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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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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

Project related to processing video, extracting object position information, and streaming data.Provides set of programs for processing video for behavioral research. Includes OAT software tool as real time position tracker which was developed by Massachusetts Institute of Technology scientists.

Proper citation: Online Animal Tracker project (RRID:SCR_021386) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/b-soid-unsupervised-behavior-analysis/

Project related to unsupervised behavior analysis.Carnegie Mellon University has shared B-SOiD, open source unsupervised algorithm for discovery of spontaneous behaviors. Includes software pipeline that pairs unsupervised pattern recognition with supervised classification to achieve fast predictions of behaviors that are not predefined by users.

Proper citation: Behavioral Segmentation of Open-field in DeepLabCut project (RRID:SCR_021410) Copy   

•   Source: SciCrunch Registry

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

University of Washington project SimBA for analysis of complex social behaviors.Used for automated behavioral scoring. Includes open source software toolkit for computer classification of complex social behaviors in experimental animals. Uses data from popular open source tracking tools in combination with small amount of behavioral annotations to create supervised machine learning classifiers that can then rapidly and accurately score behaviors across different background settings and lighting conditions.

Proper citation: Simple Behavior Analysis project (RRID:SCR_021411) Copy   

•   Source: SciCrunch Registry

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

Project related to behavior analysis.Mt.Sinai scientist developed open source video analysis pipeline for investigation of animal behavior.Used to track location, motion, and freezing of animal.

Proper citation: ezTrack project (RRID:SCR_021418) Copy   

•   Source: SciCrunch Registry

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

Project for markerless pose estimation of user defined body parts with deep learning.

Proper citation: DeepLabCut Project (RRID:SCR_021398) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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://github.com/fdechaumont/lmt-analysis

Software package for Live Mouse Tracker analysis. lmt-analysis provides all analysis tools needed to extract information from tracking performed by live mouse tracker.

Proper citation: Live Mouse Tracker analysis (RRID:SCR_021505) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   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://github.com/aspence/tmilltracker

Open source computer vision controlled treadmill system for small running animals such as insects and mice. Treadmill is controlled by Python software, allowing for flexible control of video tracking parameters, behavioral triggers, distance ran, and feedback. Used for studying locomotor behavior.

Proper citation: tmilltracker (RRID:SCR_023511) Copy   

•   Source: SciCrunch Registry

https://www.sciencedirect.com/science/article/pii/S2352289523000061

Open source automated platform for assessing working memory and prefrontal circuit function. Designed for automated, high-throughput assessments of working memory and simultaneous two-photon imaging in chronic stress studies. Physiology compatible behavioral platform designed specifically for studying circuit mechanisms underlying working memory and related cognitive functions in chronic stress states.

Proper citation: Automated 2 Photon Imaging Compatible Platform for Assessing Working Memory (RRID:SCR_023463) Copy   

•   Source: SciCrunch Registry