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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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BonZeb project Resource Report Resource Website |
BonZeb project (RRID:SCR_021388) | data or information resource, portal, project portal | Portal provides tools for investigating visuomotor integration specific to high speed kinematic tracking in small model organisms in closed loop experiments. University of Toronto scientists developed suite of Bonsai modules for specifically tracking and analyzing zebrafish movements and integrating these data with closed-loop experiments. BonZeb modules can also be used in an 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. | Tacking and analyzing zebrafish movements, integrating zebrafish movements data with closed loop experiments, zebrafish movements, OpenBehavior |
is listed by: OpenBehavior is related to: BonZeb has parent organization: University of Toronto; Ontario; Canada |
Free, Freely available | SCR_021388 | BonZeb | 2026-08-29 11:28:51 | 0 | |||||||||
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BrainGlobe project Resource Report Resource Website 1+ mentions |
BrainGlobe project (RRID:SCR_021481) | data or information resource, portal, project portal | 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. | Atlas data from multiple species, atlas data on common platform, morphological analyses, systems neuroscience, OpenBehavior | is listed by: OpenBehavior | Free, Freely available | SCR_021481 | BrainGlobe | 2026-08-29 11:28:52 | 2 | |||||||||
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Toolboxes for Spike and LFP Analysis project Resource Report Resource Website |
Toolboxes for Spike and LFP Analysis project (RRID:SCR_021478) | data or information resource, portal, project portal | 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. | List of compared toolboxes for spike and LFP analysis, connectivity analysis, dimensionality reduction, generalized linear modeling, assessing system and program requirements, quality of documentation and support, data types accepted, OpenBehavior | is listed by: OpenBehavior | DOI:10.3389/fninf.2019.00057 | Free, Freely available | SCR_021478 | Toolboxes for Spike and LFP Analysis | 2026-08-29 11:29:02 | 0 | ||||||||
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Scintillate project Resource Report Resource Website |
Scintillate project (RRID:SCR_021479) | data or information resource, portal, project portal | 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 . | Image acquisition, time series calcium imaging evaluation, calcium imaging, |
is listed by: OpenBehavior is related to: Scintillate |
DOI:10.1016/j.jneumeth.2016.08.010 | Free, Freely available | SCR_021479 | Scintillate | 2026-08-29 11:28:57 | 0 | ||||||||
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Wave Surfer project Resource Report Resource Website |
Wave Surfer project (RRID:SCR_021476) | data or information resource, portal, project portal | 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. | Neurophysiology data acquisition, neurophysiology data analysis, neurophysiology data, MATLAB, OpenBehavior |
is listed by: OpenBehavior is related to: Wave Surfer |
Free, Freely available | SCR_021476 | Wave Surfer | 2026-08-29 11:29:02 | 0 | |||||||||
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Calcium Imaging data Analysis project Resource Report Resource Website 1+ mentions |
Calcium Imaging data Analysis project (RRID:SCR_021477) | CaImAn | data or information resource, portal, project portal | Project related to calcium imaging.Provides software library, CaImAn, for one and two-photon Calcium Imaging data Analysis. | calcium imaging analysis, movie handling, motion correction, source extraction, spike deconvolution, result visualization, OpenBehavior |
is listed by: OpenBehavior is related to: Calcium Imaging data Analysis |
DOI:10.7554/elife.38173 | Free, Freely available | SCR_021477 | Calcium Imaging data Analysis | 2026-08-29 11:28:52 | 2 | |||||||
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BonVision project Resource Report Resource Website |
BonVision project (RRID:SCR_021491) | data or information resource, portal, project portal | 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. | Creating visual environments, controlling visual environments, Bonsai, 2D environment, 3D environments, OpenBehavior |
is listed by: OpenBehavior is related to: BonVision has parent organization: University College London; London; United Kingdom |
DOI:10.1101/2020.03.09.983775 | Free, Freely available | SCR_021491 | BonVision | 2026-08-29 11:29:02 | 0 | ||||||||
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Open Source Whisking Video Database portal Resource Report Resource Website |
Open Source Whisking Video Database portal (RRID:SCR_021404) | data or information resource, portal, project portal | 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. | High speed videos, whisking behavior, freely moving rodents, infrared videography database, active sensing, OpenBehavior |
is listed by: OpenBehavior is related to: Open Source Whisking Video Database |
DOI:10.1093/gigascience/giy134 | Free, Freely available | SCR_021404 | 2026-08-29 11:29:02 | 0 | |||||||||
