We have previously described the use of microchannels (μChannels) as substrate-integrated equivalents of micropipettes and advantageous neuron-electrode interface enhancers. The use of μChannels to establish stable recording and stimulation of threading axons results in a high signal-to-noise ratio (SNR), potentially high-throughput and low-cost alternative to conventional substrate-embedded microelectrodes. Here we confirm the consistent achievement of high SNRs with μChannels and systematically characterize the impact of μChannel geometry on the measured signals via numerical simulations and in vitro experiments. We demonstrate and rationalize how channels with a length of ≤300 μm and channel cross section of ≤12 μm(2) support spontaneous formation of seals and yield spike sizes in the millivolt range. Despite the low degree of complexity involved in their fabrication and use, μChannel devices provide a single-unit mean SNR of 101 ± 76, which compares favourably with the SNR obtained from typical microelectrode arrays.

The electrophysiological characterisation of cultured neurons is of paramount importance for drug discovery, safety pharmacology and basic research in the neurosciences. Technologies offering low cost, low technical complexity and potential for scalability towards high-throughput electrophysiology on in vitro neurons would be advantageous, in particular for screening purposes. Here we describe a plastic culture substrate supporting low-complexity multi-unit loose-patch recording and stimulation of developing networks while retaining manufacturability compatible with low-cost and large-scale production. Our hybrid polydimethylsilane (PDMS)-on-polystyrene structures include chambers (6 mm in diameter) and microchannels (25 microm x 3.7 microm x 1 mm) serving as substrate-embedded recording pipettes. Somas are plated and retained in the chambers due to geometrical constraints and their processes grow along the microchannels, effectively establishing a loose-patch configuration without human intervention. We demonstrate that off-the-shelf voltage-clamp, current-clamp and extracellular amplifiers can be used to record and stimulate multi-unit activity with the aid of our dishes. Spikes up to 50 pA in voltage-clamp and 300 microV in current-clamp modes are recorded in sparse and bursting activity patterns characteristic of 1 week-old hippocampal cultures. Moreover, spike sorting employing principal component analysis (PCA) confirms that single microchannels support the recording of multiple neurons. Overall, this work suggests a strategy to endow conventional culture plasticware with added functionality to enable cost-efficient network electrophysiology.

The analysis of electrophysiological recordings often involves visual inspection of time series data to locate specific experiment epochs, mask artifacts, and verify the results of signal processing steps, such as filtering or spike detection. Long-term experiments with continuous data acquisition generate large amounts of data. Rapid browsing through these massive datasets poses a challenge to conventional data plotting software because the plotting time increases proportionately to the increase in the volume of data. This paper presents FTSPlot, which is a visualization concept for large-scale time series datasets using techniques from the field of high performance computer graphics, such as hierarchic level of detail and out-of-core data handling. In a preprocessing step, time series data, event, and interval annotations are converted into an optimized data format, which then permits fast, interactive visualization. The preprocessing step has a computational complexity of ; the visualization itself can be done with a complexity of and is therefore independent of the amount of data. A demonstration prototype has been implemented and benchmarks show that the technology is capable of displaying large amounts of time series data, event, and interval annotations lag-free with ms. The current 64-bit implementation theoretically supports datasets with up to bytes, on the x86_64 architecture currently up to bytes are supported, and benchmarks have been conducted with bytes/1 TiB or double precision samples. The presented software is freely available and can be included as a Qt GUI component in future software projects, providing a standard visualization method for long-term electrophysiological experiments.

In this thesis various methods are presented towards long-term electrophysiological monitoring of in-vitro neuron cultures in µ-channel devices. A new µ-channel device has been developed. The StarPoM device offers multiple culture chambers connected with µ-channels allowing to study communication between neuron populations. For its fabrication an advanced multi level SU-8 soft-lithography master was developed that can mold µ-channels and culture wells simultaneously. The problem of aligning features across a thick SU-8 layer has been solved by integrating a chrome mask into the substrate and then using backside exposure through the chrome mask. A long-term monitoring of neuron electrophysiological activity has been conducted continuously during 14 days in the StarPoM device. For the analysis of the recorded dataset a new software tool-chain has been created with the goal of high processing performance. The two most advanced components - O1Plot and ISI viewer - offer high performance visualization of time series data with event or interval annotation and visualization of inter-spike interval histograms for fast discovery of correlations between spike units on a device. The analysis of the 14 day recording revealed that signals can be recorded from day 4/5 onwards. While maximum spike amplitudes in kept rising during the 14 days and reached up to 3.16 mV, the average spike amplitudes reached their maximum of 0.1-0.3 mV within 6 to 8 days and then kept the amplitudes stable. To better understand the biophysics of signal generation in µ-channels, the influence of µ-channel length on signal amplitude was studied. A model based on the passive cable theory was developed showing that spike amplitude rises with channel length for µ-channels < 250 µm. In longer µ-channels, further growth of spike amplitude is inhibited by cancellation of positive and negative spike phase. Also, clogging of the µ-channel entrances by cells and debris helps to enhance signal amplification.