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

Project related to mouse tracking and analysis of mouse movements during computerized lab experiments. Provides open source software plugin to record and analyze mouse movements.

Proper citation: Mousetrap project (RRID:SCR_021456) Copy   

•   Source: SciCrunch Registry

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

Project related to saving precise times of behavioral events.Provides software tool to read MedPC data into Python and Matlab.

Proper citation: MedParse project (RRID:SCR_021455) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/offline-behavior-video-analysis/

Project related to visualizing and quantifying movement from pre-recorded videos. Provides software toolbox for visualizing and quantifying movement.Used for summarizing animal movement data as single image ( spectral time lapse algorithm) as well as automate analysis of animal movement data.

Proper citation: Quantifying Animal Movement from Pre-recorded Videos project (RRID:SCR_021436) Copy   

•   Source: SciCrunch Registry

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

Project related to computer based review of previously recorded videos or live observations. Related to study of animal and human behavior. Provides open source, multiplatform standalone program that allows user specific coding environment for computer based review of previously recorded videos or live observations.Developed by scientists from University of Turin.

Proper citation: Behavioral Observation Research Interactive Software project (RRID:SCR_021434) Copy   

•   Source: SciCrunch Registry

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

Portal provides open source, cross platform Python library that adds 3D stimulus support to all OpenGL based 2D Python stimulus libraries. Ratcave comes with resources including basic 3D object primitives and wide range of 3D light effects. Intuitive object oriented interface allows for all objects, which include meshes, lights, and cameras, can be repositioned, rotated, and scaled.

Proper citation: Ratcave project (RRID:SCR_021555) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/m-track/

Project related to tracking movement of labelled paws in grooming and freely behaving mice. Provides software toolbox for automated detection of forepaw trajectories in mice.

Proper citation: M-Track project (RRID:SCR_021433) Copy   

•   Source: SciCrunch Registry

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

Project to detect spatial navigation behavior in animals.Provides open source software for analyzing spatial navigation search strategies developed by University of British Columbia scientists.

Proper citation: Pathfinder project (RRID:SCR_021447) Copy   

•   Source: SciCrunch Registry

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

Project related to behavioral experiments.Provides software Python framework for running behavioral experiments designed by University of Oregon scientists.

Proper citation: AutoPilot project (RRID:SCR_021448) Copy   

•   Source: SciCrunch Registry

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

Project related to composing reactive and asynchronous data streams coming from video cameras, microphones, electrophysiology systems or data acquisition boards. Provides open source software tool as visual language for reactive programming.

Proper citation: Bonsai project (RRID:SCR_021443) Copy   

•   Source: SciCrunch Registry

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

Project is related to working with atlas data from multiple species on common platform.Provides collection of Python tools for working with atlas data from multiple species on common platform and for morphological analyses in systems neuroscience.

Proper citation: BrainGlobe project (RRID:SCR_021481) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/toolboxes-ephys-analysis/

Portal includes compared several toolboxes for spike and LFP analysis, connectivity analysis, dimensionality reduction, and generalized linear modeling. Discussion about major features of software available for Python and MATLAB including Brainstorm, Chronux, Elephant, FieldTrip, gramm, Spike Viewer, and SPIKY. They include succinct tables for assessing system and program requirements, quality of documentation and support, and data types accepted by each toolbox.

Proper citation: Toolboxes for Spike and LFP Analysis project (RRID:SCR_021478) Copy   

•   Source: SciCrunch Registry

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

Project related to time series calcium imaging evaluation and pre-processing. Included open source graphical viewer for time series calcium imaging evaluation and pre-processing is provided by Swedish University scientists .

Proper citation: Scintillate project (RRID:SCR_021479) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/wave-surfer/

Project related to neurophysiology data acquisition and analysis.Included open source software application for neurophysiology data acquisition and analysis is provided by Howard Hughes Medical Institute Janelia Research Campus scientists. Program is based in MatLab, and evolved from earlier open source software package called Ephus.

Proper citation: Wave Surfer project (RRID:SCR_021476) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/self-grooming-mice/

Portal provides protocol that implements JAABA, open source machine learning based behavior detection system; motr, open-source mouse trajectory tracking software; and bonsai, open source system capable of streaming and recording video. Together they use these tools to process videos of mice performing grooming behaviors in variety of behavioral setups.

Proper citation: Automated Classification of Self-grooming in Mice project (RRID:SCR_021597) Copy   

•   Source: SciCrunch Registry

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

Project related to calcium imaging.Provides software library, CaImAn, for one and two-photon Calcium Imaging data Analysis.

Proper citation: Calcium Imaging data Analysis project (RRID:SCR_021477) Copy   

•   Source: SciCrunch Registry

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

Project related to creating and controlling visual environments.Provided open source software package for creating and controlling visual environments was developed by University College London scientists.

Proper citation: BonVision project (RRID:SCR_021491) 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/attys/

Portal related to biomedical signals.Provides wearable data acquisition device with special focus on biomedical signals such as heart activity (ECG), muscle activity (EMG) and brain activity (EEG).Open source high precision bluetooth data acquisition device.

Proper citation: Attys project (RRID:SCR_021461) Copy   

•   Source: SciCrunch Registry

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

Project related to self initiated conditioning and behavior tracking in mice. Provides automated system that can track large numbers (over 25) of socially housed mice through implanted RFID chips on mice. With RFID trackers and other analyses, behavior of mice can be tracked as they train and are subsequently tested on (or self-initiate testing in) odor discrimination task over months with thousands of trials performed every day.

Proper citation: AutonoMouse project (RRID:SCR_021462) Copy   

•   Source: SciCrunch Registry