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https://edspace.american.edu/openbehavior/project/open-ephys/

Organization mission is to advance understanding of brain by promoting community ownership of neuroscience tools.Collaborative effort to develop, document, and distribute open source tools for systems neuroscience.Project aims to distribute reliable open source software as well as tools for extracellular recording and stimulation.

Proper citation: Open Ephys (RRID:SCR_021624) Copy   

•   Source: SciCrunch Registry

https://github.com/DepartmentofNeurophysiology/Matlab-Whisker-Tracker

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 (RRID:SCR_021407) Copy   

•   Source: SciCrunch Registry

https://www.eneuro.org/content/12/2/ENEURO.0444-24.2025

Low-cost implant for reliable diaphragm EMG recordings in awake, behaving rats.Diaphragm EMG implant.

Proper citation: Implant for Reliable Diaphragm EMG Recordings in Awake, Behaving Rats (RRID:SCR_026968) Copy   

•   Source: SciCrunch Registry

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

Open-source apparatus to enable continuous individual monitoring, training, and testing of rats without removing them from their social environment. This system utilizes RFID technology to track individual animals, minimizing human intervention and providing precise behavioral data.

Proper citation: One-rat Turnstile (RRID:SCR_025570) Copy   

•   Source: SciCrunch Registry

https://github.com/careylab/LocoMouse

Software kinematics analysis tool used to study movement coordination and analyzing limb, head, and tail kinematics of freely walking mice.

Proper citation: LocoMouse (RRID:SCR_021397) Copy   

•   Source: SciCrunch Registry

https://github.com/ncguilbeault/BonZeb

Open source, modular software tools for high resolution zebrafish tracking and analysis.Software suite of Bonsai modules for specifically tracking and analyzing zebrafish movements and integrating these data with closed loop experiments.Can be used in open loop fashion for collecting, analyzing, and integrating data from multiple sources in real time, or from offline sources for batch processing of pre-recorded data.

Proper citation: BonZeb (RRID:SCR_021392) Copy   

•   Source: SciCrunch Registry

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

Software tool to extract relevant features from images and use time series of these features to classify whether given behavior is present in each frame of video recording.machine learning pipeline for supervised behavior classification from raw pixels. Performs action recognition ,automated behavior classification, over frames. Used for automated behavior classification to detect and track behavior over time.

Proper citation: DeepEthogram (RRID:SCR_022355) Copy   

•   Source: SciCrunch Registry

https://github.com/SunGL001/DeepBhvTracking

Software tool as novel tracking algorithm that combines deep learning and background subtraction.

Proper citation: DeepBhvTracking (RRID:SCR_022351) Copy   

•   Source: SciCrunch Registry

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

Software Matlab based tool to visualize and analyze multimodal datasets.

Proper citation: Behavior Ensemble and Neural Trajectory Observatory (RRID:SCR_022348) Copy   

•   Source: SciCrunch Registry

https://github.com/neuroethology/MARS_Developer

Software MARS based Python pipeline used for detection, pose estimation and behavior classification in experiments of any format. Repository contains all the code you'll need to train your own version of MARS.

Proper citation: MARS Developer (RRID:SCR_022346) Copy   

•   Source: SciCrunch Registry

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

Software MATLAB based toolbox for automated quantitative analysis of ultrasonic vocalizations. Utilizes image processing libraries to detect USVs and computational vision and machine learning algorithms to classify detected USVs. Used for analysis of ultrasonic vocalizations from mice using computer vision and machine learning.

Proper citation: VocalMat (RRID:SCR_022342) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/permuco/index.html

Software R package for permutation test in linear model with nuisances variables.Used for permutation testing in regression, ANOVA, and comparison of signals.

Proper citation: Permuco (RRID:SCR_022341) Copy   

•   Source: SciCrunch Registry

https://github.com/ACCLAB/DABEST-python

Software package for data analysis using bootstrap coupled estimation. Library combining Python, R, and MATLAB for estimation statistics.

Proper citation: DABEST (RRID:SCR_022340) Copy   

•   Source: SciCrunch Registry

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

Software tool for data extraction and computation of spatial accuracy and precision of head mounted display based eye trackers. Allows for significant customization without altering source code but changes to the code allow for further alteration.

Proper citation: GazeMetrics (RRID:SCR_022338) Copy   

•   Source: SciCrunch Registry

https://github.com/BadenLab/LED-Zappelin

Open source LED controller for arbitrary spectrum visual stimulation and optogenetics during 2 photon imaging. Device that rapidly time interleaves stimulation and detection epochs during two photon imaging.

Proper citation: LED Zappelin’ (RRID:SCR_022560) Copy   

•   Source: SciCrunch Registry

https://github.com/TAMUCogLab/OpenSync

Open source platform for synchronizing multiple behavioral and physiological signals in neuroscience experiments.

Proper citation: OpenSync (RRID:SCR_022722) Copy   

•   Source: SciCrunch Registry

https://github.com/gilestrolab/ethoscope

Software R package for data analysis.Enables high throughput analysis of behavior in Drosophila and other animals.

Proper citation: EthoScopes (RRID:SCR_021507) Copy   

•   Source: SciCrunch Registry

https://github.com/mtlippert/CAVE

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 (RRID:SCR_021498) Copy   

•   Source: SciCrunch Registry

https://github.com/video-annotator/pythonvideoannotator-module-idtrackerai

Software tool as Python Video Annotator software.Agorithm and tracking software that features two deep networks.Tracks animal identification and tracks when animals touch or cross paths in front of one another.

Proper citation: idtracker.ai (RRID:SCR_021499) Copy   

•   Source: SciCrunch Registry

https://github.com/MatthewBCooke/Pathfinder/

Open source software for analyzing spatial navigation search strategies.

Proper citation: Pathfinder (RRID:SCR_021520) Copy   

•   Source: SciCrunch Registry