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Correction: Hard real-time closed-loop electrophysiology with the Real-Time eXperiment Interface (RTXI)

2017 PLoS Computational Biology  
Patel YA, George A, Dorval AD, White JA, Christini DJ, Butera RJ (2017) Hard real-time closed-loop electrophysiology with the Real-Time eXperiment Interface (RTXI RTXI).  ...  PLOS Computational Biology Staff (2017) Correction: Hard real-time closed-loop electrophysiology with the Real-Time eXperiment Interface (  ... 
doi:10.1371/journal.pcbi.1005656 pmid:28715502 pmcid:PMC5513696 fatcat:lk4ppxekyrejrllgp7nwh735he

Hard real-time closed-loop electrophysiology with the Real-Time eXperiment Interface (RTXI)

Yogi A. Patel, Ansel George, Alan D. Dorval, John A. White, David J. Christini, Robert J. Butera, Timothée Poisot
2017 PLoS Computational Biology  
The Real-Time eXperiment Interface (RTXI) is an open source software platform for achieving hard real-time data acquisition and closed-loop control in biological experiments while retaining the flexibility  ...  The Real-Time Experiment Interface (RTXI, http://www.rtxi.org, Fig 1) is an open source software platform for hard RT, closed-loop data acquisition (DAQ) and experimental control in biological experiments  ...  Most importantly, the authors would like to thank the RTXI user-community and greater open-source hardware/software communities for continued feedback, interest, and use of RTXI.  ... 
doi:10.1371/journal.pcbi.1005430 pmid:28557998 pmcid:PMC5469488 fatcat:qjys7ijbanhrja3rgcxy6xjuum

Dynamic Clamp in Cardiac and Neuronal Systems Using RTXI [chapter]

Francis A. Ortega, Robert J. Butera, David J. Christini, John A. White, Alan D. Dorval
2014 Msphere  
In this chapter, we provide an overview of designing and implementing a dynamic clamp experiment using the Real-Time eXperiment Interface (RTXI), an open-source software system tailored for real-time biological  ...  While its applications are broad, the approach is straightforward: synthesizing traditional patch clamp, computational modeling, and closed-loop feedback control to simulate a cellular conductance.  ...  The dynamic clamp software must operate on the same time scale as the currents it is trying to mimic. Hard real-time operating systems allows for execution of these tasks at a guaranteed timing.  ... 
doi:10.1007/978-1-4939-1096-0_21 pmid:25023319 pmcid:PMC4880480 fatcat:f6ykxxv46nbo5njwkonkphixj4

Real-time Experiment Interface for biological control applications

R J Lin, J Bettencourt, J A White, D J Christini, R J Butera
2010 2010 Annual International Conference of the IEEE Engineering in Medicine and Biology  
The Real-time Experiment Interface (RTXI) is a fast and versatile real-time biological experimentation system based on Real-Time Linux.  ...  RTXI is currently used extensively for two experiment types: dynamic patch clamp and closed-loop stimulation pattern control in neural and cardiac single cell electrophysiology.  ...  Acknowledgments This work was supported by the National Institutes of Health under Grant 2-R01RR020115-05.  ... 
doi:10.1109/iembs.2010.5627397 pmid:21096883 pmcid:PMC3647344 fatcat:4dsyj5dw3baa3ijcomxjeqhqxe

Closed Loop Experiment Manager (CLEM)—An Open and Inexpensive Solution for Multichannel Electrophysiological Recordings and Closed Loop Experiments

Hananel Hazan, Noam E. Ziv
2017 Frontiers in Neuroscience  
There is growing need for multichannel electrophysiological systems that record from and interact with neuronal systems in near real-time.  ...  We then present our own solution, which we refer to as Closed Loop Experiments Manager (CLEM).  ...  AUTHOR CONTRIBUTIONS HH coded the software, analyzed its performance and wrote the manuscript. NEZ conceived the project, coded the software, and wrote the manuscript.  ... 
doi:10.3389/fnins.2017.00579 pmid:29093659 pmcid:PMC5651259 fatcat:ed5y2is3fjhcbasyij6ad5ixoy

