SpikeInterface, a unified framework for spike sorting | bioRxiv

Given the importance of understanding single-neuron activity, much development has been directed towards improving the performance and automation of spike sorting. These developments, however, introduce new challenges, such as file format incompatibility and reduced interoperability, that hinder benchmarking and preclude reproducible analysis. To address these limitations, we developed SpikeInterface, a Python framework designed to unify preexisting spike sorting technologies into a single codebase and to standardize extracellular data file operations. With a few lines of code and regardless of the underlying data format, researchers can: run, compare, and benchmark most modern spike sorting algorithms; pre-process, post-process, and visualize extracellular datasets; validate, curate, and export sorting outputs; and more. In this paper, we provide an overview of SpikeInterface and, with applications to both real and simulated extracellular datasets, demonstrate how it can improve the accessibility, reliability, and reproducibility of spike sorting in preparation for the widespread use of large-scale electrophysiology.

Source: SpikeInterface, a unified framework for spike sorting | bioRxiv

Functional and structural properties of highly responsive somatosensory neurons in mouse barrel cortex | bioRxiv

Sparse population activity is a hallmark of supra-granular sensory neurons in neocortex. The mechanisms underlying sparseness are not well understood because a direct link between the neurons activated in vivo and their cellular properties investigated in vitro has been missing. We used two-photon calcium imaging to identify a subset of neurons in layer L2/3 (L2/3) of mouse primary somatosensory cortex that are highly active following principal whisker vibrotactile stimulation. These high responders were then tagged using photoconvertible green fluorescent protein for subsequent targeting in the brain slice using intracellular patch-clamp recordings and biocytin staining. This approach allowed us to investigate the structural and functional properties of high responders that distinguish them from less active control cells. Compared to less responsive L2/3 neurons, high responders displayed increased levels of stimulus-evoked and spontaneous activity, elevated noise and spontaneous pair-wise correlations, and stronger coupling to the population response. Intrinsic excitability was reduced in high responders, while other electrophysiological and morphological parameters were unchanged. Thus, the choice of which neurons participate in stimulus encoding may largely be determined by network connectivity rather than by cellular structure and function.

Source: Functional and structural properties of highly responsive somatosensory neurons in mouse barrel cortex | bioRxiv

Functional Logic of Layer 2/3 Inhibitory Connectivity in the Ferret Visual Cortex: Neuron

Scholl et al. examine the functional connectivity of layer 2/3 inhibitory inputs ontosingle neurons in the ferret visual cortex. This study argues against a simple ruledescribing the arrangement of inhibitory inputs supplied by layer 2/3 circuits.

Source: Functional Logic of Layer 2/3 Inhibitory Connectivity in the Ferret Visual Cortex: Neuron

Genetically Defined Functional Modules for Spatial Orienting in the Mouse Superior Colliculus: Current Biology

Masullo and Mariotti et al. uncover the existence of genetically defined neurons inthe superior colliculus responsible for the execution of three-dimensional reorientingmovements. These neurons are clustered in anatomically defined modules, giving originto a discretely organized and selectively addressable spatial-motor indexing system.

Source: Genetically Defined Functional Modules for Spatial Orienting in the Mouse Superior Colliculus: Current Biology

Dissociation between Postrhinal Cortex and Downstream Parahippocampal Regions in the Representation of Egocentric Boundaries: Current Biology

Gofman et al. describe pure egocentric boundary cells in the postrhinal cortex anddissociate it from other hippocampal regions using a GLM. This finding corroboratesthe idea that a coordinate transformation from egocentric to world-based coordinates,driven by head direction cells, underlies the formation of downstream border cells.

Source: Dissociation between Postrhinal Cortex and Downstream Parahippocampal Regions in the Representation of Egocentric Boundaries: Current Biology

Closed-loop control of gamma oscillations in the amygdala demonstrates their role in spatial memory consolidation | Nature Communications

Gamma is a ubiquitous brain rhythm hypothesized to support cognitive, perceptual, and mnemonic functions by coordinating neuronal interactions. While much correlational evidence supports this hypothesis, direct experimental tests have been lacking. Since gamma occurs as brief bursts of varying frequencies and durations, most existing approaches to manipulate gamma are either too slow, delivered irrespective of the rhythm’s presence, not spectrally specific, or unsuitable for bidirectional modulation. Here, we overcome these limitations with an approach that accurately detects and modulates endogenous gamma oscillations, using closed-loop signal processing and optogenetic stimulation. We first show that the rat basolateral amygdala (BLA) exhibits prominent gamma oscillations during the consolidation of contextual memories. We then boost or diminish gamma during consolidation, in turn enhancing or impairing subsequent memory strength. Overall, our study establishes the role of gamma oscillations in memory consolidation and introduces a versatile method for studying fast network rhythms in vivo.

