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https://github.com/denisecailab/ezTrack

Open source video analysis pipeline for investigation of animal behavior. Platform independent set of behavior analysis pipelines using interactive Python ( (iPython/Jupyter Notebook) that researchers with no prior programming experience can use.

Proper citation: ezTrack (RRID:SCR_021496) Copy   

•   Source: SciCrunch Registry

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

Project related to dispensing precise volumes of fluid over precise timescales.System components include syringe holder and control board with syringe pump controller and programming library.Syringe pump controller was developed by American University scientists.

Proper citation: Precision Syringe Pump Controller project (RRID:SCR_021493) Copy   

•   Source: SciCrunch Registry

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

Project related to study of orientation behavior and neural circuit functions, through creation and analysis of small, freely moving animals in virtual realities. Provides virtual reality tool system for behavioral and neural circuit studies of small animals.Closed loop platform to study unrestrained sensorimotor behavior.

Proper citation: Pi Virtual Reality System project (RRID:SCR_021490) Copy   

•   Source: SciCrunch Registry

https://github.com/oculomatic/oculomatic-release

Software tool for high speed eye tracking for Point Gray USB3.0 cameras.Oculomatic software tracks eye position within acquired image frame at frame rate dictated by image sensor.

Proper citation: Oculomatic (RRID:SCR_021525) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/open-tes/

Project is related to transcranial Electrical Stimulation.Included system contains aluminum box stimulator with banana connectors for both anode and cathode on front panel,power supply on rear, power switch and serial port, LCD screen and three buttons on top panel that are used to input settings for stimulator. Device for delivering non-invasive neuromodulation techniques such as transcranial direct current stimulation. If device is used for certain types of tDCS (otDCS and tPCs) or external triggering, computer control must be used. Microcontroller is used to regulate operating speed and pulse width modulation switching frequency administrated by device.

Proper citation: Open-tES project (RRID:SCR_021487) Copy   

•   Source: SciCrunch Registry

https://github.com/MatthewBCooke/Pathfinder/

Open source software for analyzing spatial navigation search strategies.

Proper citation: Pathfinder (RRID:SCR_021520) Copy   

•   Source: SciCrunch Registry

https://wavesurfer.janelia.org/

Open source software application for neurophysiology data acquisition and analysis. Program is based in MatLab, and evolved from earlier open source software package called Ephus.

Proper citation: Wave Surfer (RRID:SCR_021529) Copy   

•   Source: SciCrunch Registry

https://github.com/fchampalimaud/optical-lickometer

Low-cost open-source lickometer that combines restricted infrared beam defined by optical fibers, with poke design that allows easy access to the tongue while limiting access of other body parts and external light sources. This device also includes features for detecting nose pokes and presenting visual cues during behavioral tasks. Used to study lick microstructure in combination with other techniques, such as imaging of neural activity, in freely moving mice.

Proper citation: High-Precision Optical Fiber-Based Lickometer (RRID:SCR_026392) Copy   

•   Source: SciCrunch Registry

https://github.com/asoronow/belljar/tree/main

Software mouse brain histology tool for neuroscientists. Semiautomated registration and cell counting tool for mouse neurohistology analysis.

Proper citation: Bell Jar (RRID:SCR_026912) Copy   

•   Source: SciCrunch Registry

https://github.com/Imbrosci/synaptic-vesicles-detection

Software tool as Python based synaptic vesicle classifier algorithm to identify neurotransmitter vesicles in electron microscopy images using Pytorch.

Proper citation: Synaptic Vesicles Detection (RRID:SCR_024910) Copy   

•   Source: SciCrunch Registry

https://github.com/munoztd0/Mouthpiecegusto

3D printed pacifier shaped mouthpiece for fMRI compatible gustometers to deliver up to eight liquids during fMRI task. Can be utilized to study flavor, taste reactivity, reward or punishment with food, conditioning, and neurodegenerative conditions such as Alzheimers and Parkinsons, since taste and smell senses diminish early into disease acquisition.

