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

Project related to videographic processing of head fixed rodent behaviors. Provides software toolbox for unsupervised video analysis of rodent behavior.

Proper citation: FaceMap project (RRID:SCR_021428) Copy   

•   Source: SciCrunch Registry

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

Project related to distraction free behavioral acquisition. Provides imaging setup for distraction free behavioral acquisition with automated tracking using open source ImageJ software and workflow for extraction of behavioral endpoints of zebrafish. Used for online tracking of larval zebrafish at high framerates.Provides user interface to run experiments as well as flexible design to allow definition of arbitrary open- and closed- loop experiments.

Proper citation: ZebraTrack project (RRID:SCR_021429) Copy   

•   Source: SciCrunch Registry

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

Project about synchronizing video and neural signals. Provides software Python toolbox for interactive characterization in neuroscience.Software tool used to review and annotate signal data synchronized with video, performs simple initial analyses including signal filtering and spike detection, supports variety of file formats.

Proper citation: neurotic project (RRID:SCR_021403) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/deepfly3d/

Project related to deep learning based pose estimator for studying how neural circuits control limbed behaviors in tethered Drosophila. Includes Deep Fly image annotation tool for pose estimation and to permit further correction of 2D pose estimates, which are automatically converted to 3D pose.

Proper citation: DeepFly3D project (RRID:SCR_021400) Copy   

•   Source: SciCrunch Registry

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

Project features single board real time input/output system including touch sensing joysticks to quantify mouse forelimb trajectories with micron millisecond spatiotemporal resolution, which resolves mouse forelimb kinematics and further allows extraction of primitives. Joystick increases spatial precision, and reduces displacement force. Joystick is then integrated into automated home cage system to train mice in center out reach task.

Proper citation: RodentJoystick (RRID:SCR_023482) Copy   

•   Source: SciCrunch Registry

https://github.com/compsy/ACTman/

Software R library to automate labor intensive actigraphy data preprocessing and analyses steps while improving transparency, reproducibility, and scalability over software suites traditionally used in actigraphy research practice. Provides streamlined preprocessing while validating circadian rhythm and sleep analysis.

Proper citation: ACTman (RRID:SCR_023119) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/?s=pyPhotometry

Open source Python based hardware and software for fiber photometry data acquisition. System includes compact, low cost, data acquisition board built around Micropython microcontroller, and cross platform graphical user interface for controlling acquisition and visualising signals. Can acquire two analog and two digital signals, and control two external LEDs via built in LED drivers. Time division multiplexed illumination allows independent readout of fluorescence evoked by different excitation wavelengths from single photoreceiver signal.

Proper citation: pyPhotometry (RRID:SCR_022940) Copy   

•   Source: SciCrunch Registry

https://github.com/PeyracheLab/pynapple

Software object oriented, lightweight and standalone Python toolbox for neural data analysis. Its core features five versatile timeseries objects from Pandas library, allowing it the versatility to be used with most raw neuroscience data types and produce some common analysis forms.

Proper citation: Pynapple (RRID:SCR_023312) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/kloostermannerflab/

Open source software tool for closed loop neuroscientific experiments capable of sub-millisecond response latency over high-rate streaming data acquired from high-count multi-electrode arrays. Used for processing and controlling closed-loop neuroscience data.

Proper citation: Falcon (RRID:SCR_023199) Copy   

•   Source: SciCrunch Registry

https://rupertoverall.net/ColonyTrack/

Software R package to process raw data from ColonyRack system. In addition to generating pre processed data and quality control information, range of high level metrics are calculated together with convenient tools for analysis.

Proper citation: ColonyTrack (RRID:SCR_023026) Copy   

•   Source: SciCrunch Registry

https://github.com/vivian-imbriotis/rpg

Software Python package written for Raspberry Pi for displaying visual stimuli and to provide real time feedback on stimulus timing. High performance python library for displaying drifting gratings on Raspberry Pi 3.

Proper citation: Raspberry Pi Grating (RRID:SCR_023157) Copy   

•   Source: SciCrunch Registry

https://github.com/KimchiLab/OpBoxPhys

Open source electrophysiology hardware and software package for simultaneous EEG and EMG acquisition from multiple subjects.

Proper citation: OpBox (RRID:SCR_023269) Copy   

•   Source: SciCrunch Registry

https://github.com/borglandlab/RunningWheel/

Open source, printable, open faced running wheels for mice residing in home cage that is automated to collect locomotor information such as distance traveled, wheel direction, and velocity. Running wheel system available on GitHub contains code and information to create and run running wheels. System consists of 3D printed wheel, Raspberry Pi 0 W, and supporting components.

Proper citation: Open Face Homecage Running Wheel (RRID:SCR_023642) Copy   

•   Source: SciCrunch Registry

https://github.com/namboodirilab/B-CALM

Open source system for behavioral control based on Arduino Mega microcontroller and MATLAB based graphical interface and analysis code. Behavior controller optimized and customized for associative learning and memory tasks. Provided software should be able to control many different types of hardware for different task configurations.

Proper citation: B-CALM (RRID:SCR_023884) Copy   

•   Source: SciCrunch Registry

https://github.com/TomGeorge1234/RatInABox

Software Python toolkit for modelling locomotion and neuronal activity in continuous environments. Used to model realistic rodent locomotion and generate synthetic electrophysiological data from spatially modulated cell types.

Proper citation: RatInABox (RRID:SCR_023682) Copy   

•   Source: SciCrunch Registry

https://github.com/DepartmentofNeurophysiology/Matlab-Whisker-Tracker

Shared database of videos featuring juvenile and adult male rats and adult male mice exploring stationary objects.This dataset includes wide variety of experimental conditions including genetic, pharmacological, and sensory deprivation interventions to explore how active sensing behavior is modulated by different factors. Database of high speed videos of whisking behavior in freely moving rodents.Open source high speed infrared videography database to study principles of active sensing in freely navigating rodents.

Proper citation: Open Source Whisking Video Database (RRID:SCR_021407) Copy   

•   Source: SciCrunch Registry

https://github.com/haiderlab/DP-Lick-Detector

Distribution package for Dual Port Lick Detector.Package includes files relevant to building lick detector.

Proper citation: Dual Port Lick Detector (RRID:SCR_021521) Copy   

•   Source: SciCrunch Registry

https://github.com/AdaptiveMotorControlLab/Camera_Control

Open source software package that allows video to be recorded in sync with behavior. Python GUI and scripts allows investigators to record from multiple imaging source camera feeds with associated timestamps for each frame. Python API to record video system timestamps from Imaging Source USB cameras. Package requires Windows 10, Anaconda, and Git, and is compatible with Imaging Source USB3 cameras. Part of Camera Control project.

Proper citation: Camera Control (RRID:SCR_021614) Copy   

•   Source: SciCrunch Registry

https://github.com/wildrootlab/SHARCQ

Software tools to register histological section images and cell count locations to mouse brain atlas. Semi automated workflow and GUI for automated brain slice histology alignment, registration, and cell quantification. Used to explore Allen Mouse Brain Atlas, register asymmetric slice images to atlas using manual input, and analyze region of interest data by registering locations of fluorescently labeled cells to standardized regions of Atlas.

Proper citation: SHARCQ (RRID:SCR_022498) Copy   

•   Source: SciCrunch Registry

https://github.com/jellen44/AutomaticSleepScoringTool

Software pipeline for sleep researchers to perform automatic sleep scoring for rodents. Artificial neural network for automated behavioral state classification in rats.

Proper citation: AutomaticSleepScoringTool (RRID:SCR_022300) Copy   

•   Source: SciCrunch Registry