Source: Closed-loop control of gamma oscillations in the amygdala demonstrates their role in spatial memory consolidation | Nature Communications

The Imposition of Value on Odor: Transient and Persistent Representations of Odor Value in Prefrontal Cortex | bioRxiv

The representation of odor in olfactory cortex (piriform) is distributive and unstructured and can only be afforded behavioral significance upon learning. We performed 2-photon imaging to examine the representation of odors in piriform and in two downstream stations, the orbitofrontal cortex (OFC) and medial prefrontal cortex (mPFC), as mice learned olfactory associations. In piriform we observed minor changes in neural activity unrelated to learning. In OFC, 30% of the neurons acquired robust responses to conditioned stimuli (CS+) after learning, and these responses were gated by context and internal state. The representation in OFC, however, diminished after learning and persistent representations of CS+ and CS− odors emerged in mPFC. Optogenetic silencing indicates that these two brain structures function sequentially to consolidate the learning of appetitive associations. These data demonstrate the transformation of a representation of odor identity in piriform into transient and persistent representations of value in the prefrontal cortex.

Source: The Imposition of Value on Odor: Transient and Persistent Representations of Odor Value in Prefrontal Cortex | bioRxiv

Flexible and accurate decoding of neural populations through stochastic comodulation | bioRxiv

Sensory-guided behavior requires reliable encoding of information (from stimuli to neural responses) and flexible decoding (from neural responses to behavior). In typical decision tasks, a small subset of cells within a large population encode task-relevant stimulus information and need to be identified by later processing stages for relevant information to be transmitted. A statistically optimal decoder (e.g., maximum likelihood) can utilize task-relevant cells for any given task configuration, but relies on complete knowledge of the relationship between the task and the stimulus-response and noise properties of the encoding population. The brain could learn an optimal decoder for a task through supervised learning (i.e., regression), but this typically requires many training trials, and thus lacks the flexibility of humans or animals, that can rapidly adjust to changes in task parameters or structure. Here, we propose a novel decoding solution based on functionally targeted stochastic modulation. Population recordings during different discrimination tasks have revealed that a substantial portion of trial-to-trial variability in cell responses can be explained by stochastic modulatory signals that are shared, and that seem to preferentially target task-informative neurons ([Rabinowitz et al., 2015][1]). The variability introduced by these modulators corrupts the encoded stimulus signal, but we propose that it also serves as a label for the informative neurons, allowing the decoder to solve the identification problem. We show in simulations of a modulated Poisson spiking model that a linear decoder with readout weights proportional to the estimated neuron-specific strength of modulation achieves performance close to an optimal decoder. [1]: #ref-22

Source: Flexible and accurate decoding of neural populations through stochastic comodulation | bioRxiv

Context-dependent decision making in a premotor circuit | bioRxiv

Cognitive capacities afford contingent associations between sensory information and behavioral responses. We studied this problem using an olfactory delayed match to sample task whereby a sample odor specifies the association between a subsequent test odor and rewarding action. Multi-neuron recordings revealed representations of the sample and test odors in olfactory sensory and association cortex, which were sufficient to identify the test odor as match/non-match. Yet, inactivation of a downstream premotor area (ALM), but not orbitofrontal cortex, confined to the epoch preceding the test odor, led to gross impairment. Olfactory decisions that were not context dependent were unimpaired. Therefore, ALM may not receive the outcome of a match/non-match decision from upstream areas but contextual information—the identity of the sample—to establish the mapping between test odor and action. A novel population of pyramidal neurons in ALM layer 2 may mediate this process.

Source: Context-dependent decision making in a premotor circuit | bioRxiv

Reconstruction of 1,000 Projection Neurons Reveals New Cell Types and Organization of Long-Range Connectivity in the Mouse Brain: Cell

An efficient pipeline for brain-wide imaging and morphological reconstruction of individualneurons, including long-range projection neurons, is presented along with a searchabledatabase containing more than 1,000 fully reconstructed neurons in the mouse neocortex,hippocampus, thalamus, and hypothalamus.

Source: Reconstruction of 1,000 Projection Neurons Reveals New Cell Types and Organization of Long-Range Connectivity in the Mouse Brain: Cell