Optical mapping system with real-time control capability

Shahriar Iravanian, David J. Christini
2007 American Journal of Physiology. Heart and Circulatory Physiology  
As previously reported, we have developed a hard real-time software system [originally known as RTLab; now known as real-time experimental interface (RTXI); www.rtxi.org] that accomplishes the stringent  ...  REAL-TIME, CLOSED-LOOP intervention is an emerging experiment-control method that promises to provide invaluable new insight into cardiac electrophysiology.  ...  GRANTS This work was supported by the Division of Research Resources Grant R01-RR-020115, the National Science Foundation Grant PHY-0513389, and the Kenny Gordon Foundation.  ... 
doi:10.1152/ajpheart.00588.2007 pmid:17644571 fatcat:wwa75fgrvjdfbetb7m4ph32kjq

Open Ephys: an open-source, plugin-based platform for multichannel electrophysiology

Joshua H Siegle, Aarón Cuevas López, Yogi A Patel, Kirill Abramov, Shay Ohayon, Jakob Voigts
2017 Journal of Neural Engineering  
We thank Filipe Carvalho of the Champalimaud Institute and Andrew Seddon and Melissa Hough of CircuitHub, Inc. for helping with hardware distribution.  ...  Acknowledgments We wish to thank the founders of the Allen Institute for Brain Science, Paul G. Allen and Jody Allen, for their vision, encouragement and support.  ...  Programming the GUI for use with a real-time operating system, as RTXI has done in their closed-loop electrophysiology software (see next section), would further reduce processing latencies, but would  ... 
doi:10.1088/1741-2552/aa5eea pmid:28169219 fatcat:qjnqlqfz7vcuvgsemkr3pzg6ue

The Past, Present, and Future of Real-Time Control in Cellular Electrophysiology

Jennifer A. Bauer, Katherine M. Lambert, John A. White
2014 IEEE Transactions on Biomedical Engineering  
The technological driver of these advances was the voltage-clamp method, an early and extremely influential form of real-time control in electrophysiology.  ...  For over 60 years, real-time control has been an important technique in the study of excitable cells. Two such control-based technologies are reviewed here.  ...  This work was supported by the National Institutes of Health (R01 MH085074, R01 NS078331, R01 EB016407) and the State of Utah.  ... 
doi:10.1109/tbme.2014.2314619 pmid:24710815 pmcid:PMC4086259 fatcat:yspnvyau4jetlhwxfdx4vvsksy

Neural ensemble communities: open-source approaches to hardware for large-scale electrophysiology

Joshua H Siegle, Gregory J Hale, Jonathan P Newman, Jakob Voigts
2015 Current Opinion in Neurobiology  
Key interfaces within multichannel electrophysiology platforms. Overview of the main components and interfaces in multichannel electrophysiology systems.  ...  One often-overlooked factor when selecting a platform for largescale electrophysiology is whether or not a particular data acquisition system is 'open' or 'closed': that is, whether or not the system's  ...  JPN was supported by the Center for Brains, Minds and Machines (CBMM), funded by the USA National Science Foundation STC award CCF-1231216.  ... 
doi:10.1016/j.conb.2014.11.004 pmid:25528614 pmcid:PMC4447530 fatcat:v4zhm2vozfh7xbtbtlfj3fy2du

Dynamic clamp with StdpC software

Ildikó Kemenes, Vincenzo Marra, Michael Crossley, Dávid Samu, Kevin Staras, György Kemenes, Thomas Nowotny
2011 Nature Protocols  
The software enables the configuration and operation of a wide range of complex and fully automated dynamic clamp experiments via an intuitive and powerful interface with a minimal initial lead-time of  ...  Use of this protocol does not require specialist hardware, costly commercial software, experience in real time operating systems or a strong programming background.  ...  Pinto for the initial development work of Dynclamp 2/4, the early predecessor of StdpC, and to A. Szücs for years of testing StdpC. This work was financed partially by an RCUK fellowship to TN.  ... 
doi:10.1038/nprot.2010.200 pmid:21372819 pmcid:PMC3188375 fatcat:fzyhq3hpvzbprjxwyhw6qn6llq