Proper citation: 3DP Gustometer (RRID:SCR_025010) Copy   

•   Source: SciCrunch Registry

https://github.com/mmgxw3/pipetteFindingCNN

Software application for convolutional neural network that assesses pipette positioning before patch clamp is begun to minimize patch clamping errors in electrophysiology experiments. Used for detecting pipette positioning and making patch clamping procedures.

Proper citation: Pipette Finding CNN (RRID:SCR_024992) Copy   

•   Source: SciCrunch Registry

https://github.com/gchelini87/SEB3R

Software tool to automate and standardize ethologically driven observation of freely moving mice. Identifies different postures of mice and associates them with emotions, offering detailed analysis of their movements frame by frame. Used for tracking mouse body language and studying emotional behaviors.

Proper citation: SEB3R (RRID:SCR_025161) Copy   

•   Source: SciCrunch Registry

https://github.com/LurLab-UCI/HERBs

Open source hardware and software solution for flexible implementation of complex behaviors in head-fixed mice. Low cost and requires little to no programming experience. Allows neural activity to be seen during testing, which will show relations between neuronal activity and behavior during tasks such as alternative forced choice, GoNoGo, and sensory stimulus presentation.

Proper citation: HERBs (RRID:SCR_025381) Copy   

•   Source: SciCrunch Registry

https://github.com/ZuAh/Custom-fitting-of-implants

Tutorial to custom-design and -fit implants to continuous and discontinuous skull surfaces. Universal Guide for Skull Extraction and Custom-Fitting of Implants to Continuous and Discontinuous Skulls.

Proper citation: Custom-fitting-of-implants (RRID:SCR_025270) Copy   

•   Source: SciCrunch Registry

https://github.com/MaSoMoTr/MaSoMoTr

Markerless video-based tool to simultaneously track two interacting mice of the same appearance in controlled settings for quantifying behaviors such as different types of sniffing, touching, and locomotion to improve tracking accuracy under these settings without increased human effort. It incorporates conventional handcrafted tracking and deep-learning-based techniques. The tool is trained on small number of manually annotated images from basic experimental setup and outputs body masks and coordinates of the snout and tail-base for each mouse.

Proper citation: Markerless Mouse Tracking for Social Experiments (RRID:SCR_025368) Copy   

•   Source: SciCrunch Registry

https://github.com/mcmelo22/Licktech/tree/main

Lickometer system based on open-source hardware platform with user-friendly interface software, capable of simultaneously receiving data from eight automated cages with two drinking bottles each. Device to acquire high-quality and detailed data. Adaptable to new types of sensors or other neuroscience tools capable of measuring brain activity simultaneously to the behavior.

Proper citation: Lickometer Box (RRID:SCR_025248) Copy   

•   Source: SciCrunch Registry

https://github.com/jfrie/FARESHARE

Open source device for fluid tracking in socially housed rats. Device uses RFID and custom hardware to individually measure and record each rat's fluid consumption and licking microstructure.

Proper citation: FARESHARE (RRID:SCR_025330) Copy   

•   Source: SciCrunch Registry

https://github.com/Aharoni-Lab/Ephys-Miniscope

Miniaturized calcium imaging microscope with integrated dense electrode technology for synchronous acquisition of neural activity across distant regions of the brain. Device based off open-sourced UCLA Miniscope to synchronously measure single cell activity at or near spike-time resolution across distant brain regions in freely behaving mice. Used to perform calcium imaging, with dense electrode electrophysiological recording, allowing simultaneous recordings from two remote brain regions in freely behaving mouse.

Proper citation: E-Scope (RRID:SCR_025396) Copy   

•   Source: SciCrunch Registry

https://github.com/BerezhnoyD/Reaching_Task_VAI/

Open source hardware-software platform for analyzing reaching movement kinematics in mice. Used for studying fine motor skills in mice performing reach-to-grasp task. Behavioral platform uses readily available and 3D-printed components and was designed to be affordable and universally reproducible. Provides schematics, 3D models, code, and assembly instructions.

Proper citation: ReachOut (RRID:SCR_025502) Copy   

•   Source: SciCrunch Registry