A brain-wide map of neural activity during complex behaviour.

A key challenge in neuroscience is understanding how neurons in hundreds of interconnected brain regions integrate sensory inputs with previous expectations to initiate movements and make decisions. It is difficult to meet this challenge if different laboratories apply different analyses to different recordings in different regions during different behaviours. Here we report a comprehensive set of recordings from 621,733 neurons recorded with 699 Neuropixels probes across 139 mice in 12 laboratories.

Brain-wide representations of prior information in mouse decision-making.

The neural representations of prior information about the state of the world are poorly understood. Here, to investigate them, we examined brain-wide Neuropixels recordings and widefield calcium imaging collected by the International Brain Laboratory. Mice were trained to indicate the location of a visual grating stimulus, which appeared on the left or right with a prior probability alternating between 0.

A multimodal approach for visualization and identification of electrophysiological cell types .

Neurons of different types perform diverse computations and coordinate their activity during sensation, perception, and action. While electrophysiological recordings can measure the activity of many neurons simultaneously, identifying cell types during these experiments remains difficult. To identify cell types, we developed PhysMAP, a framework that weighs multiple electrophysiological modalities simultaneously to obtain interpretable multimodal representations.

A customised combination of environmental enrichment reduces aggression in CD-1 male mice.

Murine aggression has profound implications on animal welfare and husbandry. This report examines how three distinct combinations of environmental enrichment - wheel, igloo and tunnel; wheel, igloo, and tunnel with nesting; and tunnel with nesting - affect aggressive behaviour in CD-1 male mice. We found that combining wheel/igloo/tunnel enrichment with nesting or replacing the wheel/igloo with two tunnels while maintaining the nesting enrichment reduced aggression.

A scalable, all-optical method for mapping synaptic connectivity with cell-type specificity.

Single-cell transcriptomics has uncovered the enormous heterogeneity of cell types that compose each region of the mammalian brain, but describing how such diverse types connect to form functional circuits has remained challenging. Current methods for measuring the probability and strength of cell-type specific connectivity motifs principally rely on low-throughput whole-cell recording approaches. The recent development of optical tools for perturbing and observing neural circuit activity, now notably including genetically encoded voltage indicators, presents an exciting opportunity to employ optical methods to greatly increase the throughput with which circuit connectivity can be mapped physiologically.

Molecular and Spatial Organization of the Primary Olfactory System and its Responses to Social Odors.

The detection of olfactory cues is essential to signal food, predators, and social encounters. To determine how the sensory detection of physiologically relevant odors is systematically mapped into the mouse primary olfactory system, we used Multiplexed Error Robust Fluorescent Hybridization (MERFISH) to construct a molecular atlas of odorant receptor (OR) expression in the main olfactory epithelium (MOE) and olfactory bulb (OB). We comprehensively quantified the expression of the mouse OR repertoire and uncovered stereotypical gradients of sensory neuron distribution in the MOE along two, central-to-peripheral and basal-to-apical, axes.

Expansion-assisted selective plane illumination microscopy for nanoscale imaging of centimeter-scale tissues.

Recent advances in tissue processing, labeling, and fluorescence microscopy are providing unprecedented views of the structure of cells and tissues at sub-diffraction resolutions and near single molecule sensitivity, driving discoveries in diverse fields of biology, including neuroscience. Biological tissue is organized over scales of nanometers to centimeters. Harnessing molecular imaging across intact, three-dimensional samples on this scale requires new types of microscopes with larger fields of view and working distance, as well as higher throughput.

Proprioceptive limit detectors mediate sensorimotor control of the leg.

Many animals possess mechanosensory neurons that fire when a limb nears the limit of its physical range, but the function of these proprioceptive limit detectors remains poorly understood. Here, we investigate a class of proprioceptors on the leg called hair plates. Using calcium imaging in behaving flies, we find that a hair plate on the fly coxa (CxHP8) detects the limits of anterior leg movement.

A multidimensional distributional map of future reward in dopamine neurons.

