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https://edspace.american.edu/openbehavior/project/3dtracker/, http://www.3dtracker.org/
Project related to markerless computerized behavioral analysis for laboratory animals.Provides open source 3D video based behavioral analysis system for neuroscience. System includes open source software tool for 3D-video based markerless computerized behavioral analysis.
Proper citation: 3DTracker project (RRID:SCR_021440) Copy
https://edspace.american.edu/openbehavior/project/lincom/
Project related to animal behavior in complex mazes.Provides software MATLAB package for linearization of place fields in complex mazes.
Proper citation: LinCoM project (RRID:SCR_021438) Copy
https://edspace.american.edu/openbehavior/project/ethowatcher/
Project related to video tracking, detailed ethography, and extraction of kinematic variables from digital video files of laboratory animals.Provides computational tool developed at Federal University of Santa Catarina.
Proper citation: EthoWatcher project (RRID:SCR_021435) Copy
https://edspace.american.edu/openbehavior/project/automated-rodent-tracker-art/
Project related to development of automated rodent tracking position and movement. Provides software tool to automatically track rodent.Used to track head movements, body movements and also aspects of body size.Identifies certain behaviours from video footage, such as rotations, moving forwards, interacting with objects and staying still.
Proper citation: Automated Rodent Tracker project (RRID:SCR_021432) Copy
https://edspace.american.edu/openbehavior/project/deepsqueak/
Project related to rodent social communication through repertoire of ultrasonic vocalizations. Provides deep learning based system for quantification of Ultrasonic Vocalizations.Includes software MATLAB package for high throughput USV detection, classification, and analysis.
Proper citation: DeepSqueak project (RRID:SCR_021450) Copy
https://edspace.american.edu/openbehavior/project/camera-control/
Portal provides Python based camera software GUI developed by Harvard University scientists. Open source software package that allows video to be recorded in sync with behavior. Python API to record video system timestamps from Imaging Source USB cameras.
Proper citation: Camera Control project (RRID:SCR_021569) Copy
https://edspace.american.edu/openbehavior/project/rigbox/
Project related to streamlining behavioral neuroscience experiments.Provides open source software MATLAB toolbox for running behavioral neuroscience experiments and managing data.Used for probing neurons and behavior.
Proper citation: Rigbox project (RRID:SCR_021444) Copy
https://edspace.american.edu/openbehavior/project/freemovr/
Portal related to virtual reality for freely moving animals.Provides virtual reality system set up for unrestrained animals.System developed by University of Frieburg scientists. This Virtual Reality system can be used with number of different species including mice, zebrafish, and Drosophila.
Proper citation: FreemoVR project (RRID:SCR_021551) Copy
https://edspace.american.edu/openbehavior/project/pyper/
Project related to motion tracking of specimen in open field. Provides software tool for motion tracking.Used to track path of object of interest in live feed from camera or recorded video. Used to track rodents in open field maze as well as retina of mice.New version of Pyper allows to customise image processing to track different kind of objects.
Proper citation: Pyper project (RRID:SCR_021431) Copy
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
https://github.com/BrettHewitt/ART
Software tool to automatically track rodent position and movement.Used to track head movements, body movements and also aspects of body size. It is able to identify certain behaviours from video footage too, such as rotations, moving forwards, interacting with objects and staying still.
Proper citation: Automated Rodent Tracker (RRID:SCR_021510) Copy
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
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
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
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
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
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
https://github.com/NeLy-EPFL/LiftPose3D
Software tool for transforming 2D poses to 3D coordinates on labaratory animals. Used for kinematic studies of laboratory animals. Tracking movements in three dimensions from behaving flies, mice, rats, and non-human primates.
Proper citation: LiftPose3D (RRID:SCR_023049) Copy
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
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
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