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

Software MATLAB based toolbox for automated quantitative analysis of ultrasonic vocalizations. Utilizes image processing libraries to detect USVs and computational vision and machine learning algorithms to classify detected USVs. Used for analysis of ultrasonic vocalizations from mice using computer vision and machine learning.

Proper citation: VocalMat (RRID:SCR_022342) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/permuco/index.html

Software R package for permutation test in linear model with nuisances variables.Used for permutation testing in regression, ANOVA, and comparison of signals.

Proper citation: Permuco (RRID:SCR_022341) Copy   

•   Source: SciCrunch Registry

https://github.com/ACCLAB/DABEST-python

Software package for data analysis using bootstrap coupled estimation. Library combining Python, R, and MATLAB for estimation statistics.

Proper citation: DABEST (RRID:SCR_022340) Copy   

•   Source: SciCrunch Registry

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

Software tool for data extraction and computation of spatial accuracy and precision of head mounted display based eye trackers. Allows for significant customization without altering source code but changes to the code allow for further alteration.

Proper citation: GazeMetrics (RRID:SCR_022338) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/pyos-5/

Open source operant box system optimized for use with tethered animals. System includes hardware and software. Control electronics are build on pyControl, controlling custom PCB integrating 5 infra-red break-beam sensors and 5 stimulus LEDs, single nose-poke for reward receptacle, stepper motor for control of custom peristaltic pump for reward delivery, audio board for tone generation through attached speaker, house light and fan, LED driver for optogenetic stimulation, and bidirectional communication with external devices via TTL pulses.

Proper citation: pyOS-5 project (RRID:SCR_022335) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/MatsumotoJ/usvcam

Open source acoustic camera system for measuring ultrasound communication in rodents. System includes small phased microphone array combined with camera and comprises USV segmentation algorithms with modification for overlapping vocalizations that results in high accuracy. Enables simpler and faster USV localization and assignment.

Proper citation: USVCAM (RRID:SCR_022747) Copy   

•   Source: SciCrunch Registry

https://github.com/denisecailab/minian

Software miniscope analysis pipeline that requires low memory and computational demand so it can be run without specialized hardware. Offers interactive visualization that allows users to see how parameters in each step of pipeline affect output.

Proper citation: Minian (RRID:SCR_022601) Copy   

•   Source: SciCrunch Registry

https://github.com/TAMUCogLab/OpenSync

Open source platform for synchronizing multiple behavioral and physiological signals in neuroscience experiments.

Proper citation: OpenSync (RRID:SCR_022722) 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

https://rupertoverall.net/ColonyTrack/

Software R package to process raw data from ColonyRack system. In addition to generating pre processed data and quality control information, range of high level metrics are calculated together with convenient tools for analysis.

Proper citation: ColonyTrack (RRID:SCR_023026) Copy   

•   Source: SciCrunch Registry

https://github.com/vivian-imbriotis/rpg

Software Python package written for Raspberry Pi for displaying visual stimuli and to provide real time feedback on stimulus timing. High performance python library for displaying drifting gratings on Raspberry Pi 3.

Proper citation: Raspberry Pi Grating (RRID:SCR_023157) 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/KimchiLab/OpBoxPhys

Open source electrophysiology hardware and software package for simultaneous EEG and EMG acquisition from multiple subjects.

Proper citation: OpBox (RRID:SCR_023269) 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