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https://github.com/sgoldenlab/simba

Open source software toolkit for computer classification of complex social behaviors in experimental animals.

Proper citation: Simple Behavior Analysis (RRID:SCR_021413) 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/3doc/

Project related to animals learned perform action in order to achieve reward. Fully 3D printable chamber able to perform operant conditioning using off-the-shelf, low-cost optical and electronic components, that can be reproduced rigorously in any laboratory equipped with 3D printer.

Proper citation: 3DOC (RRID:SCR_021547) Copy   

•   Source: SciCrunch Registry

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

Automated surgical instrument for brain tissue aspiration.Instrument for microendoscope implantation. Utilizes robotic control of needle connected to vacuum pump to aspirate brain tissue. System consists of robotic surgical instrument built around commercially available stereotaxic instrument and open source MATLAB-based GUI for control.

Proper citation: AutoStereota (RRID:SCR_022330) Copy   

•   Source: SciCrunch Registry

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

Open source video recording system for acquiring video data that is scalable, flexible, and affordable.Utilizes Raspberry Pi (RPi) miniature computer and 8-megapixel Camera Board that allows for greater manipulation of recording parameters. System may be accessed on GitHub.

Proper citation: Pi-based Remote Acquisition Technology for Motion Capture project (RRID:SCR_022325) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/raspi-aud-generator/

Stimulation system for auditory EEG experiments using Raspberry Pi3 B+ board, HiFiBerry audio card to enhance sound quality and trigger tone latency, and custom Python library to generate auditory stimuli.

Proper citation: Raspberry Pi based auditory stimulus generator (RRID:SCR_022343) Copy   

•   Source: SciCrunch Registry

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

Interactive software for visualizing and uncovering function of circuits created from large scale fruit fly brain data. Interactive computing platform for studying function of executable circuits constructed from fruit fly brain data.

Proper citation: FlyBrainLab (RRID:SCR_022337) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/modular-led-displays/

Provides customized display systems used in neuroscientific studies in insects and other small animals. System includes custom built modular LED panels and software. LED panels of various sizes can be arranged/grouped in different shapes for diverse setups. System provides millisecond refresh, precise synchronization, customizable color combinations, and varied display configurations and addresses most technical challenges of small animal vision experiments and is thoroughly documented for replicability.

Proper citation: Modular LED Displays project (RRID:SCR_022704) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/pi-usb-cam/

Project related to video recording.Provides system for high throughput video capture. Pi USB Cam system includes low cost Raspberry Pi microcomputer, DIY electronics peripherals, freely available open-source firmware, and custom 3D-printed casings.

Proper citation: Pi USB Cam project (RRID:SCR_022834) 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/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/LINCellularNeuroscience/VAME

Software Python tool to cluster behavioral signals obtained from pose estimation tools. Unsupervised probabilistic deep learning framework capable of finding behavioral motifs in pose estimation data. Capable of augmenting quantitative behavioral analyses of data derived from standard pose-estimation software packages. Written based on core functions from DeepLabCut, and readily works with pose data from that package. Can also work with data from other pose estimation packages such as SLEAP.

Proper citation: Variational Embedding of Animal Motion (RRID:SCR_022477) Copy   

•   Source: SciCrunch Registry

https://github.com/earnestt1234/SipperViz

Software Python GUI for graphing measures of liquid ingestion in rodents from Sippers. Python GUI for visualizing Sipper data.

Proper citation: SipperViz (RRID:SCR_022463) 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://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://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://edspace.american.edu/openbehavior/project/openeyetrack/

Project related to measurement of fast eye movement dynamics.Tracking eye position in head fixed applications system created by scientists from Boston University. Includes software tool as part of multithreaded eye tracker and Teledyne DALSA Camera with GigE-V framework APIs for Linux.

Proper citation: openEyeTrack project (RRID:SCR_021399) Copy   

•   Source: SciCrunch Registry

https://github.com/YttriLab/B-SOID

Software pipeline that pairs unsupervised pattern recognition with supervised classification to achieve fast predictions of behaviors that are not predefined by users.Unsupervised learning algorithm that discovers and classifies actions based on inherent statistics of data points provided.

Proper citation: Behavioral Segmentation of Open-field in DeepLabCut (RRID:SCR_021385) Copy   

•   Source: SciCrunch Registry

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

Project related to involvement in larval zebrafish behavioral experiments.Provides integrated system for stimulation, tracking and closed loop behavioral experiments. Provides timed stimulus presentation, interfacing with external devices and simultaneous real time tracking of behavioral parameters such as position, orientation, tail and eye motion in both freely swimming and head restrained preparations.

Proper citation: Stytra project (RRID:SCR_021416) Copy   

•   Source: SciCrunch Registry