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https://github.com/Optophys-Lab/FreiBox/tree/main/Commutator_FreiBox2022
Affordable commutator that is equipped with novel sensing system that improves online tracking of cable rotations without impairing the 1-photon calcium imaging via Miniscope. Commutator to allow freely moving behaviors while recording neural activity from platforms such as Miniscope V4 and OpenEphys. Used to perform calcium imaging.
Proper citation: commutator (RRID:SCR_023919) Copy
https://github.com/Optophys-Lab/FreiBox
Versatile open source behavioral system for investigating neuronal correlates of behavioral flexibility via 1-Photon Imaging in freely moving mice. Behavioral testing platform consists of FreiBox, novel low-cost Arduino behavioral setup, controlled by custom Python interface and integrates new licking sensor (strain gauge lickometer) for controlling spatial licking behavioral tasks.
Proper citation: Freibox (RRID:SCR_023918) Copy
https://github.com/nickpetersen93/LIQ_HD
Arduino code, 3D print design files, and tutorial video on how to build LIQ HD system. Open source tool for recording undisturbed two-bottle drinking behavior in home cage environment. All designs and software are open source to allow other researchers to build on the system and adapt LIQ HD to their animal home cages.
Proper citation: Lick Instance Quantifier Home cage Device (RRID:SCR_023802) Copy
https://github.com/singerlabgt/BrainWAVE
Code to program and run flicker stimulation on BrainWAVE stimulator device. This brain oscillation stimulating software can be adapted across subjects and integrated into variety of experimental designs like electrophysiology, neuroimaging, EEG, MRI. Flexible method for noninvasive stimulation of brain rhythms across species. Used to measure effects of rhythmic brain activity on behavior.
Proper citation: BrainWAVE (RRID:SCR_024396) Copy
https://github.com/VioletteChiara/AnimalTA
Software video tracking tool for tracking and analysing animal movement in different environments.
Proper citation: AnimalTA (RRID:SCR_023784) Copy
https://github.com/zelanolab/hfoapp
Software for detecting and identifying high frequency oscillations observed in EEG recordings. MATLAB based graphical user interface for High Frequency Oscillation marking.
Proper citation: HFOApp (RRID:SCR_024864) Copy
https://github.com/mtu-most/linear-actuator
Code and model files for open source linear actuator. Part of Pearce Lab Syringe Pump system.
Proper citation: linear actuator (RRID:SCR_021613) Copy
https://github.com/KravitzLab/ROBucket
Software tool as ROBucket source code.
Proper citation: Rodent Operant Bucket (RRID:SCR_021610) Copy
https://github.com/jf-lab/chendoscope
Software tool as part of CHEndoscope. Acquisition software that interfaces with CHEndoscope Ximea USB camera. This code is compatible with Linux and Windows systems.
Proper citation: chendoscope (RRID:SCR_021616) Copy
https://github.com/jamieboyd/AutoHeadFix
Software Python code for automated control of behavioural apparatus and imaging for mice in home cage environment.Part of Homecage Task Training and Mesoscale Imaging system.
Proper citation: AutoHeadFix (RRID:SCR_021617) Copy
https://github.com/bsbrl/craniobot
Software tool as part of Craniobot system.Generates, sends, and receives commands to communicate with the Craniobot.
Proper citation: craniobot (RRID:SCR_021609) Copy
https://murphylab.med.ubc.ca/automated-homecages/
Software tool as part of Automated Home Cage Functional Imaging system.
Proper citation: Automated Home-Cage Functional Imaging (RRID:SCR_021607) Copy
https://github.com/dublon/scintillate
Open source graphical viewer for time series calcium imaging evaluation and pre-processing.
Proper citation: Scintillate (RRID:SCR_021531) Copy
https://github.com/ribeiro-lab/flyPAD-fpga
FPGA code for running main board of flyPAD. Code written in VHDL using Quartus 2 web edition software.
Proper citation: flyPAD (RRID:SCR_021522) Copy
Operant Box code
Proper citation: pyOS-5 (RRID:SCR_022336) Copy
https://github.com/portugueslab/stytra
Open source software Python package to control stimulation and track behaviour.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 (RRID:SCR_021500) Copy
https://github.com/openworm/tracker-commons
Software tool as repository of documentation, software, and discussions to share worm tracking data and analysis routines.Open access repository for storing, accessing, and filtering data; interchange format for notating single or multi worm behavior; and file formats written in Python for feature extraction, review, and analysis.
Proper citation: Worm Behavior Platform (RRID:SCR_021501) Copy
https://github.com/olivierfriard/BORIS
Open source event logging software for video/audio coding and live observations.Multiplatform standalone program that allows user specific coding environment for computer based review of previously recorded videos or live observations.
Proper citation: Behavioral Observation Research Interactive Software (RRID:SCR_021509) Copy
https://github.com/chenxinfeng4/ArControl
Software tool as Arduino UNO/Mega based, visual programming and real-time behavioral platform for neuroscience. It can run Go/No-Go, 2AFPC and Optogenetic stimulation tasks. Stand alone and intuitive Gaphical User Interface application.Part of ArControl system.
Proper citation: ArControl (RRID:SCR_021605) Copy
Open source software package for creating and controlling visual environments.Software package for Bonsai which allows for control of 2D and 3D environments.
Proper citation: BonVision (RRID:SCR_021534) Copy
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