Initial conditions combine with sensory evidence to induce decision-related dynamics in premotor cortex

Assessing cross-contamination in spike-sorted electrophysiology data

Recent advances in extracellular electrophysiology now facilitate the recording of spikes from hundreds or thousands of neurons simultaneously. This has necessitated both the development of new computational methods for spike sorting and better methods to determine spike sorting accuracy. One longstanding method of assessing the false discovery rate (FDR) of spike sorting - the rate at which spikes are misassigned to the wrong cluster - has been the rate of inter-spike-interval (ISI) violations. Despite their near ubiquitous usage in spike sorting, our understanding of how exactly ISI violations relate to FDR, as well as best practices for using ISI violations as a quality metric, remain limited. Here, we describe an analytical solution that can be used to predict FDR from ISI violation rate. We test this model in silico through Monte Carlo simulation, and apply it to publicly available spike-sorted electrophysiology datasets. We find that the relationship between ISI violation rate and FDR is highly nonlinear, with additional dependencies on firing rate, the correlation in activity between neurons, and contaminant neuron count. Predicted median FDRs in public datasets were found to range from 3.1% to 50.0%. We find that stochasticity in the occurrence of ISI violations as well as uncertainty in cluster-specific parameters make it difficult to predict FDR for single clusters with high confidence, but that FDR can be estimated accurately across a population of clusters. Our findings will help the growing community of researchers using extracellular electrophysiology assess spike sorting accuracy in a principled manner.