Pynapple, a toolbox for data analysis in neuroscience.

Datasets collected in neuroscientific studies are of ever-growing complexity, often combining high-dimensional time series data from multiple data acquisition modalities. Handling and manipulating these various data streams in an adequate programming environment is crucial to ensure reliable analysis, and to facilitate sharing of reproducible analysis pipelines. Here, we present Pynapple, the PYthon Neural Analysis Package, a lightweight python package designed to process a broad range of time-resolved data in systems neuroscience.

SpikeShip: A method for fast, unsupervised discovery of high-dimensional neural spiking patterns.

Neural coding and memory formation depend on temporal spiking sequences that span high-dimensional neural ensembles. The unsupervised discovery and characterization of these spiking sequences requires a suitable dissimilarity measure to spiking patterns, which can then be used for clustering and decoding. Here, we present a new dissimilarity measure based on optimal transport theory called SpikeShip, which compares multi-neuron spiking patterns based on all the relative spike-timing relationships among neurons.

State-dependent coupling of hippocampal oscillations.

Oscillations occurring simultaneously in a given area represent a physiological unit of brain states. They allow for temporal segmentation of spikes and support distinct behaviors. To establish how multiple oscillatory components co-vary simultaneously and influence neuronal firing during sleep and wakefulness in mice, we describe a multivariate analytical framework for constructing the state space of hippocampal oscillations.

Heterogeneity of network and coding states in mouse CA1 place cells.

Theta sequences and phase precession shape hippocampal activity and are considered key underpinnings of memory formation. Theta sequences are sweeps of spikes from multiple cells, tracing trajectories from past to future. Phase precession is the correlation between theta firing phase and animal position.

Hippocampal gamma and sharp wave/ripples mediate bidirectional interactions with cortical networks during sleep.

Hippocampus-neocortex interactions during sleep are critical for memory processes: Hippocampally initiated replay contributes to memory consolidation in the neocortex and hippocampal sharp wave/ripples modulate cortical activity. Yet, the spatial and temporal patterns of this interaction are unknown. With voltage imaging, electrocorticography, and laminarly resolved hippocampal potentials, we characterized cortico-hippocampal signaling during anesthesia and nonrapid eye movement sleep.

Replay, the default mode network and the cascaded memory systems model.

The spontaneous replay of patterns of activity related to past experiences and memories is a striking feature of brain activity, as is the coherent activation of sets of brain areas - particularly those comprising the default mode network (DMN) - during rest. We propose that these two phenomena are strongly intertwined and that their potential functions overlap. In the 'cascaded memory systems model' that we outline here, we hypothesize that the DMN forms the backbone for the propagation of replay, mediating interactions between the hippocampus and the neocortex that enable the consolidation of new memories.

The Hybrid Drive: a chronic implant device combining tetrode arrays with silicon probes for layer-resolved ensemble electrophysiology in freely moving mice.

. Understanding the function of brain cortices requires simultaneous investigation at multiple spatial and temporal scales and to link neural activity to an animal's behavior. A major challenge is to measure within- and across-layer information in actively behaving animals, in particular in mice that have become a major species in neuroscience due to an extensive genetic toolkit.

Learning differentially shapes prefrontal and hippocampal activity during classical conditioning.

The ability to use sensory cues to inform goal-directed actions is a critical component of behavior. To study how sounds guide anticipatory licking during classical conditioning, we employed high-density electrophysiological recordings from the hippocampal CA1 area and the prefrontal cortex (PFC) in mice. CA1 and PFC neurons undergo distinct learning-dependent changes at the single-cell level and maintain representations of cue identity at the population level.

Reduced firing rates of pyramidal cells in the frontal cortex of APP/PS1 can be restored by acute treatment with levetiracetam.

In recent years, aberrant neural oscillations in various cortical areas have emerged as a common physiological hallmark across mouse models of amyloid pathology and patients with Alzheimer's disease. However, much less is known about the underlying effect of amyloid pathology on single cell activity. Here, we used high-density silicon probe recordings from frontal cortex area of 9-month-old APP/PS1 mice to show that local field potential power in the theta and beta band is increased in transgenic animals, whereas single-cell firing rates, specifically of putative pyramidal cells, are significantly reduced.

Unsupervised clustering of temporal patterns in high-dimensional neuronal ensembles using a novel dissimilarity measure.

Temporally ordered multi-neuron patterns likely encode information in the brain. We introduce an unsupervised method, SPOTDisClust (Spike Pattern Optimal Transport Dissimilarity Clustering), for their detection from high-dimensional neural ensembles. SPOTDisClust measures similarity between two ensemble spike patterns by determining the minimum transport cost of transforming their corresponding normalized cross-correlation matrices into each other (SPOTDis).

Impaired hippocampal representation of place in the Fmr1-knockout mouse model of fragile X syndrome.

