Spike sorting is a critical first step in extracting neural signals from large-scale electrophysiological data. This manuscript describes an efficient, reliable pipeline for spike sorting on dense multi-electrode arrays (MEAs), where neural signals appear across many electrodes and spike sorting currently represents a major computational bottleneck. We present several new techniques that make dense MEA spike sorting more robust and scalable.

Decoding extracellular recordings is a crucial task in electrophysiology and brain-computer interfaces. Spike sorting, which distinguishes spikes and their putative neurons from extracellular recordings, becomes computationally demanding with the increasing number of channels in modern neural probes. To address the intensive workload and complex neuron interactions, we propose E-Sort, an end-to-end neural network-based spike sorter with transfer learning and parallelizable post-processing. Our framework reduces the required number of annotated spikes for training by 44% compared to training from scratch, achieving up to 25.68% higher accuracy. Additionally, our novel post-processing algorithm is compatible with deep learning frameworks, making E-Sort significantly faster than state-of-the-art spike sorters. On synthesized Neuropixels recordings, E-Sort achieves comparable accuracy with Kilosort4 while sorting 50 seconds of data in only 1.32 seconds. Our method demonstrates robustness across various probe geometries, noise levels, and drift conditions, offering a substantial improvement in both accuracy and runtime efficiency compared to existing spike sorters.

This could be a reasonable approach. Is it used for data augmentation or not at all and just described as a potential alternative? What is the evidence that this approach is useful? The synthetic data may not be representative of real recordings.

Spike sorting is a critical first step in extracting neural signals from large-scale electrophysiological data. This manuscript describes an efficient, reliable pipeline for spike sorting on dense multi-electrode arrays (MEAs), where neural signals appear across many electrodes and spike sorting currently represents a major computational bottleneck. We present several new techniques that make dense MEA spike sorting more robust and scalable. This is accomplished by developing a neural network detection method followed by efficient outlier triaging. The clean waveforms are then used to infer the set of neural spike waveform templates through nonparametric Bayesian clustering.