Bypassing spike sorting: Density-based decoding using spike localization from dense multielectrode probes

Neural decoding and its applications to brain computer interfaces (BCI) are essential for understanding the association between neural activity and behavior. A prerequisite for many decoding approaches is spike sorting, the assignment of action potentials (spikes) to individual neurons. Current spike sorting algorithms, however, can be inaccurate and do not properly model uncertainty of spike assignments, therefore discarding information that could potentially improve decoding performance. Recent advances in high-density probes (e.g., Neuropixels) and computational methods now allow for extracting a rich set of spike features from unsorted data; these features can in turn be used to directly decode behavioral correlates. To this end, we propose a spike sorting-free decoding method that directly models the distribution of extracted spike features using a mixture of Gaussians (MoG) encoding the uncertainty of spike assignments, without aiming to solve the spike clustering problem explicitly. We allow the mixing proportion of the MoG to change over time in response to the behavior and develop variational inference methods to fit the resulting model and to perform decoding. We benchmark our method with an extensive suite of recordings from different animals and probe geometries, demonstrating that our proposed decoder can consistently outperform current methods based on thresholding (i.e. multi-unit activity) and spike sorting. Open source code is available at https://github.com/yzhang511/density_decoding.

Compression strategies for large-scale electrophysiology data

Objective.With the rapid adoption of high-density electrode arrays for recording neural activity, electrophysiology data volumes within labs and across the field are growing at unprecedented rates. For example, a one-hour recording with a 384-channel Neuropixels probe generates over 80 GB of raw data. These large data volumes carry a high cost, especially if researchers plan to store and analyze their data in the cloud. Thus, there is a pressing need for strategies that can reduce the data footprint of each experiment.Approach.Here, we establish a set of benchmarks for comparing the performance of various compression algorithms on experimental and simulated recordings from Neuropixels 1.0 (NP1) and 2.0 (NP2) probes.Main results.For lossless compression, audio codecs (FLACandWavPack) achieve compression ratios (CRs) 6% higher for NP1 and 10% higher for NP2 than the best general-purpose codecs, at the expense of decompression speed. For lossy compression, theWavPackalgorithm in 'hybrid mode' increases the CR from 3.59 to 7.08 for NP1 and from 2.27 to 7.04 for NP2 (compressed file size of ∼14% for both types of probes), without adverse effects on spike sorting accuracy or spike waveforms.Significance.Along with the tools we have developed to make compression easier to deploy, these results should encourage all electrophysiologists to apply compression as part of their standard analysis workflows.

A modular architecture for organizing, processing and sharing neurophysiology data

We describe an architecture for organizing, integrating and sharing neurophysiology data within a single laboratory or across a group of collaborators. It comprises a database linking data files to metadata and electronic laboratory notes; a module collecting data from multiple laboratories into one location; a protocol for searching and sharing data and a module for automatic analyses that populates a website. These modules can be used together or individually, by single laboratories or worldwide collaborations.

Modulation of liver canalicular transport processes by the tyrosine-kinase inhibitor genistein: implications of genistein metabolism in the rat

Rat liver cells express the multispecific organic anion transporter (cmoat, cmrp, mrp2) and P-glycoprotein (Pgp) in their canalicular membranes, proteins that are homologous to the multidrug-resistance related protein (MRP) and multidrug resistance (MDR) gene products in multidrug resistant tumor cells. We tested whether genistein, a modulator of drug resistance in tumor cells, affects biliary secretion of substrates of canalicular multispecific organic anion transporter (cmoat) (glucuronides of bilirubin and rhodamine, glutathione conjugate of bromsulphthalein) and of P-glycoprotein (Pgp) (rhodamine), respectively. Using the isolated perfused rat liver of control Wistar rats (TR+) and of a mutant strain (TR-) that expresses Pgp but not cmoat, we show that genistein effectively inhibits the secretion of anionic substrates of cmoat in Wistar rats but stimulates secretion of cationic rhodamine in TR- rats. Genistein is subject to glucuronidation and sulfatation and secretion of genistein and its metabolites stimulates bile flow in Wistar rats, but secretion is nearly absent in TR- rats. Because genistein and its metabolites are substrates for cmoat, inhibition of anion secretion by genistein is partially explained by competition for this transporter. Genistein is also a substrate of uridindiphosphate (UDP)-glucuronyltransferase isoenzyme(s). Inhibition of glucuronidation reduces the availability of bilirubin and rhodamine glucuronates for transport via cmoat, but unconjugated cationic rhodamine becomes available for transport via Pgp at an increased cellular concentration. Daidzein, a genistein analogue with no effect on protein tyrosine kinase (PTK) shows Similar effects on secretion of organic anions and cations supporting the conclusion that genistein affects transport in liver mainly through competition with other substrates at the sites of glucuronidation and transport via cmoat.

Event-related potentials to tones in the absence and presence of sleep spindles

The present study focused on event-related potentials to tones in the presence and absence of sleep spindles. Six undergraduates were studied throughout an experimental night, following an adaptation session. The event-related potentials to tone stimuli were averaged for each subject. Separate averages were determined for trials on which no sleep spindle occurred 2 s before or after a tone and trials in which spindle activity was present. Both voltage distribution maps and multivariate analysis of the waveforms produced significant differences between these conditions, which could be seen as a higher initial positive component and sustained positively over the averaged epoch in the presence of spindles. Spectral analysis indicated that this result could not solely be ascribed to residual sigma activity in the spindle-present average. The results may provide insights into the functional role of sleep spindles in humans in addition to that suggested by a neurophysiological model of inhibition.

Auditory event-related potentials to deviant stimuli during drowsiness and stage 2 sleep

Twelve subjects were tested using a 3-tone auditory oddball paradigm consisting of a standard 1000 Hz tone (P = 80%) and two deviants, namely, a 1200 Hz tone and a 2000 Hz tone (both P = 10%). Testing took place in 3 conditions: (1) attend, in which the subject had to count one of the deviant tones; (2) ignore, in which the subject read a book; and (3) sleep, in which the subject was encouraged to go to sleep during presentation of the tones. In the awake conditions stimulus deviance elicited mismatch negativity (MMN) and P3. During drowsiness, no separate mismatch negativity (MMN) could be detected, but the 2000 Hz tone evoked a broad fronto-central early negative deflection, suggesting an overlap of N1 and MMN. In the same condition, P210, N330 and P430 appeared, all being sensitive to magnitude of deviance. During stage 2, the P210, N330 and P430 amplitudes increased, most notably to the large deviant. These data indicate that differential processing of auditory inputs is maintained during drowsiness and stage 2 sleep, but do not support the notion that MMN or P3 activity comparable to the waking state occurs to oddball stimuli during this stage. It is hypothesised that during light sleep, scanning of the environment is performed by a different system than in the awake state and that during drowsiness a gradual switch between these two systems takes place.