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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
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
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
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
https://edspace.american.edu/openbehavior/project/aba/
Software semi automated brain atlas based analysis pipeline for c-Fos immunohistochemical data. Used to analyze c-Fos in multiple brain regions simultaneously.
Proper citation: Atlas Based Analysis (RRID:SCR_022339) Copy
https://edspace.american.edu/openbehavior/project/dbscorer/
Open source, MATLAB based software for forced swim test and tail suspension test video analysis.
Proper citation: DBscorer (RRID:SCR_022334) Copy
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
https://github.com/gordonberman/MotionMapper
Software tool to work on videos (not poses).Uses image analysis and multivariate statistical methods to find stereotyped behaviors in flies, mice, and other species.
Proper citation: MotionMapper (RRID:SCR_021384) Copy
https://www.nature.com/articles/srep16171#Sec20
Open source program for semi automated analysis of movement and cognitive testing in rodents. Accurately quantifies numerous parameters of movement including travel distance, speed, turning, stationary fraction and laterality. Part of MouseMove system.
Proper citation: MouseMove (RRID:SCR_021618) Copy
https://ethowatcher.paginas.ufsc.br/
Software tool for behavioral and video tracking analysis in laboratory animals. Used to support detailed ethography, video tracking, and extraction of kinematic variables from digital video files of laboratory animals.
Proper citation: EthoWatcher (RRID:SCR_021504) Copy
https://github.com/arnefmeyer/mousecam
Software Python package with functions for extracting and analyzing data recorded using camera system.Used to monitor behaviors including eye position, whisking, and ear movements in unrestrained animals.Can be mounted in combination with neural implants for recording brain activity.
Proper citation: Mousecam (RRID:SCR_021503) Copy
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
https://github.com/MouseLand/facemap
Software toolbox for unsupervised video analysis of rodent behavior.Used for videographic processing of head fixed rodent behavior.
Proper citation: FaceMap (RRID:SCR_021513) Copy
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
https://github.com/KravitzLab/fed/wiki
Flexible open-source device for measuring feeding behavior. FED measures food intake in mice. It is battery powered and designed to be used in rodent colony caging.Home cage-compatible feeding system that measures food intake with high accuracy and temporal resolution. FED offers alternative to commercial feeders, with convenience of use in tradition colony rack caging.
Proper citation: Feeding Experimentation Device project (RRID:SCR_015942) Copy
https://github.com/lvrgb777/STPoseNet
Source code for pose recognition model for laboratory mice based on yolov8. Real-time spatiotemporal network model for robust mouse pose estimation.
Proper citation: STPoseNet (RRID:SCR_026834) Copy
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
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
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
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
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