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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
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/kemerelab/ghostipy
Software signal processing and spectral analysis toolbox designed for local field potential recordings.
Proper citation: ghostipy (RRID:SCR_026231) Copy
https://github.com/Sakata-Lab/SaLSa
Software MATLAB package for analyzing and categorizing behaviors using pose estimation data. Integrates semi-automatic labeling with machine learning, specifically Long Short-Term Memory neural networks, to classify behavioral "syllables” (distinct, repeatable behaviors). Combinatory approach of semi-automatic labeling and long short-term memory to classify behavioral syllables.
Proper citation: SaLSa (RRID:SCR_026182) Copy
https://github.com/NC4Lab/NC4gate
Code for testing and operating NC4gate modules of modular gate system for autonomous control of rodent behavior. Fully customizable gate system that can be used in behavioral experiments involving rodent mazes (T-maze, Y-maze, radial arm, etc.).
Proper citation: NC4gate (RRID:SCR_026445) Copy
https://github.com/tomcatsmith19/ArucoDetection
Automated rodent behavioral scoring system, complete with 3D design files and code/software. System monitors behavioral engagement using open-source software. 3D design files and necessary software has been made available, as well as code that can be used for data analysis.
Proper citation: ArUco (RRID:SCR_026572) Copy
https://github.com/lvrgb777/STPoseNet
Source code for pose recognition model for laboratory mice based on yolov8. Real-time spatiotemporal network model for robust mouse pose estimation.
Proper citation: STPoseNet (RRID:SCR_026834) Copy
https://github.com/ThomasAkam/active_commutator
Open source active commutator for Open Ephys / Intan electrophysiology systems. Motorized device used in neuroscience research, particularly in studies involving freely moving animals, to manage wires or fibers connecting headstage or other device to external equipment. Addresses common issue of tether tangling during experiments with freely moving subjects. Relies on Hall-Effect sensor detecting rotation of cable, this information is continuously fed to Adafruit microcontroller that operates servo motor to counter-rotate cable as needed, preventing twisting and ensuring clear, uninterrupted data collection. System can also be paused, restarted, and its neutral position recalibrated with simple button presses, allowing for flexible operation.
Proper citation: Active Commutator (RRID:SCR_027098) 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://edspace.american.edu/openbehavior/project/spikeforest/
Project related to neural data analysis. Provides open-source and reproducible software suite that benchmarks performance of automated spike sorting algorithms across extensive, curated database of ground truth electrophysiological recordings, displaying results interactively on continuously updating website.
Proper citation: Spike Forest project (RRID:SCR_021472) Copy
https://edspace.american.edu/openbehavior/project/pypreclin/
Project related to preprocessing of images. Provieds software Python tool to processes raw macaque fMRI images using algorithms embedded in automatic pipeline.
Proper citation: Pypreclin project (RRID:SCR_021473) Copy
https://edspace.american.edu/openbehavior/project/mne-scan/
Project related to real time acquisition and processing of electrophysiological data.Provides software tool for acquisition and processing of electrophysiological data.
Proper citation: MNE Scan project (RRID:SCR_021470) Copy
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
https://edspace.american.edu/openbehavior/project/3dtracker/, http://www.3dtracker.org/
Project related to markerless computerized behavioral analysis for laboratory animals.Provides open source 3D video based behavioral analysis system for neuroscience. System includes open source software tool for 3D-video based markerless computerized behavioral analysis.
Proper citation: 3DTracker project (RRID:SCR_021440) Copy
https://edspace.american.edu/openbehavior/project/lincom/
Project related to animal behavior in complex mazes.Provides software MATLAB package for linearization of place fields in complex mazes.
Proper citation: LinCoM project (RRID:SCR_021438) Copy
https://edspace.american.edu/openbehavior/project/ethowatcher/
Project related to video tracking, detailed ethography, and extraction of kinematic variables from digital video files of laboratory animals.Provides computational tool developed at Federal University of Santa Catarina.
Proper citation: EthoWatcher project (RRID:SCR_021435) Copy
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