Command-line cellular electrophysiology for conventional and real-time closed-loop experiments.
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.


METHODS
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.


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.
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.
Daniele
D
Linaro
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.
João
J
Couto
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.
Michele
M
Giugliano
D000200:Action Potentials; D000465:Algorithms; D000818:Animals; D002525:Cerebellar Cortex / Q000502:physiology; D003198:Computer Simulation; D004558:Electric Stimulation / Q000379:methods; D004594:Electrophysiology / Q000379:methods*; D008959:Models, Neurological; D009474:Neurons / Q000502:physiology*; D018408:Patch-Clamp Techniques / Q000379:methods; D017966:Pyramidal Cells / Q000502:physiology; D017208:Rats, Wistar; D012815:Signal Processing, Computer-Assisted; D012984:Software; D013003:Somatosensory Cortex / Q000502:physiology; D013997:Time Factors; D046509:Tissue Culture Techniques; D014584:User-Computer Interface
Active Electrode Compensation; Cellular neurobiology; Closed-loop; Command-line interface; Current clamp; Dynamic clamp; Electrophysiology; Experimental control; Hybrid experiments; Neuroinformatics; Real-time computing; Scripted electrophysiology