RTHybrid: A Standardized and Open-Source Real-Time Software Model Library for Experimental Neuroscience

Abstract

Closed-loop technologies provide novel ways of online observation, control and bidirectional interaction with the nervous system, which help to study complex non-linear and partially observable neural dynamics. These protocols are often difficult to implement due to the temporal precision required when interacting with biological components, which in many cases can only be achieved using real-time technology. In this paper we introduce RTHybrid (www.github.com/GNB-UAM/RTHybrid), a free and open-source software that includes a neuron and synapse model library to build hybrid circuits with living neurons in a wide variety of experimental contexts. In an effort to encourage the standardization of real-time software technology in neuroscience research, we compared different open-source real-time operating system patches, RTAI, Xenomai 3 and Preempt-RT, according to their performance and usability. RTHybrid has been developed to run over Linux operating systems supporting both Xenomai 3 and Preempt-RT real-time patches, and thus allowing an easy implementation in any laboratory. We report a set of validation tests and latency benchmarks for the construction of hybrid circuits using this library. With this work we want to promote the dissemination of standardized, user-friendly and open-source software tools developed for open- and closed-loop experimental neuroscience.

A dynamic clamp protocol to artificially modify cell capacitance

“…For an existing dynamic clamp setup, the sole requirement is to implement the calculation of the clamping currents (see Equation 5 ). Otherwise, multiple open source frameworks exist that only require a dedicated computer with a data acquisition card to enable the dynamic clamp in a conventional electrophysiology setup ( Dorval et al, 2001 ; Benda et al, 2007 ; Kemenes et al, 2011 ; Linaro et al, 2015 ; Patel et al, 2017 ; Desai et al, 2017 ; Amaducci et al, 2019 ). To facilitate the usage of the technique, we provide code for the CapClamp scheme in the RELACS and RTXI frameworks (see "Data and software availability" in Appendix 1).…”

Modulation of neuronal dynamics by sustained and activity-dependent continuous-wave near-infrared laser stimulation

“…The stimulation was triggered when the area reached a specific threshold, which was predicted as in the voltage case, or hand-tuned. For the detection of the minimum point to reset the voltage area, we used an RTXI module based on RTHybrid, a real-time software that includes automatic adaptation algorithms to handle the ongoing variability of the recordings 36 , 37 , 40 available in a GitHub repository at: https://github.com/GNB-UAM/rthybrid-for-rtxi/tree/master/rthybrid_burst_analysis. The use of each mode of the protocol in the experiment was decided depending on the specific requirements of the recorded activity.…”

“…Refs. 38–42, promoting the accessibility, reproducibility, and standardization of the studies and methods. However, near-infrared (NIR) lasers have been used with fixed/periodic stimulus and, to the best of our knowledge, they have not been exploited in activity-dependent protocols.…”

A dynamic clamp protocol to artificially modify cell capacitance

“…5). Otherwise, multiple open source frameworks exist that only require a dedicated computer with a data acquisition card to enable the dynamic clamp in a conventional electrophysiology setup [47][48][49][50][51][52][53]. To facilitate the usage of the technique, we provide code for the CapClamp scheme in the RELACS and RTXI frameworks (see Appendix).…”