Curator Dashboard

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.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Software MARS based Python pipeline used for detection, pose estimation and behavior classification in experiments of any format. Repository contains all the code you'll need to train your own version of MARS.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Open source device consists of three LED matrices that can be independently controlled via open source Arduino Uno microcontroller. Matrices of LEDs are mounted above nose pokes to examine perceptual decision making in rats. Highly modifiable LED matrices for visual stimulus presentation in behavioral studies.Designs for printing these accessory devices are available in GitHub account for the project.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Open source system built around Arduino based microcontroller for analog and digital input and synchronization combined with custom printed circuit board. Hardware and Arduino-based firmware used to synchronize experimental and electrophysiological data.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Stimulation system for auditory EEG experiments using Raspberry Pi3 B+ board, HiFiBerry audio card to enhance sound quality and trigger tone latency, and custom Python library to generate auditory stimuli.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

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.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

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

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

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

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Software semi automated brain atlas based analysis pipeline for c-Fos immunohistochemical data. Used to analyze c-Fos in multiple brain regions simultaneously.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

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.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Interactive software for visualizing and uncovering function of circuits created from large scale fruit fly brain data. Interactive computing platform for studying function of executable circuits constructed from fruit fly brain data.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Operant Box code

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

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.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Open source, MATLAB based software for forced swim test and tail suspension test video analysis.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Open source software package to support rt-fMRI via data in formats generated by Siemens, Philips, and GE. Used to support real time functional magnetic resonance imaging.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Software tool as generalist algorithm for cell and nucleus segmentation.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Software Pyton scripts to run computerised task of Reaction Time. Scripts, together with their instructions and scoresheets.Used for assessment of RTs that is freely available, compatible with all operating systems, without license and activation costs, and based on open source software platform.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Automated surgical instrument for brain tissue aspiration.Instrument for microendoscope implantation. Utilizes robotic control of needle connected to vacuum pump to aspirate brain tissue. System consists of robotic surgical instrument built around commercially available stereotaxic instrument and open source MATLAB-based GUI for control.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Non invasive, infrared activity and sleep measurement system that uses passive infrared sensors and Arduino microprocessor. Publication provides protocol for assembling COMPASS as well as provides support protocols and python scripts for data analysis, best practices for optimum results, troubleshooting, and alternative protocols for different use scenarios.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Software Python package for visualizing and interacting with datasets registered to brain atlases. Used for visualization of neuroanatomical and morphological data.

• Resource
• SciCrunch
• 4 years ago - submitted by Edyta Vieth