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.
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.
J Neurosci Methods. 2014 Jun 15;230:5-19. doi: 10.1016/j.jneumeth.2014.04.003. Epub 2014 Apr 24.
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.
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.
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.
We compare lcg with two open source toolboxes, RTXI and RELACS.
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.
当前的电生理实验软件工具在灵活性方面存在限制，并且很少为动态钳位和混合实验等高级技术提供足够的支持，因此这些技术仅限于在神经信息学方面具有专业知识的实验室。
我们开发了 lcg，这是一个基于命令行界面 (CLI) 的软件套件，允许执行标准和高级电生理实验。经典电压和电流钳实验的刺激协议通过简洁灵活的元描述来定义，该描述允许将复杂波形表示为基本子波形的分段参数分解，从而抽象刺激硬件。为了执行复杂的实验，lcg 提供了一组基本构建块，可以将它们相互连接以产生各种实验范例。
我们展示了使用 lcg 进行的各种细胞电生理实验，从自动应用电流钳协议来描述神经元的基本电生理特性，到动态钳位、响应钳位和混合实验。我们最后展示了 CLI 背后的脚本功能如何适合将实验试验集成到复杂的工作流程中，在这些工作流程中，实际实验、在线数据分析和计算模型无缝集成。
我们将 lcg 与两个开源工具箱 RTXI 和 RELACS 进行了比较。
我们相信 lcg 将极大地促进简单和复杂实验的标准化和可重复性。此外，从长远来看，CLI 提高的效率将对实验社区带来巨大的好处。