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DeepFly3D Resource Report Resource Website 1+ mentions |
DeepFly3D (RRID:SCR_021402) | data processing software, image analysis software, software application, software resource | 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. | Image annotation, pose tracking, pose estimation, motor circuit, behavioral measure, accurate 3D pose estimation, OpenBehavior |
is listed by: OpenBehavior is related to: DeepFly3D project |
DOI:10.7554/elife.48571 | Free, Available for download, Freely Available | https://edspace.american.edu/openbehavior/project/deepfly3d/ | SCR_021402 | 2026-08-29 11:28:51 | 1 | ||||||||
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Argus Resource Report Resource Website 1+ mentions |
Argus (RRID:SCR_021585) | data or information resource, portal, project portal, software resource | Portal provides software tool for analysis and quantification of both single and socially interacting zebrafish. Software data extraction and analysis tool built in open source R language for tracking zebrafish behavior. | Analysis, quantification, socially interacting zebrafish, OpenBehavior |
is listed by: OpenBehavior is listed by: SoftCite is related to: Argus |
DOI:10.3758/s13428-018-1083-y | Free, Freely available | SCR_021619 | SCR_021585 | 2026-08-29 11:28:57 | 1 | ||||||||
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MouseMove project Resource Report Resource Website |
MouseMove project (RRID:SCR_021581) | data or information resource, portal, project portal | Portal provides MouseMove software system used to analyze Open Field behavior of mice after experimental stroke to show reduced locomotor activity and to quantify laterality deficits. System is used in combination with open source program ImageJ and MTrack2 plugin to analyze pre recorded Open Field test video. System has two downloadable components, ImageJ macro and separate program with custom built MouseMove GUI. ImageJ is used to subtract background video from experiment and create image of animals total trajectory. MouseMove GUI then completes detailed analysis of movement patterns, measuring fractional time spent stationary, distance traveled, speed mean and various details of laterality. | Open Field behavior analysis, mice after experimental stroke, reduced locomotor activity, quantify laterality deficits, OpenBehavior |
is listed by: OpenBehavior is related to: MouseMove |
DOI:10.1038/srep16171 | Free, Freely available | SCR_021581 | MouseMove system | 2026-08-29 11:29:03 | 0 | ||||||||
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Ratcave project Resource Report Resource Website |
Ratcave project (RRID:SCR_021555) | data or information resource, portal, project portal | 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. | Cognitive psychology, stimuli to subjects, response record, Python, 3D graphics library, OpenBehavior |
is listed by: OpenBehavior is related to: Ratcave |
DOI:10.3758/s13428-019-01245-x | Free, Freely available | SCR_021555 | Ratcave | 2026-08-29 11:28:57 | 0 | ||||||||
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Automated Classification of Self-grooming in Mice project Resource Report Resource Website 1+ mentions |
Automated Classification of Self-grooming in Mice project (RRID:SCR_021597) | data or information resource, portal, project portal | 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. | grooming behavior, behavior detection protocol, JAABA behavior detection system, motr mouse trajectory tracking software, bonsai streaming and recording video, OpenBehavior | is listed by: OpenBehavior | DOI:10.1016/j.jneumeth.2017.05.026 | Free, Freely available | SCR_021597 | Automated Classification of Self-grooming in Mice | 2026-08-29 11:28:53 | 1 | ||||||||
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MedParse Resource Report Resource Website |
MedParse (RRID:SCR_021528) | data processing software, software application, software resource | 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. | Read MedPC data, Python, Matlab, behavioral events, time event codes, OpenBehavior |
is listed by: OpenBehavior is related to: MedParse project |
Free, Available for download, Freely Available | https://edspace.american.edu/openbehavior/project/medparse/ | SCR_021528 | 2026-08-29 11:28:53 | 0 | |||||||||
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Wheel Running Activity acQuisition Resource Report Resource Website |
Wheel Running Activity acQuisition (RRID:SCR_023353) | WRAQ | software resource | Open source microcontroller based system for wheel running activity in mice.Used to track circadian rhythms of rodents using microcontroller, powered by lithium polymer battery, and surveys exercise activity for up to 30 days. Data can be stored on microSD card or using online server using WiFi connection. Python software provides system interface with ActogramJ to analyze chronobiological aspects of data.Repository includes guide for installing integrated developmental environment and dependent libraries for building and setting up WRAQ systems - WRAQ and WRAQ-Wifi. WRAQ and WRAQ-WiFi are based on Adafruit Adalogger and DFRobot FireBeetle ESP32 connected to 4- and 8-bit binary counters receiving signal from reed switch attached to 5-inch flying saucer respectively. | OpenBehavior, instrument, building and setting up WRAQ systems, measure mouse wheel running activity, mouse wheel running, monitor wheel running activity, | is listed by: OpenBehavior | PMID:34479979 | Free, Freely available | https://edspace.american.edu/openbehavior/project/wraq/ | SCR_023353 | WRAQ system, Wheel Running Activity acQuisition system | 2026-08-29 11:28:19 | 0 | ||||||
