µSpikeHunter: An advanced computational tool for the analysis of neuronal communication and action potential propagation in microfluidic platforms

Abstract

Understanding neuronal communication is fundamental in neuroscience, but there are few methodologies offering detailed analysis for well-controlled conditions. By interfacing microElectrode arrays with microFluidics (μEF devices), it is possible to compartmentalize neuronal cultures with a specified alignment of axons and microelectrodes. This setup allows the extracellular recording of spike propagation with a high signal-to-noise ratio over the course of several weeks. Addressing these μEF devices, we developed an advanced yet easy-to-use publically available computational tool, μSpikeHunter, which provides a detailed quantification of several communication-related properties such as propagation velocity, conduction failure, spike timings, and coding mechanisms. The combination of μEF devices and μSpikeHunter can be used in the context of standard neuronal cultures or with co-culture configurations where, for example, communication between sensory neurons and other cell types is monitored and assessed. The ability to analyze axonal signals (in a user-friendly, time-efficient, high-throughput manner) opens the door to new approaches in studies of peripheral innervation, neural coding, and neuroregeneration, among many others. We demonstrate the use of μSpikeHunter in dorsal root ganglion neurons where we analyze the presence of both anterograde and retrograde signals in μEF devices. A fully functional version of µSpikeHunter is publically available for download from https://github.com/uSpikeHunter .

Assessment and manipulation of the computational capacity of in vitro neuronal networks through criticality in neuronal avalanches

“…Avalanches were detected according to the method described by Beggs and Plenz [12]. Spikes were detected using a simple thresholding method [20] based on the standard deviation of the noise of the signal after applying a bandpass filter with a pass band of 300 Hz to 3 kHz 1 . The spike detection threshold was set to 6, 7, and 8 standard deviations below the median of the signal for the cortical networks, and the results were compared to assess the effect of the detection threshold on the classification results.…”

Sensory neurons sprouting is dependent on osteoclast-derived extracellular vesicles involving the activation of epidermal growth factor receptors

“…Although recordings of random DRG cultures have been previously demonstrated (Black et al, 2019), these are not adapted to the study of peripheral innervation. Here, we employed microElectrode-microFluidic (μEF) devices (Figure 7A), which allowed us to monitor axonal activity with great fidelity (Figure 7B) (Heiney et al, 2019; Lopes et al, 2018).…”

“…Then, treatments and recordings were performed at 6-7 DIV. This time point was chosen following preliminary studies that showed adequate electrophysiological maturation and culture viability at this stage (Heiney et al, 2019).…”

Neuronal cultures show bidirectional axonal conduction with antidromic action potentials depolarizing the soma

“…It is important to note that no study has previously attempted to characterize the signal conduction of DRG cultures (Black et al, 2019). Still, preliminary in vitro experiments using DRGs had suggested that most APs propagate orthodromically (Heiney et al, 2019). Our data shows clearly that bidirectional axonal conduction (EAP initiation/antidromic conduction in particular) must be considered when analyzing functional data from both hippocampal and DRG cultures.…”

“…The polydimethylsiloxane (PDMS) microfluidic chambers used in this study followed a design reported on our previous publications (Heiney et al, 2019; Lopes et al, 2018), with minor optimizations regarding the number of microchannels, as well as their length and width. The number of microchannels was reduced to match exactly the number of microelectrode columns (16 microchannels in total).…”