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https://edspace.american.edu/openbehavior/project/open-ephys/
Organization mission is to advance understanding of brain by promoting community ownership of neuroscience tools.Collaborative effort to develop, document, and distribute open source tools for systems neuroscience.Project aims to distribute reliable open source software as well as tools for extracellular recording and stimulation.
Proper citation: Open Ephys (RRID:SCR_021624) Copy
https://github.com/DepartmentofNeurophysiology/Matlab-Whisker-Tracker
Shared database of videos featuring juvenile and adult male rats and adult male mice exploring stationary objects.This dataset includes wide variety of experimental conditions including genetic, pharmacological, and sensory deprivation interventions to explore how active sensing behavior is modulated by different factors. Database of high speed videos of whisking behavior in freely moving rodents.Open source high speed infrared videography database to study principles of active sensing in freely navigating rodents.
Proper citation: Open Source Whisking Video Database (RRID:SCR_021407) Copy
https://www.eneuro.org/content/12/2/ENEURO.0444-24.2025
Low-cost implant for reliable diaphragm EMG recordings in awake, behaving rats.Diaphragm EMG implant.
Proper citation: Implant for Reliable Diaphragm EMG Recordings in Awake, Behaving Rats (RRID:SCR_026968) Copy
https://edspace.american.edu/openbehavior/project/ort/
Open-source apparatus to enable continuous individual monitoring, training, and testing of rats without removing them from their social environment. This system utilizes RFID technology to track individual animals, minimizing human intervention and providing precise behavioral data.
Proper citation: One-rat Turnstile (RRID:SCR_025570) Copy
https://github.com/BadenLab/LED-Zappelin
Open source LED controller for arbitrary spectrum visual stimulation and optogenetics during 2 photon imaging. Device that rapidly time interleaves stimulation and detection epochs during two photon imaging.
Proper citation: LED Zappelin’ (RRID:SCR_022560) Copy
https://github.com/ntorquet/lmt_toolkit_analysis
Open source web application created to analyze Live Mouse Tracker data easily and intuitively. Used to check reliability and to make some analysis of data from Live Mouse Tracker experiments. LMT stores data in SQLite files that requires some computer skills, but LMT-toolkit makes it easy to compute and extract behavioral profiles for each animal tested following step-by-step process.
Proper citation: Live Mouse Tracker Toolkit Analysis (RRID:SCR_024592) Copy
https://www.dropbox.com/s/wx7aicjh4is81om/HomeCageForelimbTask.py?dl=0
Software Python tool running on Raspberry Pi computer. Used for trial timing and data logging. Part of Autonomous Training of Forelimb Motor Task system.
Proper citation: Autonomous Training of a Forelimb Motor Task (RRID:SCR_021603) Copy
https://github.com/mauriciowr/OBAT
Software tool as part of Operant Box for Auditory Tasks system.
Proper citation: Operant Box for Auditory Tasks (RRID:SCR_021604) Copy
https://github.com/MaSoMoTr/MaSoMoTr
Markerless video-based tool to simultaneously track two interacting mice of the same appearance in controlled settings for quantifying behaviors such as different types of sniffing, touching, and locomotion to improve tracking accuracy under these settings without increased human effort. It incorporates conventional handcrafted tracking and deep-learning-based techniques. The tool is trained on small number of manually annotated images from basic experimental setup and outputs body masks and coordinates of the snout and tail-base for each mouse.
Proper citation: Markerless Mouse Tracking for Social Experiments (RRID:SCR_025368) Copy
https://github.com/PTMonteiro/GoFish_Ajuwon_etal_2022
Bonsai code for running GOFish platform for behavioural experiments in fish.
Proper citation: GoFish Ajuwon etal 2022 (RRID:SCR_022511) Copy
https://github.com/mmgxw3/pipetteFindingCNN
Software application for convolutional neural network that assesses pipette positioning before patch clamp is begun to minimize patch clamping errors in electrophysiology experiments. Used for detecting pipette positioning and making patch clamping procedures.
Proper citation: Pipette Finding CNN (RRID:SCR_024992) Copy
https://github.com/ZuAh/Custom-fitting-of-implants
Tutorial to custom-design and -fit implants to continuous and discontinuous skull surfaces. Universal Guide for Skull Extraction and Custom-Fitting of Implants to Continuous and Discontinuous Skulls.
Proper citation: Custom-fitting-of-implants (RRID:SCR_025270) Copy
https://github.com/NeLy-EPFL/LiftPose3D
Software tool for transforming 2D poses to 3D coordinates on labaratory animals. Used for kinematic studies of laboratory animals. Tracking movements in three dimensions from behaving flies, mice, rats, and non-human primates.
Proper citation: LiftPose3D (RRID:SCR_023049) Copy
https://m3platform.weebly.com/
Software neuroscience laboratory environment for simultaneous neuronal imaging and behavioral monitoring. McGill-Mouse-Miniscope Touchscreen Behavior Platform. Standardized approach for high throughput imaging of neuronal dynamics during behavior.
Proper citation: M3 Platform (RRID:SCR_023425) Copy
https://github.com/WinterLab-Berlin/LabNet
Open source software for parallel control over multiple behavioral systems.C++ optimized control layer software to give access to Raspberry Pi connected hardware. Suitable for time critical operations, and to be simple to expand. Used for general automation in experimental laboratories with its control PC located at some distance.
Proper citation: LabNet (RRID:SCR_023712) Copy
https://github.com/oculomatic/oculomatic-release
Software tool for high speed eye tracking for Point Gray USB3.0 cameras.Oculomatic software tracks eye position within acquired image frame at frame rate dictated by image sensor.
Proper citation: Oculomatic (RRID:SCR_021525) Copy
https://github.com/AdaptiveMotorControlLab/Camera_Control
Open source software package that allows video to be recorded in sync with behavior. Python GUI and scripts allows investigators to record from multiple imaging source camera feeds with associated timestamps for each frame. Python API to record video system timestamps from Imaging Source USB cameras. Package requires Windows 10, Anaconda, and Git, and is compatible with Imaging Source USB3 cameras. Part of Camera Control project.
Proper citation: Camera Control (RRID:SCR_021614) Copy
https://github.com/jellen44/AutomaticSleepScoringTool
Software pipeline for sleep researchers to perform automatic sleep scoring for rodents. Artificial neural network for automated behavioral state classification in rats.
Proper citation: AutomaticSleepScoringTool (RRID:SCR_022300) Copy
https://github.com/haiderlab/DP-Lick-Detector
Distribution package for Dual Port Lick Detector.Package includes files relevant to building lick detector.
Proper citation: Dual Port Lick Detector (RRID:SCR_021521) Copy
https://github.com/wildrootlab/SHARCQ
Software tools to register histological section images and cell count locations to mouse brain atlas. Semi automated workflow and GUI for automated brain slice histology alignment, registration, and cell quantification. Used to explore Allen Mouse Brain Atlas, register asymmetric slice images to atlas using manual input, and analyze region of interest data by registering locations of fluorescently labeled cells to standardized regions of Atlas.
Proper citation: SHARCQ (RRID:SCR_022498) Copy
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