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https://github.com/Whitlock-Group/HERBS

Open source, extendable, intuitive and interactive software platform for image visualisation and image registration. Python based GUI for histological E-data registration in brain space.

Proper citation: Histological E data Registration in rodent Brain Spaces (RRID:SCR_022776) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/3d-printed-superfusion-chamber/

Project consists of suite of 3D-printed tools including superfusion chamber with independent brain presser and animal stand. Modular device that facilitates transfer of pharmacological agents and brain access for electrodes and/or lenses for imaging. Provides stable conditions for electrophysiological and neuroimaging recordings. Device can be print either in-house or through 3d-printing service.

Proper citation: 3D Printed Superfusion Chamber (RRID:SCR_022901) Copy   

•   Source: SciCrunch Registry

https://github.com/spoonsso/dannce

Convolutional neural network that calculates 3D positions of user-defined anatomical landmarks on behaving animals from videos taken at multiple angles. Works on recorded video data from multiple cameras. Used for 3D markerless pose estimation and tracking.

Proper citation: DANNCE (RRID:SCR_023061) Copy   

•   Source: SciCrunch Registry

https://github.com/neurobio-hiroshima/WRAQ

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.

Proper citation: Wheel Running Activity acQuisition (RRID:SCR_023353) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   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

https://edspace.american.edu/openbehavior/project/autoreward2/

Project related to detection and rewarding rodents in modified T-maze task. System designed to detect and reward rodents in modified T maze provided by Ruhr University Bochum, Germany scientists.

Proper citation: Autoreward2 project (RRID:SCR_021460) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/bpm-biosignals/

Portal as educational resource regarding construction and implementation of bioamplifiers as well as interpretation of biosignals.

Proper citation: BPM Biosignals project (RRID:SCR_021459) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/automated-mouse-homecage-two-bottle-choice-test/

Project related to assessing preferences by mice among fluids in their homecages.Provided system includes homecage fitted apparatus for automated, photobeam based detection of licks in two bottle choice task. Used for automated mouse homecage two bottle choice test.

Proper citation: Automated mouse homecage two bottle choice test project (RRID:SCR_021457) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/closed-loop-system/

Portal includes system for combined behavioral tracking, electrophysiology, and closed loop stimulation provided by University of Oslo scientists.Integrates Bonsai and Open Ephys with multiple modules.Provides guide for setting up this system.

Proper citation: Closed Loop System project (RRID:SCR_021475) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/usv-detector/

Project related to ultrasonic vocalizations detection. Provides device designed for automatic detection of 50kHz ultrasonic vocalizations.

Proper citation: Ultrasonic Vocalizations Detector project (RRID:SCR_021471) Copy   

•   Source: SciCrunch Registry

https://ethowatcher.paginas.ufsc.br/

Software tool for behavioral and video tracking analysis in laboratory animals. Used to support detailed ethography, video tracking, and extraction of kinematic variables from digital video files of laboratory animals.

Proper citation: EthoWatcher (RRID:SCR_021504) Copy   

•   Source: SciCrunch Registry

https://www.feldmanlab.org/

Project related to function of cerebral cortex. Included model system for studying cortical function is provided by UC Berkeley scientists. System includes lickometer which employs infrared beam and sensor to minimize electrical noise artifacts during neurophysiology experiments and can be easily mounted in micromanipulator for precise and repeatable positioning.Open source lickometer was designed in conjunction with open source water delivery system.Together, these provide basic hardware for DIY behavioral assay and reward system for mice.

Proper citation: Feldman Lab Lickometer project (RRID:SCR_021469) Copy   

•   Source: SciCrunch Registry