Midbrain dopamine neurons (DANs) signal reward-prediction errors that teach recipient circuits about expected rewards. However, DANs are thought to provide a substrate for temporal difference (TD) reinforcement learning (RL), an algorithm that learns the mean of temporally discounted expected future rewards, discarding useful information about experienced distributions of reward amounts and delays. Here we present time-magnitude RL (TMRL), a multidimensional variant of distributional RL that learns the joint distribution of future rewards over time and magnitude.

Enhancer AAV toolbox for accessing and perturbing striatal cell types and circuits.

We present an enhancer-AAV toolbox for accessing and perturbing striatal cell types and circuits. Best-in-class vectors were curated for accessing major striatal neuron populations including medium spiny neurons (MSNs), direct- and indirect-pathway MSNs, Sst-Chodl, Pvalb-Pthlh, and cholinergic interneurons. Specificity was evaluated by multiple modes of molecular validation, by three different routes of virus delivery, and with diverse transgene cargos.

Reproducibility of in vivo electrophysiological measurements in mice.

Understanding brain function relies on the collective work of many labs generating reproducible results. However, reproducibility has not been systematically assessed within the context of electrophysiological recordings during cognitive behaviors. To address this, we formed a multi-lab collaboration using a shared, open-source behavioral task and experimental apparatus.

Imaging 3D cell cultures with optical microscopy.

Three-dimensional (3D) cell cultures have gained popularity in recent years due to their ability to represent complex tissues or organs more faithfully than conventional two-dimensional (2D) cell culture. This article reviews the application of both 2D and 3D microscopy approaches for monitoring and studying 3D cell cultures. We first summarize the most popular optical microscopy methods that have been used with 3D cell cultures.

Glutamate indicators with increased sensitivity and tailored deactivation rates.

Identifying the input-output operations of neurons requires measurements of synaptic transmission simultaneously at many of a neuron's thousands of inputs in the intact brain. To facilitate this goal, we engineered and screened 3365 variants of the fluorescent protein glutamate indicator iGluSnFR3 in neuron culture, and selected variants in the mouse visual cortex. Two variants have high sensitivity, fast activation (< 2 ms) and deactivation times tailored for recording large populations of synapses (iGluSnFR4s, 153 ms) or rapid dynamics (iGluSnFR4f, 26 ms).

Far-red fluorescent genetically encoded calcium ion indicators.

Genetically encoded calcium ion (Ca) indicators (GECIs) are widely-used molecular tools for functional imaging of Ca dynamics and neuronal activities with single-cell resolution. Here we report the design and development of two far-red fluorescent GECIs, FR-GECO1a and FR-GECO1c, based on the monomeric far-red fluorescent proteins mKelly1 and mKelly2. FR-GECOs have excitation and emission maxima at ~596 nm and ~644 nm, respectively, display large responses to Ca in vitro (ΔF/F = 6 for FR-GECO1a, 18 for FR-GECO1c), are bright under both one-photon and two-photon illumination, and have high affinities (apparent K = 29 nM for FR-GECO1a, 83 nM for FR-GECO1c) for Ca.

DELTA: a method for brain-wide measurement of synaptic protein turnover reveals localized plasticity during learning.

Synaptic plasticity alters neuronal connections in response to experience, which is thought to underlie learning and memory. However, the loci of learning-related synaptic plasticity, and the degree to which plasticity is localized or distributed, remain largely unknown. Here we describe a new method, DELTA, for mapping brain-wide changes in synaptic protein turnover with single-synapse resolution, based on Janelia Fluor dyes and HaloTag knock-in mice.

Foundry-fabricated dual-color nanophotonic neural probes for photostimulation and electrophysiological recording.

Significance: Compact tools capable of delivering multicolor optogenetic stimulation to deep tissue targets with sufficient span, spatiotemporal resolution, and optical power remain challenging to realize. Here, we demonstrate foundry-fabricated nanophotonic neural probes for blue and red photostimulation and electrophysiological recording, which use a combination of spatial multiplexing and on-shank wavelength demultiplexing to increase the number of on-shank emitters.

Aim: We demonstrate silicon (Si) photonic neural probes with 26 photonic channels and 26 recording sites, which were fabricated on 200-mm diameter wafers at a commercial Si photonics foundry.

