useful to conduct research in all the fields where access to brain areas is needed.

Proper citation: Customized Guide Cannulas (RRID:SCR_023941) Copy   

•   Source: SciCrunch Registry

https://www.eneuro.org/content/10/8/ENEURO.0212-23.2023

Simple, lightweight, and low cost customizable multielectrode array for Local Field Potential recordings. Used to collect LFP data from different brain regions simultaneously in rats. Can be modified to record single unit and multiunit activity in addition to LFP activity using both wired and wireless neural data acquisition systems.

Proper citation: Customizable Multielectrode Array (RRID:SCR_024551) Copy   

•   Source: SciCrunch Registry

https://github.com/lapphe/raspberry_rat

Software Python platform for recording, converting, and uploading videos to cloud and for performing scheduled video recordings. Repository also includes wiki section with comprehensive guide to setting up Raspberry Pis for this purpose. Raspberry Pis are often cheaper than camcorder and can produce HD video. They are also equipped with infrared camera, making them ideal for recordings of animals that are active in low light conditions.

Proper citation: Rasberry rat (RRID:SCR_023467) 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/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/HanLabBU/micro-control-final

Teensy microcontroller based interface for optical imaging camera control during behavioral experiments.

Proper citation: Teensy-Based Interface (RRID:SCR_021602) 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/danbider/lightning-pose

Software video centric package for direct video manipulation. Semi supervised animal pose estimation algorithm, Bayesian post processing approach and deep learning package. Improved animal pose estimation via semi-supervised learning, Bayesian ensembling, and cloud-native open-source tools.

Proper citation: Lightning Pose (RRID:SCR_024480) Copy   

•   Source: SciCrunch Registry