Fragile X syndrome (FXS) is an X-chromosome linked intellectual disability and the most common known inherited single gene cause of autism spectrum disorder (ASD). Building upon demonstrated deficits in neuronal plasticity and spatial memory in FXS, we investigated how spatial information processing is affected in vivo in an FXS mouse model (Fmr1-KO). Healthy hippocampal neurons (so-called place cells) exhibit place-related activity during spatial exploration, and their firing fields tend to remain stable over time.

Functional coupling networks inferred from prefrontal cortex activity show experience-related effective plasticity.

Functional coupling networks are widely used to characterize collective patterns of activity in neural populations. Here, we ask whether functional couplings reflect the subtle changes, such as in physiological interactions, believed to take place during learning. We infer functional network models reproducing the spiking activity of simultaneously recorded neurons in prefrontal cortex (PFC) of rats, during the performance of a cross-modal rule shift task (task epoch), and during preceding and following sleep epochs.

Abnormal hippocampal theta and gamma hypersynchrony produces network and spike timing disturbances in the Fmr1-KO mouse model of Fragile X syndrome.

Neuronal networks can synchronize their activity through excitatory and inhibitory connections, which is conducive to synaptic plasticity. This synchronization is reflected in rhythmic fluctuations of the extracellular field. In the hippocampus, theta and gamma band LFP oscillations are a hallmark of the processing of spatial information and memory.

The Yin and Yang of Memory Consolidation: Hippocampal and Neocortical.

While hippocampal and cortical mechanisms of memory consolidation have long been studied, their interaction is poorly understood. We sought to investigate potential interactions with respect to trace dominance, strengthening, and interference associated with postencoding novelty or sleep. A learning procedure was scheduled in a watermaze that placed the impact of novelty and sleep in opposition.

Effects of Arc/Arg3.1 gene deletion on rhythmic synchronization of hippocampal CA1 neurons during locomotor activity and sleep.

The activity-regulated cytoskeletal-associated protein/activity regulated gene (Arc/Arg3.1) is crucial for long-term synaptic plasticity and memory formation. However, the neurophysiological substrates of memory deficits occurring in the absence of Arc/Arg3.

A Multichannel Recording System with Optical Stimulation for Closed-Loop Optogenetic Experiments.

Selective perturbation of the activity of specific cell types in the brain tissue is essential in understanding the function of neuronal circuits involved in cognition and behavior and might also provide therapeutic neuromodulation strategies. Such selective neuronal addressing can be achieved through the optical activation of light-sensitive proteins called opsins that are expressed in specific cell populations through genetic methods-hence the name "optogenetics." In optogenetic experiments, the electrical activity of the targeted cell populations is optically triggered and monitored using arrays of microelectrodes.

CA2: it's about time-and episodes.

In this issue of Neuron, Mankin et al. (2015) show that CA2, an oft-neglected hippocampal subregion, has place representations that change from one episode to the next, even as the spatial environment does not. This finding may help explain how time is encoded in episodic memories.

How to detect the Granger-causal flow direction in the presence of additive noise?

Granger-causality metrics have become increasingly popular tools to identify directed interactions between brain areas. However, it is known that additive noise can strongly affect Granger-causality metrics, which can lead to spurious conclusions about neuronal interactions. To solve this problem, previous studies have proposed the detection of Granger-causal directionality, i.

Single-trial properties of place cells in control and CA1 NMDA receptor subunit 1-KO mice.

The NMDA receptor plays a key role in synaptic plasticity and its disruption leads to impaired spatial representation in the CA1 area of the hippocampus, with place cells exhibiting larger place fields (McHugh et al., 1996). Place fields are defined by the spatial and nonspatial inputs of a given place and context, by intrinsic network processes, such as phase precession, but also by the matching of these inputs to a pre-existing spatial representation.

How the amygdala affects emotional memory by altering brain network properties.

The amygdala has long been known to play a key role in supporting memory for emotionally arousing experiences. For example, classical fear conditioning depends on neural plasticity within this anterior medial temporal lobe region. Beneficial effects of emotional arousal on memory, however, are not restricted to simple associative learning.

Oscillatory dynamics and place field maps reflect hippocampal ensemble processing of sequence and place memory under NMDA receptor control.

Place coding in the hippocampus requires flexible combination of sensory inputs (e.g., environmental and self-motion information) with memory of past events.

Light sleep versus slow wave sleep in memory consolidation: a question of global versus local processes?

Sleep is strongly involved in memory consolidation, but its role remains unclear. 'Sleep replay', the active potentiation of relevant synaptic connections via reactivation of patterns of network activity that occurred during previous experience, has received considerable attention. Alternatively, sleep has been suggested to regulate synaptic weights homeostatically and nonspecifically, thereby improving the signal:noise ratio of memory traces.

Estimation of the entropy based on its polynomial representation.

Estimating entropy from empirical samples of finite size is of central importance for information theory as well as the analysis of complex statistical systems. Yet, this delicate task is marred by intrinsic statistical bias. Here we decompose the entropy function into a polynomial approximation function and a remainder function.