Neuropixels 2.0: A miniaturized high-density probe for stable, long-term brain recordings

Recording many neurons for a long time The ultimate aim of chronic recordings is to sample from the same neuron over days and weeks. However, this goal has been difficult to achieve for large populations of neurons. Steinmetz et al. describe the development and testing of Neuropixels 2.0. This new electrophysiological recording tool is a miniaturized, high-density probe for both acute and long-term experiments combined with sophisticated software algorithms for fully automatic post hoc computational stabilization. The technique also provides a strategy for extending the number of recorded sites beyond the number of available recording channels. In freely moving animals, extremely large numbers of individual neurons could thus be followed and tracked with the same probe for weeks and occasionally months. Science, this issue p. eabf4588 An approach has been developed that allows recording from the same neurons in a freely behaving animal for weeks and months. INTRODUCTION Electrode arrays based on complementary metal-oxide semiconductor silicon fabrication technology, such as Neuropixels probes, have enabled recordings of thousands of individual neurons in the living brain. These tools have led to discoveries about the brain-wide correlates of perception and action, primarily when used in acute, head-fixed recordings. To study the dynamics of neuronal processing across time scales, however, it is necessary to record from neurons over weeks and months, ideally during unrestrained behavior and in small animals, such as mice. RATIONALE To this end, we designed a miniaturized probe, called Neuropixels 2.0, with 5120 recording sites distributed over four shanks. The probe and headstage were miniaturized to about one-third of the original size (i.e., the size of the Neuropixels 1.0 probe), so that two probes and their single headstage weigh only ~1.1 g, without loss of channel count (384 channels per probe). Using two four-shank probes provides 10,240 recording sites in one implant. To achieve stable recordings despite brain movement, we optimized the recording site arrangement. The probe has a denser, linearized geometry that allows for post hoc computational motion correction using a newly designed algorithm. This algorithm, implemented in the Kilosort 2.5 software package, determines the motion over time from the spiking data and corrects it with spatial resampling, as in image registration. RESULTS To validate these probes for long-term recordings, we implanted them chronically in 21 rats and mice in six laboratories. Twenty of these 21 implants succeeded and yielded neurons over weeks and months while retaining good signal quality. The probes were reliably recoverable using newly engineered implant fixture designs. To test the performance of the motion correction algorithm, we performed recordings with known imposed motion of the probe relative to the brain. The algorithm improved the yield of stable neurons and largely eliminated the impact of motion on the recording. A version of this algorithm allowed the recording of neurons stably across days. We assessed this by “fingerprinting” individual chronically recorded neurons in the primary visual cortex using their distinctive visual responses to a battery of images. Neuron tracking was >90% successful for up to 2 weeks and >80% successful for up to 2 months. CONCLUSION This work demonstrates a suite of electrophysiological tools comprising a miniaturized high-density probe, recoverable chronic implant fixtures, and algorithms for automatic post hoc motion correction. These tools enable an order-of-magnitude increase in the number of sites that can be recorded in small animals, such as mice, and the ability to record from them stably over long time scales. Neuropixels 2.0 probes allow unprecedented recordings. (A) Comparison of the Neuropixels 1.0 and 2.0 device designs. The Neuropixels 2.0 device is miniaturized and has four shanks. Two probes can be hosted per headstage. (B) Pattern of spiking activity across the cortex (Ctx), hippocampus (HC), and thalamus (Th) recorded over >300 days. (C) Example spiking rasters from two Neuropixels 2.0 probes chronically implanted in a mouse, showing spikes recorded on 6144 of the 10,240 sites available across the two probes. Eight sequential recordings (different colors) were performed from 768 channels each. Measuring the dynamics of neural processing across time scales requires following the spiking of thousands of individual neurons over milliseconds and months. To address this need, we introduce the Neuropixels 2.0 probe together with newly designed analysis algorithms. The probe has more than 5000 sites and is miniaturized to facilitate chronic implants in small mammals and recording during unrestrained behavior. High-quality recordings over long time scales were reliably obtained in mice and rats in six laboratories. Improved site density and arrangement combined with newly created data processing methods enable automatic post hoc correction for brain movements, allowing recording from the same neurons for more than 2 months. These probes and algorithms enable stable recordings from thousands of sites during free behavior, even in small animals such as mice.