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

Portal provides software tool for analysis and quantification of both single and socially interacting zebrafish. Software data extraction and analysis tool built in open source R language for tracking zebrafish behavior.

Proper citation: Argus (RRID:SCR_021585) Copy   

•   Source: SciCrunch Registry

https://github.com/NeLy-EPFL/DeepFly3D

Software tool as PyTorch and PyQT5 implementation of 2D-3D tethered Drosophila pose estimation. Image annotation tool used for pose estimation and appendage tracking. Provides interface for pose estimation and to permit further correction of 2D pose estimates, which are automatically converted to 3D pose.

Proper citation: DeepFly3D (RRID:SCR_021402) Copy   

•   Source: SciCrunch Registry

https://github.com/LaubachLab/MedParse

Software tool to read MedPC data into Python and Matlab. MedPC code for saving precise times of behavioral events and MatLab and Python functions to convert MedPC data into time event codes.

Proper citation: MedParse (RRID:SCR_021528) 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

https://edspace.american.edu/openbehavior/project/eco-hab/

Portal provides open source, RFID-based system for automated measurement and analysis of social preference and in-cohort sociability in mice. System was developed by Nencki Institute of Experimental Biology scientists.

Proper citation: Eco-HAB (RRID:SCR_021588) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/oculomatic-eye-tracking/

Project related to investigate mechanisms of oculomotor behavior.Included system is provided by New York University scientists to track eye movement.System includes camera module, lens, IR-Light source, mounting solution, data acquisition device, and general purpose PC. System consists of open source software and modular hardware solution to eye tracking for use in humans and non-human primates.

Proper citation: Oculomatic Eye Tracking project (RRID:SCR_021465) Copy   

•   Source: SciCrunch Registry

https://github.com/scimemia/M-Track

Software toolbox for automated detection of forepaw trajectories in mice.Open source code to simultaneously track movement of individual paws during spontaneous grooming episodes and walking in multiple freely behaving mice/rats.

Proper citation: M-Track (RRID:SCR_021508) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/moving-wall-box-mwb/

Portal provides Moving Wall Box system used to testing strategy task where mouse is repeatedly forced to jump over small ice by slowly moving walls whereby presence of animal is automatically sensed via balances and analyzed by microcontroller board which in turn controls movements of walls. Device provided by Max Planck Institute of Psychiatry scientist. Used for repeated assessment of fear coping strategies.

Proper citation: Moving Wall Box (RRID:SCR_021559) Copy   

•   Source: SciCrunch Registry

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

Software package for MATLAB that makes motion correction, segmentation, signal extraction and dimension reduction, analysis, and visualization of calcium imaging data easy to implement. Open source toolbox for analysis of calcium imaging data.

Proper citation: EZcalcium (RRID:SCR_022354) Copy   

•   Source: SciCrunch Registry

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

Software Python toolbox that makes fiber photometry data analysis intuitive and light on programming.Used to measure neural activity of freely behaving animals.

Proper citation: GuPPy (RRID:SCR_022353) Copy   

•   Source: SciCrunch Registry

https://github.com/crtwomey/paws

Statistical software platform for automated scoring of pain in mice.Software R package takes paw trajectory data in response to stimulus and provides automated scoring of pain.

Proper citation: Pain Assessment at Withdrawal Speeds (RRID:SCR_022350) Copy   

•   Source: SciCrunch Registry

https://github.com/sgoldenlab/simba

Open source software toolkit for computer classification of complex social behaviors in experimental animals.

Proper citation: Simple Behavior Analysis (RRID:SCR_021413) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/neuroethology-tools/

Software Python pipeline for automated detection, pose estimation, and behavior classification in socially interacting mice.Used for pose estimation and behavior quantification in pairs of freely behaving mice.

Proper citation: Mouse Action Recognition System (RRID:SCR_022347) Copy   

•   Source: SciCrunch Registry

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

Software pipeline for video analysis. Deep learning Swiss knife for behavioral data analysis.Performs segmentation, identification, pose-estimation and classification of complex behaviour. Used for analysis of behavior of multiple animals in complex environments.

Proper citation: SIPEC (RRID:SCR_022364) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/timed-pressure-control/

System uses Arduino microcontroller to control relay module that operates solenoid valve which all sit in 3D printed housing. Solenoid works in conjunction with flowmeter regulator to allow for controlled flow of pressurized air into target. Timing of distensions is controlled via either custom Python based UI, or by triggered TTL pulse.Timed pressure control hardware and software used for delivery of air mediated distensions in animal models.

Proper citation: Timed pressure control hardware and software for delivery of air mediated distensions in animal models (RRID:SCR_022363) Copy   

•   Source: SciCrunch Registry

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

Software tool as multi subject keypoint detection library for real time pose estimation.Used to track behavior of monkeys in natural environments, without disrupting their typical pattern of behavior. Deep learning software system for body, face, hands, and foot estimation in monkeys.

Proper citation: OpenPose (RRID:SCR_022362) Copy   

•   Source: SciCrunch Registry

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

Open source animal tracking software tool. Used to visually track movement of multiple animals at once.

Proper citation: TRex (RRID:SCR_022361) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/3doc/

Project related to animals learned perform action in order to achieve reward. Fully 3D printable chamber able to perform operant conditioning using off-the-shelf, low-cost optical and electronic components, that can be reproduced rigorously in any laboratory equipped with 3D printer.

Proper citation: 3DOC (RRID:SCR_021547) Copy   

•   Source: SciCrunch Registry

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

Software tool enables closed loop behavioral experiments using deep learning based markerless, real time posture detection.Closed loop behavioral experiment toolkit using pose estimation of body parts.

Proper citation: DLStream (RRID:SCR_022359) Copy   

•   Source: SciCrunch Registry

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

Open source software package to support rt-fMRI via data in formats generated by Siemens, Philips, and GE. Used to support real time functional magnetic resonance imaging.

Proper citation: Pyneal (RRID:SCR_022333) Copy   

•   Source: SciCrunch Registry