How Do Spike Collisions Affect Spike Sorting Performance?

Juxtacellular recordings from identified neurons in the mouse locus coeruleus

The locus coeruleus (LC) is the primary source of noradrenergic transmission in the mammalian central nervous system. This small pontine nucleus consists of a densely packed nuclear core-which contains the highest density of noradrenergic neurons-embedded within a heterogeneous surround of non-noradrenergic cells. This local heterogeneity, together with the small size of the LC, has made it particularly difficult to infer noradrenergic cell identity based on extracellular sampling of in vivo spiking activity. Moreover, the relatively high cell density, background activity and synchronicity of LC neurons have made spike identification and unit isolation notoriously challenging. In this study, we aimed at bridging these gaps by performing juxtacellular recordings from single identified neurons within the mouse LC complex. We found that noradrenergic neurons (identified by tyrosine hydroxylase, TH, expression; TH-positive) and intermingled putatively non-noradrenergic (TH-negative) cells displayed similar morphologies and responded to foot shock stimuli with excitatory responses; however, on average, TH-positive neurons exhibited more prominent foot shock responses and post-activation firing suppression. The two cell classes also displayed different spontaneous firing rates, spike waveforms and temporal spiking properties. A logistic regression classifier trained on spontaneous electrophysiological features could separate the two cell classes with 76% accuracy. Altogether, our results reveal in vivo electrophysiological correlates of TH-positive neurons, which can be useful for refining current approaches for the classification of LC unit activity.

Modeling realistic synaptic inputs of CA1 hippocampal pyramidal neurons and interneurons via Adaptive Generalized Leaky Integrate-and-Fire models

Computational models of brain regions are crucial for understanding neuronal network dynamics and the emergence of cognitive functions. However, current supercomputing limitations hinder the implementation of large networks with millions of morphological and biophysical accurate neurons. Consequently, research has focused on simplified spiking neuron models, ranging from the computationally fast Leaky Integrate and Fire (LIF) linear models to more sophisticated non-linear implementations like Adaptive Exponential (AdEX) and Izhikevic models, through Generalized Leaky Integrate and Fire (GLIF) approaches. However, in almost all cases, these models are tuned (and can be validated) only under constant current injections and they may not, in general, also reproduce experimental findings under variable currents. This study introduces an Adaptive GLIF (A-GLIF) approach that addresses this limitation by incorporating a new set of update rules. The extended A-GLIF model successfully reproduces both constant and variable current inputs, and it was validated against the results obtained using a biophysical accurate model neuron. This enhancement provides researchers with a tool to optimize spiking neuron models using classic experimental traces under constant current injections, reliably predicting responses to synaptic inputs, which can be confidently used for large-scale network implementations.

Spike sorting with Kilosort4

Spike sorting is the computational process of extracting the firing times of single neurons from recordings of local electrical fields. This is an important but hard problem in neuroscience, made complicated by the nonstationarity of the recordings and the dense overlap in electrical fields between nearby neurons. To address the spike-sorting problem, we have been openly developing the Kilosort framework. Here we describe the various algorithmic steps introduced in different versions of Kilosort. We also report the development of Kilosort4, a version with substantially improved performance due to clustering algorithms inspired by graph-based approaches. To test the performance of Kilosort, we developed a realistic simulation framework that uses densely sampled electrical fields from real experiments to generate nonstationary spike waveforms and realistic noise. We found that nearly all versions of Kilosort outperformed other algorithms on a variety of simulated conditions and that Kilosort4 performed best in all cases, correctly identifying even neurons with low amplitudes and small spatial extents in high drift conditions.

A Modular Implementation to Handle and Benchmark Drift Correction for High-Density Extracellular Recordings

High-density neural devices are now offering the possibility to record from neuronal populations in vivo at unprecedented scale. However, the mechanical drifts often observed in these recordings are currently a major issue for "spike sorting," an essential analysis step to identify the activity of single neurons from extracellular signals. Although several strategies have been proposed to compensate for such drifts, the lack of proper benchmarks makes it hard to assess the quality and effectiveness of motion correction. In this paper, we present a benchmark study to precisely and quantitatively evaluate the performance of several state-of-the-art motion correction algorithms introduced in the literature. Using simulated recordings with induced drifts, we dissect the origins of the errors performed while applying a motion correction algorithm as a preprocessing step in the spike sorting pipeline. We show how important it is to properly estimate the positions of the neurons from extracellular traces in order to correctly estimate the probe motion, compare several interpolation procedures, and highlight what are the current limits for motion correction approaches.