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https://github.com/CaT-zTools/CaT-z_Software
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.
Proper citation: CaT-z (RRID:SCR_023399) Copy
https://github.com/KumarLabJax/JABS-behavior-classifier
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.
Proper citation: JAX Animal Behavior System (RRID:SCR_023721) Copy
https://www.eneuro.org/content/9/5/ENEURO.0099-22.2022
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.
Proper citation: Customized Guide Cannulas (RRID:SCR_023941) Copy
https://github.com/bkntr/brainways
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.
Proper citation: Brainways (RRID:SCR_024402) Copy
https://www.eneuro.org/content/10/5/ENEURO.0127-22.2023
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.
Proper citation: PyMouseTracks (RRID:SCR_024453) Copy
https://www.eneuro.org/content/10/8/ENEURO.0212-23.2023
Simple, lightweight, and low cost customizable multielectrode array for Local Field Potential recordings. Used to collect LFP data from different brain regions simultaneously in rats. Can be modified to record single unit and multiunit activity in addition to LFP activity using both wired and wireless neural data acquisition systems.
Proper citation: Customizable Multielectrode Array (RRID:SCR_024551) Copy
https://github.com/EwellNeuroLab?tab=repositories
Low cost platform for multianimal chronic Local Field Potential video monitoring with Graphical User Interface for seizure detection and behavioral scoring. Enables chronic monitoring of several animals simultaneously, synchronizes bilateral local field potential and video streams in real time, and parses recorded data into manageable file sizes. Hardware solution leverages Intan and Open Ephys acquisition systems and software solution is implemented in Bonsai. Data are synchronized and parsed in Bonsai, allowing for flexibility and scalability of up to 128 channels per animal. The use of Intan adapter board for LFP video recordings allows compatibility with large variety of recording devices. Custom made electrodes and cables were components for the chronic LFP recordings. Used as acquisition system for long term video neurophysiology recordings.
Proper citation: LFP Monitoring (RRID:SCR_024428) Copy
https://edspace.american.edu/openbehavior/project/optimouse/
Project related to individual mice positions analysis, specifically their nose positions. Includes software tool for analysis of mouse position data designed by Hebrew University scientists. Provides open source software to analyze positions of individual mice, specifically their nose positions, in behavioral arena with the goal of minimizing error.
Proper citation: Optimouse project (RRID:SCR_021463) Copy
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
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
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
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
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
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
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
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
https://edspace.american.edu/openbehavior/project/deepbehavior/
Project related to behavior tracking and analysis. Provides deep learning toolbox that automates taking high speed quality video to track behavior in rodents and humans.
Proper citation: DeepBehavior project (RRID:SCR_021387) Copy
https://edspace.american.edu/openbehavior/project/worm-behavior-platform/
Project related to sharing worm tracking data and analysis routines.Open access repository for storing, accessing, filtering data and analysis.
Proper citation: Worm Behavior Platform project (RRID:SCR_021420) Copy
https://edspace.american.edu/openbehavior/project/sleap/
Collection of tools to do video analysis in behavioral neuroscience applications.Offers open source software tools including SLEAP, LEAP and MotionMapper.
Proper citation: SLEAP, LEAP and MotionMapper project (RRID:SCR_021383) Copy
Project related to tracking individual animals in large collective groups.Provides algorithm and software for tracking individuals in large collectives of unmarked animals.Tracks animal identification and tracks when animals touch or cross paths in front of one another.
Proper citation: idtracker.ai project (RRID:SCR_021417) Copy
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