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

Project related to calcium imaging.Provide open source tool for combined analysis of head mounted calcium imaging and behavior. Used to analyze imaging data from head mounted microscopes simultaneously with behavioral data.

Proper citation: Calcium ActiVity Explorer project (RRID:SCR_021419) Copy   

•   Source: SciCrunch Registry

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

Project related to high speed tracking of animals.Provides software tool for tracking organisms.Can handle one or several animals in one or several environments.Used for fish, insects, rodents, etc.

Proper citation: ToxTrac project (RRID:SCR_021424) 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://edspace.american.edu/openbehavior/project/open-source-whisking-video-database/

Portal provides shared database of videos featuring juvenile and adult male rats and adult male mice exploring stationary objects.This dataset includes wide variety of experimental conditions including genetic, pharmacological, and sensory deprivation interventions to explore how active sensing behavior is modulated by different factors. Database of high speed videos of whisking behavior in freely moving rodents.Open source high speed infrared videography database to study principles of active sensing in freely navigating rodents.

Proper citation: Open Source Whisking Video Database portal (RRID:SCR_021404) 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://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://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/pavca/

Project related to tracking behavior. Used to identify subgroups of individuals that differentially attribute incentive value to food cue. Includes apparatus for studying Pavlovian conditioned approach behavior. Customized rat PavCA chambers are constructed based on modular devices purchased from Med-Associates. Code used to operate equipment and collect data was written using Med-Associates’ MEDSTATE programming language. This program is then loaded into Med-PC V operating program, also created by Med-Associates.

Proper citation: PavCA project (RRID:SCR_022508) 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