A prospective code for value in the serotonin system.

The in vivo responses of dorsal raphe nucleus serotonin neurons to emotionally salient stimuli are a puzzle. Existing theories centring on reward, surprise, salience and uncertainty individually account for some aspects of serotonergic activity but not others. Merging ideas from reinforcement learning theory with recent insights into the filtering properties of the dorsal raphe nucleus, here we find a unifying perspective in a prospective code for value.

Relative timing and coupling of neural population bursts in large-scale recordings from multiple neuron populations.

The onset of a sensory stimulus elicits transient bursts of activity in neural populations, which are presumed to convey information about the stimulus to downstream populations. The time at which these synchronized bursts reach their peak is highly variable across stimulus presentations, but the relative timing of bursts across interconnected brain regions may be less variable, especially for regions that are strongly functionally coupled. We developed a simple analytical framework that obtains good estimates of population burst times on a trial-by-trial basis, and of the correlations in the timing of evoked population bursts across areas.

A non-Hebbian code for episodic memory.

Hebbian plasticity has long dominated neurobiological models of memory formation. Yet, plasticity rules operating on one-shot episodic memory timescales rarely depend on both pre- and postsynaptic spiking, challenging Hebbian theory in this crucial regime. Here, we present an episodic memory model governed by a simpler rule depending only on presynaptic activity.

Neuropixels Opto: Combining high-resolution electrophysiology and optogenetics.

High-resolution extracellular electrophysiology is the gold standard for recording spikes from distributed neural populations, and is especially powerful when combined with optogenetics for manipulation of specific cell types with high temporal resolution. We integrated these approaches into prototype Neuropixels Opto probes, which combine electronic and photonic circuits. These devices pack 960 electrical recording sites and two sets of 14 light emitters onto a 1 cm shank, allowing spatially addressable optogenetic stimulation with blue and red light.

Computation-through-Dynamics Benchmark: Simulated datasets and quality metrics for dynamical models of neural activity.

A primary goal of systems neuroscience is to discover how ensembles of neurons transform inputs into goal-directed behavior, a process known as neural computation. A powerful framework for understanding neural computation uses neural dynamics - the rules that describe the temporal evolution of neural activity - to explain how goal-directed input-output transformations occur. As dynamical rules are not directly observable, we need computational models that can infer neural dynamics from recorded neural activity.

A brainstem map of orofacial rhythms.

Rhythmic orofacial movements, such as eating, drinking, or vocalization, are controlled by distinct premotor oscillator networks in the brainstem. Orofacial movements must be coordinated with rhythmic breathing to avoid aspiration and because they share muscles. Understanding how brainstem circuits coordinate rhythmic motor programs requires neurophysiological measurements in behaving animals.

MEDiCINe: Motion Correction for Neural Electrophysiology Recordings.

Electrophysiology recordings from the brain using laminar multielectrode arrays allow researchers to measure the activity of many neurons simultaneously. However, laminar microelectrode arrays move relative to their surrounding neural tissue for a variety of reasons, such as pulsation, changes in intracranial pressure, and decompression of neural tissue after insertion. Inferring and correcting for this motion stabilizes the recording and is critical to identify and track single neurons across time.

Experience-dependent reorganization of inhibitory neuron synaptic connectivity.

Organisms continually tune their perceptual systems to the features they encounter in their environment. We have studied how ongoing experience reorganizes the synaptic connectivity of neurons in the olfactory (piriform) cortex of the mouse. We developed an approach to measure synaptic connectivity , training a deep convolutional network to reliably identify monosynaptic connections from the spike-time cross-correlograms of 4.

Differential impacts of germline and adult aggrecan knockout in PV+ neurons on perineuronal nets and PV+ neuronal function.

Perineuronal nets (PNNs) are a condensed form of extracellular matrix primarily found around parvalbumin-expressing (PV+) interneurons. The postnatal maturation of PV+ neurons is accompanied with the formation of PNNs and reduced plasticity. Alterations in PNN and PV+ neuron function have been described for mental disorders such as schizophrenia and autism.