Dataset Information

OPETH: Open Source Solution for Real-Time Peri-Event Time Histogram Based on Open Ephys.

ABSTRACT: Single cell electrophysiology remains one of the most widely used approaches of systems neuroscience. Decisions made by the experimenter during electrophysiology recording largely determine recording quality, duration of the project and value of the collected data. Therefore, online feedback aiding these decisions can lower monetary and time investment, and substantially speed up projects as well as allow novel studies otherwise not possible due to prohibitively low throughput. Real-time feedback is especially important in studies that involve optogenetic cell type identification by enabling a systematic search for neurons of interest. However, such tools are scarce and limited to costly commercial systems with high degree of specialization, which hitherto prevented wide-ranging benefits for the community. To address this, we present an open-source tool that enables online feedback during electrophysiology experiments and provides a Python interface for the widely used Open Ephys open source data acquisition system. Specifically, our software allows flexible online visualization of spike alignment to external events, called the online peri-event time histogram (OPETH). These external events, conveyed by digital logic signals, may indicate photostimulation time stamps for in vivo optogenetic cell type identification or the times of behaviorally relevant events during in vivo behavioral neurophysiology experiments. Therefore, OPETH allows real-time identification of genetically defined neuron types or behaviorally responsive populations. By allowing "hunting" for neurons of interest, OPETH significantly reduces experiment time and thus increases the efficiency of experiments that combine in vivo electrophysiology with behavior or optogenetic tagging of neurons.

SUBMITTER: Szell A

PROVIDER: S-EPMC7251067 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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OPETH: Open Source Solution for Real-Time Peri-Event Time Histogram Based on Open Ephys.

Széll András A Martínez-Bellver Sergio S Hegedüs Panna P Hangya Balázs B

Frontiers in neuroinformatics 20200520

Single cell electrophysiology remains one of the most widely used approaches of systems neuroscience. Decisions made by the experimenter during electrophysiology recording largely determine recording quality, duration of the project and value of the collected data. Therefore, online feedback aiding these decisions can lower monetary and time investment, and substantially speed up projects as well as allow novel studies otherwise not possible due to prohibitively low throughput. Real-time feedbac ...[more]

PMID: 32508613

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Project description:BackgroundInertial measurements (IMUs) facilitate the measurement of human motion outside the motion laboratory. A commonly used open-source software for musculoskeletal simulation and analysis of human motion, OpenSim, includes a tool to enable kinematics analysis of IMU data. However, it only enables offline analysis, i.e., analysis after the data has been collected. Extending OpenSim's functionality to allow real-time kinematics analysis would allow real-time feedback for the subject during the measurement session and has uses in e.g., rehabilitation, robotics, and ergonomics.MethodsWe developed an open-source software library for real-time inverse kinematics (IK) analysis of IMU data using OpenSim. The software library reads data from IMUs and uses multithreading for concurrent calculation of IK. Its operation delays and throughputs were measured with a varying number of IMUs and parallel computing IK threads using two different musculoskeletal models, one a lower-body and torso model and the other a full-body model. We published the code under an open-source license on GitHub.ResultsA standard desktop computer calculated full-body inverse kinematics from treadmill walking at 1.5 m/s with data from 12 IMUs in real-time with a mean delay below 55 ms and reached a throughput of more than 90 samples per second. A laptop computer had similar delays and reached a throughput above 60 samples per second with treadmill walking. Minimal walking kinematics, motion of lower extremities and torso, were calculated from treadmill walking data in real-time with a throughput of 130 samples per second on the laptop and 180 samples per second on the desktop computer, with approximately half the delay of full-body kinematics.ConclusionsThe software library enabled real-time inverse kinematical analysis with different numbers of IMUs and customizable musculoskeletal models. The performance results show that subject-specific full-body motion analysis is feasible in real-time, while a laptop computer and IMUs allowed the use of the method outside the motion laboratory.

Dataset Information

OPETH: Open Source Solution for Real-Time Peri-Event Time Histogram Based on Open Ephys.

Publications

OPETH: Open Source Solution for Real-Time Peri-Event Time Histogram Based on Open Ephys.

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