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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
https://github.com/danbider/lightning-pose
Software video centric package for direct video manipulation. Semi supervised animal pose estimation algorithm, Bayesian post processing approach and deep learning package. Improved animal pose estimation via semi-supervised learning, Bayesian ensembling, and cloud-native open-source tools.
Proper citation: Lightning Pose (RRID:SCR_024480) Copy
https://edspace.american.edu/openbehavior/project/ezcalcium/
Software package for MATLAB that makes motion correction, segmentation, signal extraction and dimension reduction, analysis, and visualization of calcium imaging data easy to implement. Open source toolbox for analysis of calcium imaging data.
Proper citation: EZcalcium (RRID:SCR_022354) Copy
https://edspace.american.edu/openbehavior/project/guppy/
Software Python toolbox that makes fiber photometry data analysis intuitive and light on programming.Used to measure neural activity of freely behaving animals.
Proper citation: GuPPy (RRID:SCR_022353) Copy
https://github.com/crtwomey/paws
Statistical software platform for automated scoring of pain in mice.Software R package takes paw trajectory data in response to stimulus and provides automated scoring of pain.
Proper citation: Pain Assessment at Withdrawal Speeds (RRID:SCR_022350) Copy
https://edspace.american.edu/openbehavior/project/neuroethology-tools/
Software Python pipeline for automated detection, pose estimation, and behavior classification in socially interacting mice.Used for pose estimation and behavior quantification in pairs of freely behaving mice.
Proper citation: Mouse Action Recognition System (RRID:SCR_022347) Copy
https://edspace.american.edu/openbehavior/project/pavca/
Project related to tracking behavior. Used to identify subgroups of individuals that differentially attribute incentive value to food cue. Includes apparatus for studying Pavlovian conditioned approach behavior. Customized rat PavCA chambers are constructed based on modular devices purchased from Med-Associates. Code used to operate equipment and collect data was written using Med-Associates’ MEDSTATE programming language. This program is then loaded into Med-PC V operating program, also created by Med-Associates.
Proper citation: PavCA project (RRID:SCR_022508) Copy
https://edspace.american.edu/openbehavior/project/sipec/
Software pipeline for video analysis. Deep learning Swiss knife for behavioral data analysis.Performs segmentation, identification, pose-estimation and classification of complex behaviour. Used for analysis of behavior of multiple animals in complex environments.
Proper citation: SIPEC (RRID:SCR_022364) Copy
https://edspace.american.edu/openbehavior/project/mmop/
Software tool as multi subject keypoint detection library for real time pose estimation.Used to track behavior of monkeys in natural environments, without disrupting their typical pattern of behavior. Deep learning software system for body, face, hands, and foot estimation in monkeys.
Proper citation: OpenPose (RRID:SCR_022362) Copy
https://edspace.american.edu/openbehavior/project/trex/
Open source animal tracking software tool. Used to visually track movement of multiple animals at once.
Proper citation: TRex (RRID:SCR_022361) Copy
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