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Command-line cellular electrophysiology for conventional and real-time closed-loop experiments.
Linaro, Daniele; Couto, João; Giugliano, Michele.
Afiliación
  • Linaro D; Theoretical Neurobiology and Neuroengineering Laboratory, Department of Biomedical Sciences, University of Antwerp, B-2610 Wilrijk, Belgium; Neuro-Electronics Research Flanders (NERF), B-3001 Leuven, Belgium. Electronic address: daniele.linaro@uantwerpen.be.
  • Couto J; Theoretical Neurobiology and Neuroengineering Laboratory, Department of Biomedical Sciences, University of Antwerp, B-2610 Wilrijk, Belgium; Neuro-Electronics Research Flanders (NERF), B-3001 Leuven, Belgium.
  • Giugliano M; Theoretical Neurobiology and Neuroengineering Laboratory, Department of Biomedical Sciences, University of Antwerp, B-2610 Wilrijk, Belgium; Neuro-Electronics Research Flanders (NERF), B-3001 Leuven, Belgium; Department of Computer Science, University of Sheffield, S1 4DP Sheffield, UK; Brain Mind Institute, EPFL, CH-1015 Lausanne, Switzerland.
J Neurosci Methods ; 230: 5-19, 2014 Jun 15.
Article en En | MEDLINE | ID: mdl-24769169
BACKGROUND: Current software tools for electrophysiological experiments are limited in flexibility and rarely offer adequate support for advanced techniques such as dynamic clamp and hybrid experiments, which are therefore limited to laboratories with a significant expertise in neuroinformatics. NEW METHOD: We have developed lcg, a software suite based on a command-line interface (CLI) that allows performing both standard and advanced electrophysiological experiments. Stimulation protocols for classical voltage and current clamp experiments are defined by a concise and flexible meta description that allows representing complex waveforms as a piece-wise parametric decomposition of elementary sub-waveforms, abstracting the stimulation hardware. To perform complex experiments lcg provides a set of elementary building blocks that can be interconnected to yield a large variety of experimental paradigms. RESULTS: We present various cellular electrophysiological experiments in which lcg has been employed, ranging from the automated application of current clamp protocols for characterizing basic electrophysiological properties of neurons, to dynamic clamp, response clamp, and hybrid experiments. We finally show how the scripting capabilities behind a CLI are suited for integrating experimental trials into complex workflows, where actual experiment, online data analysis and computational modeling seamlessly integrate. COMPARISON WITH EXISTING METHODS: We compare lcg with two open source toolboxes, RTXI and RELACS. CONCLUSIONS: We believe that lcg will greatly contribute to the standardization and reproducibility of both simple and complex experiments. Additionally, on the long run the increased efficiency due to a CLI will prove a great benefit for the experimental community.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Interfaz Usuario-Computador / Programas Informáticos / Electrofisiología / Neuronas Tipo de estudio: Prognostic_studies Límite: Animals Idioma: En Revista: J Neurosci Methods Año: 2014 Tipo del documento: Article Pais de publicación: Países Bajos
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Interfaz Usuario-Computador / Programas Informáticos / Electrofisiología / Neuronas Tipo de estudio: Prognostic_studies Límite: Animals Idioma: En Revista: J Neurosci Methods Año: 2014 Tipo del documento: Article Pais de publicación: Países Bajos