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https://www.sciencedirect.com/science/article/pii/S2352289523000061

Open source automated platform for assessing working memory and prefrontal circuit function. Designed for automated, high-throughput assessments of working memory and simultaneous two-photon imaging in chronic stress studies. Physiology compatible behavioral platform designed specifically for studying circuit mechanisms underlying working memory and related cognitive functions in chronic stress states.

Proper citation: Automated 2 Photon Imaging Compatible Platform for Assessing Working Memory (RRID:SCR_023463) Copy   

•   Source: SciCrunch Registry

https://www.instructables.com/3D-Printed-Syringe-Pump-Rack/

System includes 3D Printed Syringe Pump Rack composed by 5 Syringe Pumps to have 2 continuous flow systems and one remaining pump. Syringe Pump is used to gradually administer small amounts of fluid to patient or for use in chemical and biomedical research. Main features include Open hardware/software, Extremely compact size ( 7cm movement range ), High precision lead screw and nut, Simple to use (command line interface), Simple to replicate, Minimal clean Design.

Proper citation: 3D Printed Multi Pump System (RRID:SCR_023575) Copy   

•   Source: SciCrunch Registry

https://github.com/JosePardoVazquez/RatHeadphones

Repository for highly controlled sound presentation in freely moving rats. Provides all necessary information for building, adjusting, and using Ratphones to reliably present auditory stimulation to freely moving rats. Used for 3D printing of headphones designed for auditory psychophysics in behaving rats.

Proper citation: RatHeadphones (RRID:SCR_023667) Copy   

•   Source: SciCrunch Registry

https://github.com/borglandlab/RunningWheel/

Open source, printable, open faced running wheels for mice residing in home cage that is automated to collect locomotor information such as distance traveled, wheel direction, and velocity. Running wheel system available on GitHub contains code and information to create and run running wheels. System consists of 3D printed wheel, Raspberry Pi 0 W, and supporting components.

Proper citation: Open Face Homecage Running Wheel (RRID:SCR_023642) Copy   

•   Source: SciCrunch Registry

https://github.com/namboodirilab/B-CALM

Open source system for behavioral control based on Arduino Mega microcontroller and MATLAB based graphical interface and analysis code. Behavior controller optimized and customized for associative learning and memory tasks. Provided software should be able to control many different types of hardware for different task configurations.

Proper citation: B-CALM (RRID:SCR_023884) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/fdechaumont/lmt-analysis

Software package for Live Mouse Tracker analysis. lmt-analysis provides all analysis tools needed to extract information from tracking performed by live mouse tracker.

Proper citation: Live Mouse Tracker analysis (RRID:SCR_021505) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://bitbucket.org/kloostermannerflab/

Open source software tool for closed loop neuroscientific experiments capable of sub-millisecond response latency over high-rate streaming data acquired from high-count multi-electrode arrays. Used for processing and controlling closed-loop neuroscience data.

Proper citation: Falcon (RRID:SCR_023199) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry