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https://github.com/delcasso/hope
Softwre tool as part of Hybrid-drive combining Optogenetics, Pharmacology, and Electrophysiology project for brain implant.
Proper citation: Hybrid-drive combining Optogenetics, Pharmacology, and Electrophysiology (RRID:SCR_021606) Copy
https://github.com/flatironinstitute/CaImAn
Open source software tool for scalable calcium imaging data analysis. Used for large scale calcium imaging analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.
Proper citation: Calcium Imaging data Analysis (RRID:SCR_021533) Copy
https://hackaday.io/project/181604-mri-stereoscope
Project provides miniature mirror stereoscope system for MRI-scanner. System takes advantage of commonly used display equipment, MRI head coil, and display screen. Miniature Wheatstone stereoscope is used for human neuroimaging.
Proper citation: MRI-stereoscope project (RRID:SCR_021655) Copy
https://spikeforest.flatironinstitute.org/about
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 (RRID:SCR_021532) Copy
https://edspace.american.edu/openbehavior/project/openfeeder/
Project related to studying reward and feeding behavior. Provides open source automatic feeding system that can be customized for food types from seeds to pellets.System integrates plexiglass tubes, Arduino Uno, motor driver, and piezo sensor to reliably deliver accurate amounts of food, and can also be built using 3D printed parts.
Proper citation: OpenFeeder (RRID:SCR_021552) Copy
Project related to auditory behavioral task data collection.Provided high throughput operant conditioning in mouse homecage system was developed by University of Maryland,College Park, scientists.Automated system for training up to hundreds of mice in auditory behavioral task features custom Matlab GUI running on desktop which connects to Raspberry Pi to administer auditory stimuli from USB soundcard and collects auditory data as well as licking data from water spout with commercially available capacitive sensors. Parts list and build instructions are readily available from paper and associated GitHub repository.
Proper citation: ToneBox (RRID:SCR_021548) Copy
https://edspace.american.edu/openbehavior/project/touchscreen-cognition-mousebytes/
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_021549) Copy
https://github.com/ratcave/ratcave
Software 3D graphics python package for cognitive psychology experiments. Open source, cross platform Python library that adds 3D stimulus support to all OpenGL-based 2D Python stimulus libraries. These libraries include VisionEgg, Psychopy, Pyglet, and PyGam.
Proper citation: Ratcave (RRID:SCR_021599) Copy
https://github.com/mne-tools/mne-cpp
Software tool for real time processing of electrophysiological data.
Proper citation: MNE Scan (RRID:SCR_021530) Copy
https://github.com/yorambenshaul/optimouse
Software tool for analysis of mouse position data.Open source software to analyze positions of individual mice, specifically their nose positions, in behavioral arena with the goal of minimizing error.
Proper citation: Optimouse (RRID:SCR_021527) Copy
https://github.com/mtu-most/linear-actuator
Code and model files for open source linear actuator. Part of Pearce Lab Syringe Pump system.
Proper citation: linear actuator (RRID:SCR_021613) Copy
https://github.com/KravitzLab/ROBucket
Software tool as ROBucket source code.
Proper citation: Rodent Operant Bucket (RRID:SCR_021610) Copy
https://github.com/jf-lab/chendoscope
Software tool as part of CHEndoscope. Acquisition software that interfaces with CHEndoscope Ximea USB camera. This code is compatible with Linux and Windows systems.
Proper citation: chendoscope (RRID:SCR_021616) Copy
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/DeNardoLab/BehaviorDEPOT
Software tool for automated behavioral detection based on markerless pose tracking. Behavioral analysis tool to first compile and clean point-tracking output from DeepLabCut, and then classify behavioral epochs using custom behavior classifiers. Used to detect frame by frame behavior from video time series and can analyze results of common experimental assays, including fear conditioning, decision-making in T-maze, open field, elevated plus maze, and novel object exploration. Calculates kinematic and postural statistics from keypoint tracking data from pose estimation software outputs.
Proper citation: BehaviorDEPOT (RRID:SCR_023602) Copy
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