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https://github.com/compsy/ACTman/

Software R library to automate labor intensive actigraphy data preprocessing and analyses steps while improving transparency, reproducibility, and scalability over software suites traditionally used in actigraphy research practice. Provides streamlined preprocessing while validating circadian rhythm and sleep analysis.

Proper citation: ACTman (RRID:SCR_023119) Copy   

•   Source: SciCrunch Registry

https://github.com/PeyracheLab/pynapple

Software object oriented, lightweight and standalone Python toolbox for neural data analysis. Its core features five versatile timeseries objects from Pandas library, allowing it the versatility to be used with most raw neuroscience data types and produce some common analysis forms.

Proper citation: Pynapple (RRID:SCR_023312) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://mousebytes.ca/home

Open access database for all cognitive data collected from touchscreen related tasks. Performs data comparison and interactive data visualization for any data uploaded onto the site. There are also guidelines and video tutorials available.

Proper citation: Mousebytes (RRID:SCR_017904) Copy   

•   Source: SciCrunch Registry

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

Project related to processing video, extracting object position information, and streaming data.Provides set of programs for processing video for behavioral research. Includes OAT software tool as real time position tracker which was developed by Massachusetts Institute of Technology scientists.

Proper citation: Online Animal Tracker project (RRID:SCR_021386) Copy   

•   Source: SciCrunch Registry

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

Project for markerless pose estimation of user defined body parts with deep learning.

Proper citation: DeepLabCut Project (RRID:SCR_021398) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/deepfly3d/

Project related to deep learning based pose estimator for studying how neural circuits control limbed behaviors in tethered Drosophila. Includes Deep Fly image annotation tool for pose estimation and to permit further correction of 2D pose estimates, which are automatically converted to 3D pose.

Proper citation: DeepFly3D project (RRID:SCR_021400) 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

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://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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/Imbrosci/synaptic-vesicles-detection

Software tool as Python based synaptic vesicle classifier algorithm to identify neurotransmitter vesicles in electron microscopy images using Pytorch.

Proper citation: Synaptic Vesicles Detection (RRID:SCR_024910) Copy   

•   Source: SciCrunch Registry

https://github.com/munoztd0/Mouthpiecegusto

3D printed pacifier shaped mouthpiece for fMRI compatible gustometers to deliver up to eight liquids during fMRI task. Can be utilized to study flavor, taste reactivity, reward or punishment with food, conditioning, and neurodegenerative conditions such as Alzheimers and Parkinsons, since taste and smell senses diminish early into disease acquisition.

Proper citation: 3DP Gustometer (RRID:SCR_025010) Copy   

•   Source: SciCrunch Registry

https://github.com/gchelini87/SEB3R

Software tool to automate and standardize ethologically driven observation of freely moving mice. Identifies different postures of mice and associates them with emotions, offering detailed analysis of their movements frame by frame. Used for tracking mouse body language and studying emotional behaviors.

Proper citation: SEB3R (RRID:SCR_025161) Copy   

•   Source: SciCrunch Registry

https://github.com/mcmelo22/Licktech/tree/main

Lickometer system based on open-source hardware platform with user-friendly interface software, capable of simultaneously receiving data from eight automated cages with two drinking bottles each. Device to acquire high-quality and detailed data. Adaptable to new types of sensors or other neuroscience tools capable of measuring brain activity simultaneously to the behavior.

Proper citation: Lickometer Box (RRID:SCR_025248) Copy   

•   Source: SciCrunch Registry

https://github.com/LurLab-UCI/HERBs

Open source hardware and software solution for flexible implementation of complex behaviors in head-fixed mice. Low cost and requires little to no programming experience. Allows neural activity to be seen during testing, which will show relations between neuronal activity and behavior during tasks such as alternative forced choice, GoNoGo, and sensory stimulus presentation.

Proper citation: HERBs (RRID:SCR_025381) Copy   

•   Source: SciCrunch Registry

https://github.com/Aharoni-Lab/Ephys-Miniscope

Miniaturized calcium imaging microscope with integrated dense electrode technology for synchronous acquisition of neural activity across distant regions of the brain. Device based off open-sourced UCLA Miniscope to synchronously measure single cell activity at or near spike-time resolution across distant brain regions in freely behaving mice. Used to perform calcium imaging, with dense electrode electrophysiological recording, allowing simultaneous recordings from two remote brain regions in freely behaving mouse.

Proper citation: E-Scope (RRID:SCR_025396) Copy   

•   Source: SciCrunch Registry

https://github.com/jfrie/FARESHARE

Open source device for fluid tracking in socially housed rats. Device uses RFID and custom hardware to individually measure and record each rat's fluid consumption and licking microstructure.

Proper citation: FARESHARE (RRID:SCR_025330) Copy   

•   Source: SciCrunch Registry