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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
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
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
https://edspace.american.edu/openbehavior/project/aba/
Software semi automated brain atlas based analysis pipeline for c-Fos immunohistochemical data. Used to analyze c-Fos in multiple brain regions simultaneously.
Proper citation: Atlas Based Analysis (RRID:SCR_022339) Copy
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
https://edspace.american.edu/openbehavior/project/dbscorer/
Open source, MATLAB based software for forced swim test and tail suspension test video analysis.
Proper citation: DBscorer (RRID:SCR_022334) Copy
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
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
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
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
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://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/pidose/
Project related to oral drug administration to group housed mice. Provides open source system for oral drug administration to group housed mice. System includes home cage attached device that weighs individual animals and administers daily dosage of drug solution based on each animal bodyweight through their drinking water. Group housed mice are identified through use of RFID tagging and receive both regular water and drug solution drops by licking at spout within PiDose module.
Proper citation: PiDose project (RRID:SCR_021441) Copy
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
https://edspace.american.edu/openbehavior/project/homecage-2bottle-choice/
Project related to studies of liquid ingestive behaviors used in neuroscience to investigate reward related behavior, metabolism, and circadian biology. Provides automated home cage sipper device for monitoring liquid ingestive behavior in rodents developed by Washington University, St. Louis scientists. Homecage fitted apparatus for automated, photobeam based detection of licks in two bottle choice task.
Proper citation: Automated Home Cage Rodent Two bottle Choice Test project (RRID:SCR_021445) Copy
https://edspace.american.edu/openbehavior/project/pasta/, https://github.com/ikodvanj/ratPASTA/
Project related to multifunctional neurobehavioral system developed by scientists at University of Zagreb School of Medicine, Zagreb, Croatia.System includes hardware and software tools.Provides software package for processing and visualising data from startle experiments in rodents or experiments measuring grip strength in rodents.
Proper citation: Platform for Acoustic STArtle project (RRID:SCR_021446) Copy
https://github.com/gordonberman/MotionMapper
Software tool to work on videos (not poses).Uses image analysis and multivariate statistical methods to find stereotyped behaviors in flies, mice, and other species.
Proper citation: MotionMapper (RRID:SCR_021384) Copy
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
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
Software tool as real time position tracker for behavioral research. Used for processing images, extracting object position information, and streaming data to disk and/or the network in real time.
Proper citation: Online Animal Tracker (RRID:SCR_021412) Copy
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