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https://edspace.american.edu/openbehavior/project/syringe-pump/

Open source syringe pump apparatus developed by scientists from Michigan Technological University. Syringe pump is designed using freely available open source computer aided design (CAD) software and manufactured using open source RepRap 3-D printer and readily available parts.

Proper citation: Pearce Lab Syringe Pump project (RRID:SCR_021566) 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://edspace.american.edu/openbehavior/project/operant-box-auditory-tasks-obat/

Portal provides operant box designed to train small primates in auditory tasks.Device is based on computer and Arduino Mega 2560 board, named OBAT (Operant Box for Auditory Tasks), designed to present two different auditory stimuli to small primates.All schematics and software source code are available.

Proper citation: Operant Box for Auditory Tasks project (RRID:SCR_021564) Copy   

•   Source: SciCrunch Registry

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

Portal for open source operant chamber, based on Arduino microcontroller platform, that can be used to train mice to respond for reward. Designed by NIDDK scientists.Apparatus contains two nose pokes, drinking well, and solenoid controlled sucrose delivery system. Chamber can run magazine training, fixed ratio and progressive ratio training schedules, and can be programmed to run more complicated behavioral paradigms.

Proper citation: Rodent Operant Bucket project (RRID:SCR_021565) 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://github.com/flatironinstitute/CaImAn

Open source software tool for scalable calcium imaging data analysis. Used for large scale calcium imaging analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.

Proper citation: Calcium Imaging data Analysis (RRID:SCR_021533) Copy   

•   Source: SciCrunch Registry

https://hackaday.io/project/181604-mri-stereoscope

Project provides miniature mirror stereoscope system for MRI-scanner. System takes advantage of commonly used display equipment, MRI head coil, and display screen. Miniature Wheatstone stereoscope is used for human neuroimaging.

Proper citation: MRI-stereoscope project (RRID:SCR_021655) Copy   

•   Source: SciCrunch Registry

https://spikeforest.flatironinstitute.org/about

Open source and reproducible software suite that benchmarks performance of automated spike sorting algorithms across extensive, curated database of ground truth electrophysiological recordings, displaying results interactively on continuously updating website.

Proper citation: Spike Forest (RRID:SCR_021532) Copy   

•   Source: SciCrunch Registry

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

Project related to studying reward and feeding behavior. Provides open source automatic feeding system that can be customized for food types from seeds to pellets.System integrates plexiglass tubes, Arduino Uno, motor driver, and piezo sensor to reliably deliver accurate amounts of food, and can also be built using 3D printed parts.

Proper citation: OpenFeeder (RRID:SCR_021552) Copy   

•   Source: SciCrunch Registry

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/alexcwsmith/PiRATeMC

Software data management pipeline for camera synchronization and combined data directories.

Proper citation: Pi-based Remote Acquisition Technology for Motion Capture (RRID:SCR_022327) 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/lambdaloop/anipose

Software package for 3D pose estimation. Uses DeepLabCut for 2D tracking and uses triangulation methods to project pose estimations into three dimensions.Toolkit for robust markerless 3D pose estimation.

Proper citation: Anipose (RRID:SCR_023041) Copy   

•   Source: SciCrunch Registry

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://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