A reconfigurable visual-programming library for real-time closed-loop cellular electrophysiology

István Biró, Michele Giugliano
2015 Frontiers in Neuroinformatics  
closed-loop real-time control.  ...  Moreover, advanced experimental protocols requiring real-time closed-loop operation to investigate excitability, plasticity, dynamics, are largely inaccessible to users without moderate to substantial  ...  Financial support from the 7th Framework Programme of the European Commission (ICT Future Emerging Technology ENLIGHTENMENT project, contract n. 306502), the Interuniversity Attraction Poles Program initiated  ... 
doi:10.3389/fninf.2015.00017 pmid:26157385 pmcid:PMC4477165 fatcat:qh2kk7uesnfnxmynzjfsnm6p7e

Falcon: a highly flexible open-source software for closed-loop neuroscience

Davide Ciliberti, Fabian Kloosterman
2017 Journal of Neural Engineering  
Acknowledgments We are grateful to Cristian Inel for his important contrib ution in the development of a predecessor software framework, Frédéric Michon for his help with online burst detection in vivo  ...  , Joana Serpa Santos for providing the datasets used for testing online ripple detection and Nicolas Sist for his feedback on the installation and use of the software.  ...  RTXI [28] has only a single real-time thread).  ... 
doi:10.1088/1741-2552/aa7526 pmid:28548044 fatcat:g44ybgrcujc6zaurorxnswvvpu

Toward Building Hybrid Biological/in silico Neural Networks for Motor Neuroprosthetic Control

Mehmet Kocaturk, Halil Ozcan Gulcur, Resit Canbeyli
2015 Frontiers in Neurorobotics  
In order to evaluate the practicality of the BNDE for neuroprosthetic control experiments, a novel, adaptive BMI controller was developed and tested using real-time closed-loop simulations.  ...  We built the BNDE around a hard real-time system so that it is capable of creating simulated synapses from extracellularly recorded neurons to model neurons.  ...  real-Time closed-loop simulation Methods To evaluate the practicality of the BNDE for neuroprosthetic control experiments and study the performance of the B-BMI, we performed real-time closed-loop simulations  ... 
doi:10.3389/fnbot.2015.00008 pmid:26321943 pmcid:PMC4531252 fatcat:bcpjmrnbf5d5rk7ncoymyujikm

Dynamic clamp constructed phase diagram of the Hodgkin-Huxley action potential model [article]

Hillel Ori, Hananel Hazan, Eve Marder, Shimon Marom
2019 bioRxiv   pre-print
This biological-computational hybrid enabled us to explore functional relations in the parameter space, experimentally validate the phase diagram of the Hodgkin-Huxley model, and demonstrate activity-dependence  ...  Here we experimentally construct excitable membranes using the dynamic clamp and voltage-gated potassium ionic channels (Kv1.3) expressed in Xenopus oocytes.  ...  Hard real-time closed-loop electrophysiology with the Real-Time eXperiment Interface (RTXI). PLOS Computational Biology 13, 5 (2017), e1005430. [35] Rinzel, J., and Ermentrout, G. B.  ... 
doi:10.1101/766154 fatcat:pa7egtkyqjchxd2273vtluhexy

Dynamic clamp constructed phase diagram for the Hodgkin and Huxley model of excitability

Hillel Ori, Hananel Hazan, Eve Marder, Shimon Marom
2020 Proceedings of the National Academy of Sciences of the United States of America  
Here we experimentally assembled excitable membranes using the dynamic clamp and voltage-gated potassium ionic channels (Kv1.3) expressed in Xenopus oocytes.  ...  The 1950s Hodgkin and Huxley explicit formulation provides a mathematical framework for understanding excitability, as the consequence of the properties of voltage-gated sodium and potassium channels.  ...  real-time closed loop design.  ... 
doi:10.1073/pnas.1916514117 pmid:32024761 fatcat:nvciwkmjtzfmlaol7zywn3fkoi
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