Command-line Electrophysiology - A Closed-loop Approach to Single Cell Characterisation

João Couto, Daniele Linaro, Michele Giugliano


Cellular electrophysiology is the gold standard in the study of the functional properties of synapses, neurons, and microcircuits, both in vitro and in vivo. Conventional experimental paradigms, however, only marginally approximate physiologically relevant stimulus-response conditions. In fact, they are typically open-loop, as the response of the system under analysis, be it a single neuron or a small ensemble of cells, has a very limited influence on the stimulation that is applied. A general experimental framework that enables the researcher to design closed-loop experiments where the stimulation that is applied to the neuron (or network of neurons) depends on dynamical quantities related to its state is lacking. We address this by presenting a highly customisable electrophysiology data acquisition and stimulation toolbox, which allows the experimenter to perform standard voltage and current clamp protocols but also novel closed-loop paradigms, such as clamping the firing frequency or temporal firing dynamics of a (group of) neuron(s). We include also features to to deliver stimulation waveforms at specific phases of firing or of local field potentials, and to easily perform conductance-clamp, artificial ion channel injections, and hybrid experiments. As an illustrative example we use whole-cell patch clamp recordings from L5 pyramidal neurons in acute brain slices to characterise its input-output (firing frequency vs current) relation and suggest a novel closed-loop approach to this common protocol using a PID controller. By enabling closed loop experiments at several degrees of abstraction (from ion channel simulation to clamping network properties) and allowing to interface with general-purpose scripting languages, this software has the potential to boost electrophysiological research to another level of automation and protocol complexity with minimal effort by the neuroscientist.


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Paper Citation

in Harvard Style

Couto J., Linaro D. and Giugliano M. (2013). Command-line Electrophysiology - A Closed-loop Approach to Single Cell Characterisation . In - NEUROTECHNIX, ISBN , pages 0-0

in Bibtex Style

author={João Couto and Daniele Linaro and Michele Giugliano},
title={Command-line Electrophysiology - A Closed-loop Approach to Single Cell Characterisation},
booktitle={ - NEUROTECHNIX,},

in EndNote Style

TI - Command-line Electrophysiology - A Closed-loop Approach to Single Cell Characterisation
SN -
AU - Couto J.
AU - Linaro D.
AU - Giugliano M.
PY - 2013
SP - 0
EP - 0
DO -