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CaT-z Resource Report Resource Website |
CaT-z (RRID:SCR_023399) | software resource | Software tool for 3D tracking and automatic classification of rodent behavior. Used for acquisition, annotation, and automatic behavioral profile characterization of laboratory rodents' RGB-D videos. Utilizes video segmentation, tracking of body parts, and automated classification of behaviors through machine learning and computer vision methods. Setup uses low costing RGB-D cameras for tracking behaviors in various environments. Software includes GUI interfaces for video acquisition, annotation, and processing of behavioral data. Software is capable of automated behavior detection with only 30 minutes of annotated video. | 3D tracking, automatic classification, rodent behavior, behavioral analysis, individual rats, automated behavior detection, OpenBehavior | is listed by: OpenBehavior | Portugal National Funds | DOI:10.3758/s13428-020-01381-9 | Free, Available for download, Freely available | https://edspace.american.edu/openbehavior/project/cat-z/ | SCR_023399 | Classification and Tracking in depth (z) | 2026-08-29 11:28:19 | 0 | ||||||
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JAX Animal Behavior System Resource Report Resource Website 1+ mentions |
JAX Animal Behavior System (RRID:SCR_023721) | JABS | software resource | Video based phenotyping platform for laboratory mouse. Provides complete details of software and hardware, including 3D designs used for data collection. Data acquisition system consists of video collection hardware and software, behavior labeling and active learning app, and online database for sharing classifiers. Hardware and software solution collects high quality data for behavior analysis. | OpenBehavior, data acquisition system, integrated mouse phenotyping platform, behavior analysis, | is listed by: OpenBehavior | Jackson Laboratory Directors Innovation Fund ; NIDA DA041668; NIDA DA048634 |
DOI:10.1101/2022.01.13.476229 | Free, Available for download, Freely available | SCR_023721 | 2026-08-29 11:28:29 | 1 | |||||||
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Customized Guide Cannulas Resource Report Resource Website |
Customized Guide Cannulas (RRID:SCR_023941) | instrument resource | Open source modular apparatus to produce guide cannulas exploiting 3D printing technology. Step by step procedure to realize hippocampal guide cannulas. 3D-printed guide cannula implant, as well as rotary tool based cutting station for fabrication of cannulae. Useful to conduct research in all the fields where access to brain areas is needed. | OpenBehavior, apparatus, 3D-printed guide cannula implant, produce guide cannulas, brain 3D printing, hippocampal guide cannulas, hippocampal guide cannulas procedure, neuroscience, | is listed by: OpenBehavior | PMID:36104275 | Free, Freely available | SCR_023941 | 2026-08-29 11:28:32 | 0 | |||||||||
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Brainways Resource Report Resource Website 1+ mentions |
Brainways (RRID:SCR_024402) | data processing software, image analysis software, software application, software resource | Open source software that automatically registers coronal slices and quantifies fluorescent markers. Python based, AI registration algorithm for slice matching to the Waxholm rat atlas. Slice quantification can be trained on any atlas, which allows use for other subjects such as mice, zebrafish, and humans. AI-based software for registration and analysis of fluorescent markers on coronal brain slices. | OpenBehavior, slice quantification, register coronal slices, quantify fluorescent markers, slice matching to atlas, registration and analysis of fluorescent markers, coronal brain slices, | is listed by: OpenBehavior | DOI:10.1101/2023.05.25.542252 | Free, Available for download, Freely available | https://edspace.american.edu/openbehavior/project/brainways/ | SCR_024402 | 2026-08-29 11:28:09 | 1 | ||||||||
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PyMouseTracks Resource Report Resource Website |
PyMouseTracks (RRID:SCR_024453) | PMT | instrument resource, software resource, source code | Open source, adaptable tracking system for multiple rodents. Scalable and customizable system for tracking and behavior assessment consists of Raspberry Pi based video and RFID acquisition. Maximum of six rodents of any coat color can be tracked simultaneously in any user defined arena with few restrictions. For pose estimation and travel trajectory analysis, PyMouseTracks supports interfacing with open source packages such as DeepLabCut and Traja. | OpenBehavior, tracking system, tracking system for multiple rodents, Raspberry Pi based video, RFID acquisition, |
is listed by: OpenBehavior is related to: DeepLabCut |
Free, Available for download, Freely available | https://edspace.american.edu/openbehavior/project/pymousetracks/ | SCR_024453 | 2026-08-29 11:28:35 | 0 |
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